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R/FAT3DIC_function.R
In AgroR: Experimental Statistics and Graphics for Agricultural Sciences
Defines functions
FAT3DIC
Documented in
FAT3DIC
#' Analysis: DIC experiments in triple factorial
#' @description Analysis of an experiment conducted in a completely randomized design in a triple factorial scheme using analysis of variance of fixed effects.
#' @author Gabriel Danilo Shimizu, \email{shimizu@uel.br}
#' @author Leandro Simoes Azeredo Goncalves
#' @author Rodrigo Yudi Palhaci Marubayashi
#' @param f1 Numeric or complex vector with factor 1 levels
#' @param f2 Numeric or complex vector with factor 2 levels
#' @param f3 Numeric or complex vector with factor 3 levels
#' @param response Numerical vector containing the response of the experiment.
#' @param mcomp Multiple comparison test (Tukey (\emph{default}), LSD, Scott-Knott and Duncan)
#' @param quali Defines whether the factor is quantitative or qualitative (\emph{qualitative})
#' @param names.fat Allows labeling the factors 1, 2 and 3.
#' @param grau Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with three elements.
#' @param grau12 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 2, in the case of interaction f1 x f2 and qualitative factor 2 and quantitative factor 1.
#' @param grau21 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 1, in the case of interaction f1 x f2 and qualitative factor 1 and quantitative factor 2.
#' @param grau13 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 3, in the case of interaction f1 x f3 and qualitative factor 3 and quantitative factor 1.
#' @param grau31 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 1, in the case of interaction f1 x f3 and qualitative factor 1 and quantitative factor 3.
#' @param grau23 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 3, in the case of interaction f2 x f3 and qualitative factor 3 and quantitative factor 2.
#' @param grau32 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 2, in the case of interaction f2 x f3 and qualitative factor 2 and quantitative factor 3.
#' @param grau123 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 1, in the case of interaction f1 x f2 x f3 and quantitative factor 1.
#' @param grau213 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 2, in the case of interaction f1 x f2 x f3 and quantitative factor 2.
#' @param grau312 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 3, in the case of interaction f1 x f2 x f3 and quantitative factor 3.
#' @param xlab treatments name (Accepts the \emph{expression}() function)
#' @param ylab Variable response name (Accepts the \emph{expression}() function)
#' @param xlab.factor Provide a vector with two observations referring to the x-axis name of factors 1, 2 and 3, respectively, when there is an isolated effect of the factors. This argument uses `parse`.
#' @param alpha.t Significance level of the multiple comparison test (\emph{default} is 0.05)
#' @param alpha.f Level of significance of the F test (\emph{default} is 0.05)
#' @param norm Error normality test (\emph{default} is Shapiro-Wilk)
#' @param transf Applies data transformation (\emph{default} is 1; for log consider 0; `angular` for angular transformation)
#' @param constant Add a constant for transformation (enter value)
#' @param sup Number of units above the standard deviation or average bar on the graph
#' @param geom Graph type (columns or segments)
#' @param fill Defines chart color (to generate different colors for different treatments, define fill = "trat")
#' @param angulo x-axis scale text rotation
#' @param textsize Font size
#' @param labelsize Label Size
#' @param dec Number of cells
#' @param family Font family
#' @param theme ggplot2 theme (\emph{default} is theme_classic())
#' @param addmean Plot the average value on the graph (\emph{default} is TRUE)
#' @param errorbar Plot the standard deviation bar on the graph (In the case of a segment and column graph) - \emph{default} is TRUE
#' @param point This function defines whether the point must have all points ("all"), mean ("mean"), standard deviation (\emph{default} - "mean_sd") or mean with standard error ("mean_se") if quali= FALSE. For quali=TRUE, `mean_sd` and `mean_se` change which information will be displayed in the error bar.
#' @param angle.label label angle
#' @note The order of the chart follows the alphabetical pattern. Please use `scale_x_discrete` from package ggplot2, `limits` argument to reorder x-axis. The bars of the column and segment graphs are standard deviation.
#' @return The analysis of variance table, the Shapiro-Wilk error normality test, the Bartlett homogeneity test of variances, the Durbin-Watson error independence test, multiple comparison test (Tukey, LSD, Scott-Knott or Duncan) or adjustment of regression models up to grade 3 polynomial, in the case of quantitative treatments. The column chart for qualitative treatments is also returned.For significant triple interaction only, no graph is returned.
#' @note The function does not perform multiple regression in the case of two or more quantitative factors. The bars of the column and segment graphs are standard deviation.
#' @note In the final output when transformation (transf argument) is different from 1, the columns resp and respo in the mean test are returned, indicating transformed and non-transformed mean, respectively.
#' @references
#'
#' Principles and procedures of statistics a biometrical approach Steel, Torry and Dickey. Third Edition 1997
#'
#' Multiple comparisons theory and methods. Departament of statistics the Ohio State University. USA, 1996. Jason C. Hsu. Chapman Hall/CRC.
#'
#' Practical Nonparametrics Statistics. W.J. Conover, 1999
#'
#' Ramalho M.A.P., Ferreira D.F., Oliveira A.C. 2000. Experimentacao em Genetica e Melhoramento de Plantas. Editora UFLA.
#'
#' Scott R.J., Knott M. 1974. A cluster analysis method for grouping mans in the analysis of variance. Biometrics, 30, 507-512.
#'
#' Ferreira, E. B., Cavalcanti, P. P., and Nogueira, D. A. (2014). ExpDes: an R package for ANOVA and experimental designs. Applied Mathematics, 5(19), 2952.
#'
#' Mendiburu, F., and de Mendiburu, M. F. (2019). Package ‘agricolae’. R Package, Version, 1-2.
#'
#' @keywords DIC
#' @keywords Factorial
#' @export
#' @examples
#' library(AgroR)
#' data(enxofre)
#' with(enxofre, FAT3DIC(f1, f2, f3, resp))
######################################################################################
## Analise de variancia para experimentos em DIC
######################################################################################
FAT3DIC=function(f1,
f2,
f3,
response,
norm="sw",
alpha.t=0.05,
alpha.f=0.05,
quali=c(TRUE,TRUE,TRUE),
mcomp='tukey',
grau=c(NA,NA,NA),
grau12=NA, # F1/F2
grau13=NA, # F1/F3
grau23=NA, # F2/F3
grau21=NA, # F2/F1
grau31=NA, # F3/F1
grau32=NA, # F3/F2
grau123=NA,
grau213=NA,
grau312=NA,
transf=1,
constant=0,
names.fat=c("F1","F2","F3"),
ylab="Response",
xlab="",
xlab.factor=c("F1","F2","F3"),
sup=NA,
fill="lightblue",
theme=theme_classic(),
angulo=0,
family="sans",
addmean=TRUE,
errorbar=TRUE,
dec=3,
geom="bar",
textsize=12,
labelsize=4,
point="mean_sd",
angle.label=0) {
if(is.na(sup==TRUE)){sup=0.2*mean(response)}
if(angle.label==0){hjust=0.5}else{hjust=0}
if(transf==1){resp=response+constant}else{if(transf!="angular"){resp=((response+constant)^transf-1)/transf}}
# if(transf==1){resp=response+constant}else{resp=((response+constant)^transf-1)/transf}
if(transf==0){resp=log(response+constant)}
if(transf==0.5){resp=sqrt(response+constant)}
if(transf==-0.5){resp=1/sqrt(response+constant)}
if(transf==-1){resp=1/(response+constant)}
if(transf=="angular"){resp=asin(sqrt((response+constant)/100))}
ordempadronizado=data.frame(f1,f2,f3,response,resp)
resp1=resp
organiz=data.frame(f1,f2,f3,response,resp)
organiz=organiz[order(organiz$f3),]
organiz=organiz[order(organiz$f2),]
organiz=organiz[order(organiz$f1),]
f1=organiz$f1
f2=organiz$f2
f3=organiz$f3
response=organiz$response
resp=organiz$resp
fator1=f1
fator2=f2
fator3=f3
fator1a=fator1
fator2a=fator2
fator3a=fator3
requireNamespace("crayon")
requireNamespace("ggplot2")
requireNamespace("nortest")
fatores<-data.frame(fator1,fator2,fator3)
Fator1<-factor(fator1,levels=unique(fator1));
Fator2<-factor(fator2,levels=unique(fator2));
Fator3<-factor(fator3,levels=unique(fator3))
nv1<-length(summary(Fator1)); nv2<-length(summary(Fator2)); nv3<-length(summary(Fator3))
J<-(length(resp))/(nv1*nv2*nv3)
lf1<-levels(Fator1); lf2<-levels(Fator2); lf3<-levels(Fator3)
anava<-aov(resp~Fator1*Fator2*Fator3)
anavaF3<-anova(anava)
anovaF3=anavaF3
colnames(anovaF3)=c("GL","SQ","QM","Fcal","p-value")
anavares<-aov(resp~as.factor(f1)*
as.factor(f2)*
as.factor(f3),data = ordempadronizado)
respad=anavares$residuals/sqrt(anavaF3$`Mean Sq`[8])
out=respad[respad>3 | respad<(-3)]
out=names(out)
out=if(length(out)==0)("No discrepant point")else{out}
Ids=ifelse(respad>3 | respad<(-3), "darkblue","black")
residplot=ggplot(data=data.frame(respad,Ids),aes(y=respad,x=1:length(respad)))+
geom_point(shape=21,color="gray",fill="gray",size=3)+
labs(x="",y="Standardized residuals")+
geom_text(x=1:length(respad),label=1:length(respad),color=Ids,size=labelsize)+
scale_x_continuous(breaks=1:length(respad))+
theme_classic()+theme(axis.text.y = element_text(size=textsize),
axis.text.x = element_blank())+
geom_hline(yintercept = c(0,-3,3),lty=c(1,2,2),color="red",size=1)
# print(residplot)
#Teste de normalidade
norm1<-shapiro.test(anava$residuals)
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Normality of errors")))
cat(green(bold("\n------------------------------------------\n")))
print(norm1)
message(if(norm1$p.value>0.05){
black("As the calculated p-value is greater than the 5% significance level, hypothesis H0 is not rejected. Therefore, errors can be considered normal")}
else {"As the calculated p-value is less than the 5% significance level, H0 is rejected. Therefore, errors do not follow a normal distribution"})
homog1=bartlett.test(anava$residuals~paste(Fator1,Fator2,Fator3))
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Homogeneity of Variances")))
cat(green(bold("\n------------------------------------------\n")))
print(homog1)
message(if(homog1$p.value[1]>0.05){
black("As the calculated p-value is greater than the 5% significance level, hypothesis H0 is not rejected. Therefore, the variances can be considered homogeneous")}
else {"As the calculated p-value is less than the 5% significance level, H0 is rejected. Therefore, the variances are not homogeneous"})
indep=dwtest(anava)
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Independence from errors")))
cat(green(bold("\n------------------------------------------\n")))
print(indep)
message(if(indep$p.value>0.05){
black("As the calculated p-value is greater than the 5% significance level, hypothesis H0 is not rejected. Therefore, errors can be considered independent")}
else {"As the calculated p-value is less than the 5% significance level, H0 is rejected. Therefore, errors are not independent"})
cat("\n")
cat(green(bold("\n-----------------------------------------------------------------\n")))
cat(green(bold("Additional Information")))
cat(green(bold("\n-----------------------------------------------------------------\n")))
cat(paste("\nCV (%) = ",round(sqrt(anavaF3$`Mean Sq`[8])/mean(resp,na.rm=TRUE)*100,2)))
cat(paste("\nMean = ",round(mean(response,na.rm=TRUE),4)))
cat(paste("\nMedian = ",round(median(response,na.rm=TRUE),4)))
cat("\nPossible outliers = ", out)
cat("\n")
cat(green(bold("\n------------------------------------------\n")))
cat(green(italic("Analysis of Variance")))
cat(green(bold("\n------------------------------------------\n")))
anava1=as.matrix(data.frame(anovaF3))
colnames(anava1)=c("Df","Sum Sq","Mean.Sq","F value","Pr(F)" )
rownames(anava1)=c(names.fat[1],
names.fat[2],
names.fat[3],
paste(names.fat[1],"x",names.fat[2]),
paste(names.fat[1],"x",names.fat[3]),
paste(names.fat[2],"x",names.fat[3]),
paste(names.fat[1],"x",names.fat[2],"x",names.fat[3]),
"Residuals")
print(anava1,na.print = "")
cat("\n")
if(transf==1 && norm1$p.value<0.05 | transf==1 && indep$p.value<0.05 | transf==1 &&homog1$p.value<0.05){
message("\n Your analysis is not valid, suggests using a non-parametric test and try to transform the data\n")}else{}
if(transf != 1 && norm1$p.value<0.05 | transf!=1 && indep$p.value<0.05 | transf!=1 && homog1$p.value<0.05){
message("\n Your analysis is not valid, suggests using the function FATDIC.art\n")}else{}
message(if(transf !=1){blue("\nNOTE: resp = transformed means; respO = averages without transforming\n")})
if(anavaF3[4,5]>alpha.f && anavaF3[5,5]>alpha.f && anavaF3[6,5]>alpha.f && anavaF3[7,5]>alpha.f) {
graficos=list(1,2,3)
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold('Non-significant interaction: analyzing the simple effects')))
cat(green(bold("\n------------------------------------------\n")))
fatores<-data.frame('fator 1'=fator1,'fator 2' = fator2,'fator 3' = fator3)
for(i in 1:3){
if(quali[i]==TRUE && anavaF3[i,5]<=alpha.f) {
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
cat(green(bold("\n------------------------------------------\n")))
if(mcomp=='tukey'){letra=TUKEY(resp,fatores[,i],anavaF3[8,1],anavaF3[8,3],alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="sk"){
nrep=table(fatores[,i])[1]
medias=sort(tapply(resp,fatores[i],mean, na.rm=TRUE),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3[8,1],
nrep = nrep,
QME = anavaF3[8,3],
alpha = alpha.t)
letra1=data.frame(resp=medias,groups=sk)
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="duncan"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- duncan(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="lsd"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- LSD(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
teste=if(mcomp=="tukey"){"Tukey HSD"}else{
if(mcomp=="sk"){"Scott-Knott"}else{
if(mcomp=="lsd"){"LSD-Fischer"}else{
if(mcomp=="duncan"){"Duncan"}}}}
cat(green(italic(paste("Multiple Comparison Test:",teste,"\n"))))
print(letra1)
cat(green(bold("\n------------------------------------------\n")))
#=====================================================
if(point=="mean_sd"){desvio=tapply(response, c(fatores[i]), sd, na.rm=TRUE)[rownames(letra1)]}
if(point=="mean_se"){desvio=(tapply(response, c(fatores[i]), sd, na.rm=TRUE)/
sqrt(tapply(response, c(fatores[i]), length)))[rownames(letra1)]}
dadosm=data.frame(letra1,
media=tapply(response, c(fatores[i]), mean, na.rm=TRUE)[rownames(letra1)],
desvio=desvio)
dadosm$trats=factor(rownames(dadosm),
levels = unique(unlist(fatores[i])))
dadosm$limite=dadosm$media+dadosm$desvio
dadosm=dadosm[as.character(unique(unlist(fatores[i]))),]
if(addmean==TRUE){dadosm$letra=paste(format(dadosm$media,digits = dec),dadosm$groups)}
if(addmean==FALSE){dadosm$letra=dadosm$groups}
media=dadosm$media
desvio=dadosm$desvio
trats=dadosm$trats
letra=dadosm$letra
if(geom=="bar"){grafico=ggplot(dadosm,
aes(x=trats,
y=media))
if(fill=="trat"){grafico=grafico+
geom_col(aes(fill=trats),
color=1)}else{grafico=grafico+
geom_col(aes(fill=trats),
fill=fill,color=1)}
if(errorbar==TRUE){grafico=grafico+
geom_text(aes(y=media+sup+
if(sup<0){-desvio}else{desvio},
label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==FALSE){grafico=grafico+
geom_text(aes(y=media+sup,label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==TRUE){grafico=grafico+
geom_errorbar(data=dadosm,
aes(ymin=media-desvio,
ymax=media+desvio,color=1),
color="black",width=0.3)}
grafico=grafico+
theme+
ylab(ylab)+
xlab(parse(text = xlab.factor[i]))+
theme(text = element_text(size=textsize,color="black", family = family),
axis.text = element_text(size=textsize,color="black", family = family),
axis.title = element_text(size=textsize,color="black", family = family),
legend.position = "none")
print(grafico)}
# ================================
# grafico de segmentos
# ================================
if(geom=="point"){grafico=ggplot(dadosm,
aes(x=trats,
y=media))
if(fill=="trat"){grafico=grafico+
geom_point(aes(color=trats))}
else{grafico=grafico+
geom_point(aes(color=trats),color=fill,size=4)}
if(errorbar==TRUE){grafico=grafico+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==FALSE){grafico=grafico+
geom_text(aes(y=media+sup,label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==TRUE){grafico=grafico+
geom_errorbar(data=dadosm,
aes(ymin=media-desvio,
ymax=media+desvio,color=1),
color="black",width=0.3)}
grafico=grafico+theme+
ylab(ylab)+
xlab(parse(text = xlab.factor[i]))+
theme(text = element_text(size=textsize,color="black", family = family),
axis.text = element_text(size=textsize,color="black", family = family),
axis.title = element_text(size=textsize,color="black", family = family),
legend.position = "none")
print(grafico)}
}
if(anavaF3[i,5]>alpha.f) {
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
cat(green(bold("\n------------------------------------------\n")))
mean.table<-mean_stat(response,fatores[,i],mean)
colnames(mean.table)<-c('Levels','Mean')
print(mean.table)
grafico=NA}
if(quali[i]==FALSE && anavaF3[i,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
cat(green(bold("\n------------------------------------------\n")))
dose=as.numeric(as.vector(unlist(fatores[,i])))
grafico=polynomial(dose,resp,grau = grau[i],
DFres= anavaF3[8,1],SSq = anavaF3[8,2],ylab = ylab,xlab = parse(text = xlab.factor[i]),point = point)[[1]]
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial\" command\n"))
cat(green(bold("\n------------------------------------------")))}
cat('\n')
graficos[[1]]=residplot
graficos[[i+1]]=grafico
}
}
if(anavaF3[7,5]>alpha.f && anavaF3[4,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Interaction",paste(names.fat[1],'*',names.fat[2],sep='')," significant: unfolding the interaction")))
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[1], ' inside of each level of ', names.fat[2])
cat(green(bold("\n------------------------------------------\n")))
des<-aov(resp~Fator2/Fator1+Fator3+Fator2+Fator2:Fator3+Fator1:Fator2:Fator3)
l<-vector('list',nv2)
names(l)<-names(summary(Fator2))
v<-numeric(0)
for(j in 1:nv2) {
for(i in 0:(nv1-2)) v<-cbind(v,i*nv2+j)
l[[j]]<-v
v<-numeric(0)}
des1<-summary(des,split=list('Fator2:Fator1'=l))[[1]]
des1a=des1[-c(1,2,3,length(des1[,1]),length(des1[,1])-1,length(des1[,1])-2),]
#============================
rn<-numeric(0)
for (j in 1:nv2) {
rn <- c(rn, paste(paste(names.fat[1], ":", names.fat[2],
sep = ""), lf2[j]))
}
rownames(des1a)=rn
#============================
print(des1a)
if(quali[1]==TRUE & quali[2]==TRUE){
if (mcomp == "tukey"){
tukeygrafico=c()
ordem=c()
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
tukeygrafico[[i]]=tukey$groups[levels(trati),2]
ordem[[i]]=rownames(tukey$groups[levels(trati),])
}
letra=unlist(tukeygrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "duncan"){
duncangrafico=c()
ordem=c()
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
duncangrafico[[i]]=duncan$groups[levels(trati),2]
ordem[[i]]=rownames(duncan$groups[levels(trati),])
}
letra=unlist(duncangrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "lsd"){
lsdgrafico=c()
ordem=c()
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator2 == lf2[i]],trati,
mean, na.rm=TRUE)[rownames(lsd$groups)]}
lsdgrafico[[i]]=lsd$groups[levels(trati),2]
ordem[[i]]=rownames(lsd$groups[levels(trati),])
}
letra=unlist(lsdgrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "sk"){
skgrafico=c()
ordem=c()
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !="1"){sk$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(sk)]}
skgrafico[[i]]=sk[levels(trati),2]
ordem[[i]]=rownames(sk[levels(trati),])
}
letra=unlist(skgrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}}
# Desdobramento de F2 dentro de F1
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[2], " inside of the level of ",names.fat[1])
cat(green(bold("\n------------------------------------------\n")))
# Desdobramento de F1 dentro de F2
des<-aov(resp~Fator1/Fator2+Fator3+Fator1+Fator1:Fator3+Fator1:Fator2:Fator3)
l<-vector('list',nv1)
names(l)<-names(summary(Fator1))
v<-numeric(0)
for(j in 1:nv1) {
for(i in 0:(nv2-2)) v<-cbind(v,i*nv1+j)
l[[j]]<-v
v<-numeric(0)}
des1<-summary(des,split=list('Fator1:Fator2'=l))[[1]]
des1a=des1[-c(1,2,3,length(des1[,1]),length(des1[,1])-1,length(des1[,1])-2),]
#============================
rn<-numeric(0)
for (j in 1:nv1) {
rn <- c(rn, paste(paste(names.fat[2], ":", names.fat[1],
sep = ""), lf1[j]))
}
rownames(des1a)=rn
#============================
print(des1a)
if(quali[1]==TRUE & quali[2]==TRUE){
if (mcomp == "tukey"){
tukeygrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator1 == lf1[i]],
trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
tukeygrafico1[[i]]=tukey$groups[levels(trati),2]
}
letra1=unlist(tukeygrafico1)
letra1=toupper(letra1)}
if (mcomp == "duncan"){
duncangrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
duncangrafico1[[i]]=duncan$groups[levels(trati),2]
}
letra1=unlist(duncangrafico1)
letra1=toupper(letra1)}
if (mcomp == "lsd"){
lsdgrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator1 == lf1[i]],
trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
lsdgrafico1[[i]]=lsd$groups[levels(trati),2]
}
letra1=unlist(lsdgrafico1)
letra1=toupper(letra1)}
if (mcomp == "sk"){
skgrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
# sk=sk(respi,trati,anavaF3$Df[8],anavaF3$`Sum Sq`[8],alpha.t)
if(transf !=1){sk$respo=tapply(response[Fator1 == lf1[i]],trati,
mean, na.rm=TRUE)[rownames(sk)]}
skgrafico1[[i]]=sk[levels(trati),2]
}
letra1=unlist(skgrafico1)
letra1=toupper(letra1)}}
if(quali[1] & quali[2]==TRUE){
f1=rep(levels(Fator1),e=length(levels(Fator2)))
f2=rep(unique(as.character(Fator2)),length(levels(Fator1)))
media=tapply(response,paste(Fator1,Fator2), mean, na.rm=TRUE)[unique(paste(f1,f2))]
# desvio=tapply(response,paste(Fator1,Fator2), sd, na.rm=TRUE)[unique(paste(f1,f2))]
if(point=="mean_sd"){desvio=tapply(response,paste(Fator1,Fator2), sd, na.rm=TRUE)}
if(point=="mean_se"){desvio=tapply(response,paste(Fator1,Fator2), sd, na.rm=TRUE)/
sqrt(tapply(response,paste(Fator1,Fator2), length))}
desvio=desvio[unique(paste(f1,f2))]
f1=factor(f1,levels = unique(f1))
f2=factor(f2,levels = unique(f2))
graph=data.frame(f1=f1,
f2=f2,
media,
desvio,
letra,
letra1,
numero=format(media,digits = dec))
numero=paste(graph$numero,graph$letra,graph$letra1,sep="")
graph$numero=numero
colint=ggplot(graph,
aes(x=f2,
y=media,
fill=f1))+
ylab(ylab)+xlab(xlab)+
theme+
geom_col(position = "dodge",color="black")+
labs(fill=names.fat[1])+
geom_errorbar(aes(ymin=media-desvio,
ymax=media+desvio),
width=0.3,position = position_dodge(width=0.9))+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=numero),
position = position_dodge(width=0.9),angle=angle.label, hjust=hjust,size=labelsize)+
theme(text=element_text(size=textsize,family=family),
axis.text = element_text(size=textsize,color="black",family=family),
axis.title = element_text(size=textsize,color="black",family=family))
colint1=colint
print(colint)
letras=paste(graph$letra,
graph$letra1,
sep="")
matriz=data.frame(t(matrix(paste(format(graph$media,digits = dec),letras),ncol = length(levels(Fator1)))))
rownames(matriz)=levels(Fator1)
colnames(matriz)=levels(Fator2)
cat(green(bold("\n-----------------------------------------------------------------\n")))
cat(green(bold("Final table")))
cat(green(bold("\n-----------------------------------------------------------------\n")))
print(matriz)
message(black("\nAverages followed by the same lowercase letter in the column and \nuppercase in the row do not differ by the",mcomp,"(p<",alpha.t,")"))
}
if(quali[1]==FALSE | quali[2]==FALSE){
if(quali[1]==FALSE){
if (mcomp == "tukey"){
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator1 == lf1[i]],
trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(tukey$groups)}}
if (mcomp == "duncan"){
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(duncan$groups)}}
if (mcomp == "lsd"){
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator1 == lf1[i]],
trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(lsd$groups)}}
if (mcomp == "sk"){
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator1 == lf1[i]],trati,
mean, na.rm=TRUE)[rownames(sk)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(sk)}}
}
if(quali[1]==FALSE){
Fator1=fator1a
colint1=polynomial2(Fator1,
response,
Fator2,
grau = grau12,
ylab=ylab,
xlab=xlab,
theme=theme,
DFres= anavaF3[8,1],SSq = anavaF3[8,2])}
if(quali[2]==FALSE){
if (mcomp == "tukey"){
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(tukey$groups)
}}
if (mcomp == "duncan"){
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(duncan$groups)
}}
if (mcomp == "lsd"){
lsdgrafico=c()
ordem=c()
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator2 == lf2[i]],trati,
mean, na.rm=TRUE)[rownames(lsd$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(lsd$groups)}}
if (mcomp == "sk"){
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !="1"){sk$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(sk)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(sk)
}}
}
if(quali[2]==FALSE){
Fator2=fator2a#as.numeric(as.character(Fator2))
colint1=polynomial2(Fator2,
response,
Fator1,
grau = grau21,
ylab=ylab,
xlab=xlab,
theme=theme,
DFres= anavaF3[8,1],SSq = anavaF3[8,2])}
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial2\" command\n"))
}
if(anavaF3[5,5]>alpha.f && anavaF3[6,5]>alpha.f) {
i<-3
{
if(quali[i]==TRUE && anavaF3[i,5]<=alpha.f) {
cat(green(bold("\n------------------------------------------\n")))
cat(green(italic('Analyzing the simple effects of the factor ',names.fat[3])))
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
if(mcomp=='tukey'){letra=TUKEY(resp,fatores[,i],anavaF3[8,1],anavaF3[8,3],alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="sk"){
ad=data.frame(Fator1,Fator2,Fator3)
nrep=table(fatores[,i])[1]
medias=sort(tapply(resp,fatores[i],mean, na.rm=TRUE),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3[8,1],
nrep = nrep,
QME = anavaF3[8,3],
alpha = alpha.t)
letra1=data.frame(resp=medias,groups=sk)
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="duncan"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- duncan(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="lsd"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- LSD(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
print(letra1)
cat(green(bold("\n-----------------------------------------------------------------")))
if(point=="mean_sd"){desvio=tapply(response, c(fatores[i]), sd, na.rm=TRUE)[rownames(letra1)]}
if(point=="mean_se"){desvio=(tapply(response, c(fatores[i]), sd, na.rm=TRUE)/
sqrt(tapply(response, c(fatores[i]), length)))[rownames(letra1)]}
dadosm=data.frame(letra1,
media=tapply(response, c(fatores[i]), mean, na.rm=TRUE)[rownames(letra1)],
desvio=desvio)
dadosm$Tratamentos=factor(rownames(dadosm),levels = unique(unlist(fatores[i])))
dadosm$limite=dadosm$media+dadosm$desvio
dadosm=dadosm[as.character(unique(unlist(fatores[i]))),]
if(addmean==TRUE){dadosm$letra=paste(format(dadosm$media,digits = dec),dadosm$groups)}
if(addmean==FALSE){dadosm$letra=dadosm$groups}
media=dadosm$media
desvio=dadosm$desvio
Tratamentos=dadosm$Tratamentos
letra=dadosm$letra
grafico=ggplot(dadosm,
aes(x=Tratamentos,y=media))
if(fill=="trat"){grafico=grafico+
geom_col(aes(fill=Tratamentos),color=1)}
else{grafico=grafico+
geom_col(aes(fill=Tratamentos),fill=fill,color=1)}
if(errorbar==TRUE){grafico=grafico+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=letra),
family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==FALSE){grafico=grafico+
geom_text(aes(y=media+sup,label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==TRUE){grafico=grafico+
geom_errorbar(data=dadosm,
aes(ymin=media-desvio,
ymax=media+desvio,color=1),
color="black",width=0.3)
grafico1=grafico+theme+
ylab(ylab)+
xlab(parse(text = xlab.factor[3]))+
theme(text = element_text(size=textsize,color="black", family = family),
axis.text = element_text(size=textsize,color="black", family = family),
axis.title = element_text(size=textsize,color="black", family = family),
legend.position = "none")
print(grafico1)}
}
if(quali[i]==FALSE && anavaF3[i,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat('Analyzing the simple effects of the factor ',names.fat[3])
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
grafico1=polynomial(fatores[,i], resp,grau=grau[i],
DFres= anavaF3[8,1],SSq = anavaF3[8,2],ylab = ylab,xlab = parse(text = xlab.factor[3]),point = point)[[1]]
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial\" command"))}
}
}
}
if(anavaF3[7,5]>alpha.f && anavaF3[5,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Interaction",paste(names.fat[1],'*',names.fat[3],sep='')," significant: unfolding the interaction")))
cat(green(bold("\n------------------------------------------\n")))
#Desdobramento de FATOR 1 dentro do niveis de FATOR 3
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[1], ' inside of each level of ', names.fat[3])
cat(green(bold("\n------------------------------------------\n")))
des<-aov(resp~Fator3/Fator1+Fator2+Fator3+Fator2:Fator3+Fator1:Fator2:Fator3)
l<-vector('list',nv3)
names(l)<-names(summary(Fator3))
v<-numeric(0)
for(j in 1:nv3) {
for(i in 0:(nv1-2)) v<-cbind(v,i*nv3+j)
l[[j]]<-v
v<-numeric(0)
}
des1<-summary(des,split=list('Fator3:Fator1'=l))[[1]]
des1a=des1[-c(1,2,3,length(des1[,1]),length(des1[,1])-1,length(des1[,1])-2),]
#============================
rn<-numeric(0)
for (j in 1:nv3) {
rn <- c(rn, paste(paste(names.fat[1], ":", names.fat[3],
sep = ""), lf3[j]))
}
rownames(des1a)=rn
#============================
print(des1a)
if(quali[1]==TRUE & quali[3]==TRUE){
if (mcomp == "tukey"){
tukeygrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator3 == lf3[i]],
trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
tukeygrafico[[i]]=tukey$groups[levels(trati),2]
ordem[[i]]=rownames(tukey$groups[levels(trati),])
}
letra=unlist(tukeygrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "duncan"){
duncangrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator3 == lf3[i]],
trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
duncangrafico[[i]]=duncan$groups[levels(trati),2]
ordem[[i]]=rownames(duncan$groups[levels(trati),])
}
letra=unlist(duncangrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "lsd"){
lsdgrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator3 == lf3[i]],trati,
mean, na.rm=TRUE)[rownames(lsd$groups)]}
lsdgrafico[[i]]=lsd$groups[levels(trati),2]
ordem[[i]]=rownames(lsd$groups[levels(trati),])
}
letra=unlist(lsdgrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "sk"){
skgrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
skgrafico[[i]]=sk[levels(trati),2]
ordem[[i]]=rownames(sk[levels(trati),])
}
letra=unlist(skgrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}}
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[3], " inside of the level of ",names.fat[1])
cat(green(bold("\n------------------------------------------\n")))
des<-aov(resp~Fator1/Fator3+Fator1+Fator2+Fator2:Fator1+Fator1:Fator2:Fator3)
l<-vector('list',nv1)
names(l)<-names(summary(Fator1))
v<-numeric(0)
for(j in 1:nv1) {
for(i in 0:(nv3-2)) v<-cbind(v,i*nv1+j)
l[[j]]<-v
v<-numeric(0)
}
des1<-summary(des,split=list('Fator1:Fator3'=l))[[1]]
des1a=des1[-c(1,2,3,length(des1[,1]),length(des1[,1])-1,length(des1[,1])-2),]
#============================
rn<-numeric(0)
for (j in 1:nv1) {
rn <- c(rn, paste(paste(names.fat[3], ":", names.fat[1],
sep = ""), lf1[j]))
}
rownames(des1a)=rn
#============================
print(des1a)
if(quali[1]==TRUE & quali[3]==TRUE){
if (mcomp == "tukey"){
tukeygrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
tukeygrafico1[[i]]=tukey$groups[levels(trati),2]
}
letra1=unlist(tukeygrafico1)
letra1=toupper(letra1)}
if (mcomp == "duncan"){
duncangrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
duncangrafico1[[i]]=duncan$groups[levels(trati),2]
}
letra1=unlist(duncangrafico1)
letra1=toupper(letra1)}
if (mcomp == "lsd"){
lsdgrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
mod=aov(respi~trati)
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
lsdgrafico1[[i]]=lsd$groups[levels(trati),2]
}
letra1=unlist(lsdgrafico1)
letra1=toupper(letra1)}
if (mcomp == "sk"){
skgrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
mod=aov(respi~trati)
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
skgrafico1[[i]]=sk[levels(trati),2]
}
letra1=unlist(skgrafico1)
letra1=toupper(letra1)}}
if(quali[1]==TRUE & quali[3]==TRUE){
f1=rep(levels(Fator1),e=length(levels(Fator3)))
f3=rep(unique(as.character(Fator3)),length(levels(Fator1)))
media=tapply(response,paste(Fator1,Fator3), mean, na.rm=TRUE)[unique(paste(f1,f3))]
# desvio=tapply(response,paste(Fator1,Fator3), sd, na.rm=TRUE)[unique(paste(f1,f3))]
if(point=="mean_sd"){desvio=tapply(response,paste(Fator1,Fator3), sd, na.rm=TRUE)}
if(point=="mean_se"){desvio=tapply(response,paste(Fator1,Fator3), sd, na.rm=TRUE)/
sqrt(tapply(response,paste(Fator1,Fator3), length))}
desvio=desvio[unique(paste(f1,f3))]
f1=factor(f1,levels = unique(f1))
f3=factor(f3,levels = unique(f3))
graph=data.frame(f1=f1,
f3=f3,
media,
desvio,
letra,letra1,
numero=format(media,digits = dec))
numero=paste(graph$numero,graph$letra,graph$letra1,sep="")
graph$numero=numero
colint=ggplot(graph,
aes(x=f3,
y=media,
fill=f1))+
geom_col(position = "dodge",color="black")+
ylab(ylab)+xlab(xlab)+
theme+
labs(fill=names.fat[1])+
geom_errorbar(aes(ymin=media-desvio,
ymax=media+desvio),
width=0.3,position = position_dodge(width=0.9))+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=numero),
position = position_dodge(width=0.9),angle=angle.label, hjust=hjust,size=labelsize)+
theme(text=element_text(size=textsize,family=family),
axis.text = element_text(size=textsize,color="black",family=family),
axis.title = element_text(size=textsize,color="black",family=family))
colint2=colint
print(colint)
letras=paste(graph$letra,graph$letra1,sep="")
matriz=data.frame(t(matrix(paste(format(graph$media,digits = dec),letras),ncol = length(levels(Fator1)))))
rownames(matriz)=levels(Fator1)
colnames(matriz)=levels(Fator3)
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Final table")))
cat(green(bold("\n------------------------------------------\n")))
print(matriz)
message(black("\n\nAverages followed by the same lowercase letter in the column and \nuppercase in the row do not differ by the",mcomp,"(p<",alpha.t,")"))
}
if(quali[1]==FALSE | quali[3]==FALSE){
if(quali[1]==FALSE){
if (mcomp == "tukey"){
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(tukey$groups)}}
if (mcomp == "duncan"){
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(duncan$groups)}}
if (mcomp == "lsd"){
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(lsd$groups)}}
if (mcomp == "sk"){
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(sk)}}
}
if(quali[1]==FALSE){
Fator1=fator1a#as.numeric(as.character(Fator1))
colint2=polynomial2(Fator1,
response,
Fator3,
grau = grau13,
ylab=ylab,
xlab=xlab,
theme=theme,
DFres= anavaF3[8,1],SSq = anavaF3[8,2])}
if(quali[3]==FALSE){
if (mcomp == "tukey"){
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator3 == lf3[i]],
trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(tukey$groups)}}
if (mcomp == "duncan"){
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator3 == lf3[i]],
trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(duncan$groups)}}
if (mcomp == "lsd"){
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator3 == lf3[i]],trati,
mean, na.rm=TRUE)[rownames(lsd$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(lsd$groups)}}
if (mcomp == "sk"){
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(sk)}}}
if(quali[3]==FALSE){
Fator3=fator3a#as.numeric(as.character(Fator3))
colint2=polynomial2(Fator3,
response,
Fator1,
grau = grau31,
ylab=ylab,
xlab=xlab,
theme=theme,
DFres= anavaF3[8,1],SSq = anavaF3[8,2])}
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial2\" command\n"))
}
#Checar o Fator2
if(anavaF3[4,5]>alpha.f && anavaF3[6,5]>alpha.f) {
i<-2
{
if(quali[i]==TRUE && anavaF3[i,5]<=alpha.f) {
cat(green(bold("\n------------------------------------------\n")))
cat(green(italic('Analyzing the simple effects of the factor ',names.fat[2])))
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
if(mcomp=='tukey'){letra=TUKEY(resp,fatores[,i],anavaF3[8,1],anavaF3[8,3],alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="sk"){
ad=data.frame(Fator1,Fator2,Fator3)
nrep=table(fatores[,i])[1]
medias=sort(tapply(resp,fatores[i],mean, na.rm=TRUE),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3[8,1],
nrep = nrep,
QME = anavaF3[8,3],
alpha = alpha.t)
letra1=data.frame(resp=medias,groups=sk)
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="duncan"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- duncan(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="lsd"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- LSD(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
print(letra1)
cat(green(bold("\n-----------------------------------------------------------------")))
if(point=="mean_sd"){desvio=tapply(response, c(fatores[i]), sd, na.rm=TRUE)[rownames(letra1)]}
if(point=="mean_se"){desvio=(tapply(response, c(fatores[i]), sd, na.rm=TRUE)/
sqrt(tapply(response, c(fatores[i]), length)))[rownames(letra1)]}
dadosm=data.frame(letra1,
media=tapply(response, c(fatores[i]), mean, na.rm=TRUE)[rownames(letra1)],
desvio=desvio)
dadosm$Tratamentos=factor(rownames(dadosm),levels = unique(unlist(fatores[i])))
dadosm$limite=dadosm$media+dadosm$desvio
dadosm=dadosm[as.character(unique(unlist(fatores[i]))),]
if(addmean==TRUE){dadosm$letra=paste(format(dadosm$media,digits = dec),dadosm$groups)}
if(addmean==FALSE){dadosm$letra=dadosm$groups}
media=dadosm$media
desvio=dadosm$desvio
Tratamentos=dadosm$Tratamentos
letra=dadosm$letra
grafico=ggplot(dadosm,
aes(x=Tratamentos,
y=media))
if(fill=="trat"){grafico=grafico+
geom_col(aes(fill=Tratamentos),color=1)}
else{grafico=grafico+
geom_col(aes(fill=Tratamentos),fill=fill,color=1)}
if(errorbar==TRUE){grafico=grafico+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==FALSE){grafico=grafico+
geom_text(aes(y=media+sup,label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==TRUE){grafico=grafico+
geom_errorbar(data=dadosm,aes(ymin=media-desvio,
ymax=media+desvio,color=1),
color="black",width=0.3)
grafico2=grafico+theme+
ylab(ylab)+
xlab(parse(text = xlab.factor[2]))+
theme(text = element_text(size=textsize,color="black", family = family),
axis.text = element_text(size=textsize,color="black", family = family),
axis.title = element_text(size=textsize,color="black", family = family),
legend.position = "none")
print(grafico2)}
}
if(quali[i]==FALSE && anavaF3[i,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat('Analyzing the simple effects of the factor ',names.fat[2])
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
grafico2=polynomial(fatores[,i], resp,grau=grau[i],
DFres= anavaF3[8,1],SSq = anavaF3[8,2],ylab = ylab,xlab = parse(text = xlab.factor[2]),point = point)[[1]]
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial\" command"))
}
cat('\n')
}
}
}
if(anavaF3[7,5]>alpha.f && anavaF3[6,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("\nInteraction",paste(names.fat[2],'*',names.fat[3],sep='')," significant: unfolding the interaction\n")))
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[2], ' inside of each level of ', names.fat[3])
cat(green(bold("\n------------------------------------------\n")))
des<-aov(resp~Fator3/Fator2+Fator1+Fator3+Fator1:Fator3+Fator1:Fator2:Fator3)
l<-vector('list',nv3)
names(l)<-names(summary(Fator3))
v<-numeric(0)
for(j in 1:nv3) {
for(i in 0:(nv2-2)) v<-cbind(v,i*nv3+j)
l[[j]]<-v
v<-numeric(0)
}
des1<-summary(des,split=list('Fator3:Fator2'=l))[[1]]
des1a=des1[-c(1,2,3,length(des1[,1]),length(des1[,1])-1,length(des1[,1])-2),]
#============================
rn<-numeric(0)
for (j in 1:nv3) {
rn <- c(rn, paste(paste(names.fat[2], ":", names.fat[3],
sep = ""), lf3[j]))
}
rownames(des1a)=rn
#============================
print(des1a)
cat(green(bold("\n------------------------------------------\n")))
if(quali[2]==TRUE & quali[3]==TRUE){
if (mcomp == "tukey"){
tukeygrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
mod=aov(respi~trati)
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
tukeygrafico[[i]]=tukey$groups[levels(trati),2]
ordem[[i]]=rownames(tukey$groups[levels(trati),])
}
letra=unlist(tukeygrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "duncan"){
duncangrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
duncangrafico[[i]]=duncan$groups[levels(trati),2]
ordem[[i]]=rownames(duncan$groups[levels(trati),])
}
letra=unlist(duncangrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "lsd"){
lsdgrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
lsdgrafico[[i]]=lsd$groups[levels(trati),2]
ordem[[i]]=rownames(lsd$groups[levels(trati),])
}
letra=unlist(lsdgrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "sk"){
skgrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
skgrafico[[i]]=sk[levels(trati),2]
ordem[[i]]=rownames(sk[levels(trati),])
}
letra=unlist(skgrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}}
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[3], " inside of the level of ",names.fat[2])
cat(green(bold("\n------------------------------------------\n")))
des<-aov(resp~Fator2/Fator3+Fator1+Fator2+Fator1:Fator2+Fator1:Fator2:Fator3)
l<-vector('list',nv2)
names(l)<-names(summary(Fator2))
v<-numeric(0)
for(j in 1:nv2) {
for(i in 0:(nv3-2)) v<-cbind(v,i*nv2+j)
l[[j]]<-v
v<-numeric(0)
}
des1<-summary(des,split=list('Fator2:Fator3'=l))[[1]]
des1a=des1[-c(1,2,3,length(des1[,1]),length(des1[,1])-1,length(des1[,1])-2),]
#============================
rn<-numeric(0)
for (j in 1:nv2) {
rn <- c(rn, paste(paste(names.fat[3], ":", names.fat[2],
sep = ""), lf2[j]))
}
rownames(des1a)=rn
#============================
print(des1a)
if(quali[2]==TRUE & quali[3]==TRUE){
if (mcomp == "tukey"){
tukeygrafico1=c()
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
mod=aov(respi~trati)
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
tukeygrafico1[[i]]=tukey$groups[levels(trati),2]
}
letra1=unlist(tukeygrafico1)
letra1=toupper(letra1)}
if (mcomp == "duncan"){
duncangrafico1=c()
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
duncangrafico1[[i]]=duncan$groups[levels(trati),2]
}
letra1=unlist(duncangrafico1)
letra1=toupper(letra1)}
if (mcomp == "lsd"){
lsdgrafico1=c()
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
lsdgrafico1[[i]]=lsd$groups[levels(trati),2]
}
letra1=unlist(lsdgrafico1)
letra1=toupper(letra1)}
if (mcomp == "sk"){
skgrafico1=c()
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
skgrafico1[[i]]=sk[levels(trati),2]
}
letra1=unlist(skgrafico1)
letra1=toupper(letra1)}}
if(quali[2]==TRUE & quali[3]==TRUE){
f2=rep(levels(Fator2),e=length(levels(Fator3)))
f3=rep(unique(as.character(Fator3)),length(levels(Fator2)))
media=tapply(response,paste(Fator2,Fator3), mean, na.rm=TRUE)[unique(paste(f2,f3))]
# desvio=tapply(response,paste(Fator2,Fator3), sd, na.rm=TRUE)[unique(paste(f2,f3))]
if(point=="mean_sd"){desvio=tapply(response,paste(Fator2,Fator3), sd, na.rm=TRUE)}
if(point=="mean_se"){desvio=tapply(response,paste(Fator2,Fator3), sd, na.rm=TRUE)/
sqrt(tapply(response,paste(Fator2,Fator3), length))}
desvio=desvio[unique(paste(f2,f3))]
f2=factor(f2,levels = unique(f2))
f3=factor(f3,levels = unique(f3))
graph=data.frame(f2=f2,
f3=f3,
media,
desvio,
letra,letra1,
numero=format(media,digits = dec))
numero=paste(graph$numero,graph$letra,graph$letra1,sep="")
graph$numero=numero
colint=ggplot(graph,
aes(x=f3,
y=media,
fill=f2))+
geom_col(position = "dodge",color="black")+
ylab(ylab)+xlab(xlab)+
theme+
labs(fill=names.fat[2])+
geom_errorbar(aes(ymin=media-desvio,
ymax=media+desvio),
width=0.3,position = position_dodge(width=0.9))+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=numero),
position = position_dodge(width=0.9),angle=angle.label, hjust=hjust,size=labelsize)+
theme(text=element_text(size=textsize,family=family),
axis.text = element_text(size=textsize,color="black",family=family),
axis.title = element_text(size=textsize,color="black",family=family))
colint3=colint
print(colint)
letras=paste(graph$letra,graph$letra1,sep="")
matriz=data.frame(t(matrix(paste(format(graph$media,digits = dec),letras),ncol = length(levels(Fator2)))))
rownames(matriz)=levels(Fator2)
colnames(matriz)=levels(Fator3)
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Final table")))
cat(green(bold("\n------------------------------------------\n")))
print(matriz)
message(black("\n\nAverages followed by the same lowercase letter in the column and \nuppercase in the row do not differ by the",mcomp,"(p<",alpha.t,")"))
}
if(quali[2]==FALSE | quali[3]==FALSE){
if(quali[2]==FALSE){
if (mcomp == "tukey"){
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
mod=aov(respi~trati)
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(tukey$groups)}}
if (mcomp == "duncan"){
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(duncan$groups)}}
if (mcomp == "lsd"){
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(lsd$groups)}}
if (mcomp == "sk"){
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
# sk=sk(respi,trati,anavaF3$Df[8],anavaF3$`Sum Sq`[8],alpha.t)
if(transf !=1){sk$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(sk)}}
}
if(quali[2]==FALSE){
Fator2=fator2a#as.numeric(as.character(Fator2))
colint3=polynomial2(Fator2,
response,
Fator3,
grau = grau23,
ylab=ylab,
xlab=xlab,
theme=theme,
DFres= anavaF3[8,1],SSq = anavaF3[8,2])}
if(quali[3]==FALSE){
if (mcomp == "tukey"){
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
mod=aov(respi~trati)
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(tukey$groups)}}
if (mcomp == "duncan"){
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(duncan$groups)}}
if (mcomp == "lsd"){
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(lsd$groups)}}
if (mcomp == "sk"){
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
# sk=sk(respi,trati,anavaF3$Df[8],anavaF3$`Sum Sq`[8],alpha.t)
if(transf !=1){sk$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(sk)}}
}
if(quali[3]==FALSE){
Fator3=fator3a#as.numeric(as.character(Fator3))
colint3=polynomial2(Fator3,
response,
Fator2,
grau = grau32,
ylab=ylab,
xlab=xlab,
theme=theme,
DFres= anavaF3[8,1],SSq = anavaF3[8,2])}
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial2\" command"))
}
if(anavaF3[4,5]>alpha.f && anavaF3[5,5]>alpha.f) {
i<-1
{
if(quali[i]==TRUE && anavaF3[i,5]<=alpha.f) {
cat(green(bold("\n------------------------------------------\n")))
cat(green(italic('Analyzing the simple effects of the factor ',names.fat[2])))
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
if(mcomp=='tukey'){letra=TUKEY(resp,fatores[,i],anavaF3[8,1],anavaF3[8,3],alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="sk"){
ad=data.frame(Fator1,Fator2,Fator3)
nrep=table(fatores[,i])[1]
medias=sort(tapply(resp,fatores[i],mean, na.rm=TRUE),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3[8,1],
nrep = nrep,
QME = anavaF3[8,3],
alpha = alpha.t)
letra1=data.frame(resp=medias,groups=sk)
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="duncan"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- duncan(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="lsd"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- LSD(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
print(letra1)
cat(green(bold("\n------------------------------------------\n")))
if(point=="mean_sd"){desvio=tapply(response, c(fatores[i]), sd, na.rm=TRUE)[rownames(letra1)]}
if(point=="mean_se"){desvio=(tapply(response, c(fatores[i]), sd, na.rm=TRUE)/
sqrt(tapply(response, c(fatores[i]), length)))[rownames(letra1)]}
dadosm=data.frame(letra1,
media=tapply(response, c(fatores[i]), mean, na.rm=TRUE)[rownames(letra1)],
desvio=desvio)
dadosm$Tratamentos=factor(rownames(dadosm),levels = unique(unlist(fatores[i])))
dadosm$limite=dadosm$media+dadosm$desvio
dadosm=dadosm[as.character(unique(unlist(fatores[i]))),]
if(addmean==TRUE){dadosm$letra=paste(format(dadosm$media,digits = dec),dadosm$groups)}
if(addmean==FALSE){dadosm$letra=dadosm$groups}
media=dadosm$media
desvio=dadosm$desvio
Tratamentos=dadosm$Tratamentos
letra=dadosm$letra
grafico=ggplot(dadosm,
aes(x=Tratamentos,
y=media))
if(fill=="trat"){grafico=grafico+
geom_col(aes(fill=Tratamentos),color=1)}
else{grafico=grafico+
geom_col(aes(fill=Tratamentos),fill=fill,color=1)}
if(errorbar==TRUE){grafico=grafico+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==FALSE){grafico=grafico+
geom_text(aes(y=media+sup,label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==TRUE){grafico=grafico+
geom_errorbar(data=dadosm,aes(ymin=media-desvio,
ymax=media+desvio,color=1),
color="black",width=0.3)
grafico3=grafico+theme+
ylab(ylab)+
xlab(parse(text = xlab.factor[1]))+
theme(text = element_text(size=textsize,color="black", family = family),
axis.text = element_text(size=textsize,color="black", family = family),
axis.title = element_text(size=textsize,color="black", family = family),
legend.position = "none")
print(grafico3)}
}
if(quali[i]==FALSE && anavaF3[i,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat('Analyzing the simple effects of the factor ',names.fat[2])
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
grafico3=polynomial(fatores[,i], resp,grau=grau[i],
DFres= anavaF3[8,1],SSq = anavaF3[8,2],ylab = ylab,xlab=parse(text = xlab.factor[1]),point = point)[[1]]
print(grafico3)
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial\" command"))
}
cat('\n')
}
}
}
if(anavaF3[7,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Interaction",paste(names.fat[1],'*',names.fat[2],'*',names.fat[3],sep='')," significant: unfolding the interaction")))
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[1], ' inside of each level of ', names.fat[2], 'and',names.fat[3])
cat(green(bold("\n------------------------------------------\n")))
m1=aov(resp~(Fator2*Fator3)/Fator1)
anova(m1)
pattern <- c(outer(levels(Fator2), levels(Fator3),
function(x,y) paste("Fator2",x,":Fator3",y,":",sep="")))
des.tab <- sapply(pattern, simplify=FALSE,
grep, x=names(coef(m1)[m1$assign==4]))
des1.tab <- summary(m1, split = list("Fator2:Fator3:Fator1" = des.tab))
desd=des1.tab[[1]][-c(1,2,3,4),]
desd=data.frame(desd[-length(rownames(desd)),])
# rownames(desd)=cbind(paste("Fator2:",rep(levels(Fator2),length(levels(Fator3))),
# "Fator3:",rep(levels(Fator3),e=length(levels(Fator2)))))
#
rownames(desd)=cbind(paste(names.fat[2],":",rep(levels(Fator2),length(levels(Fator3))),
names.fat[3],":",rep(levels(Fator3),e=length(levels(Fator2)))))
colnames(desd)=c("Df", "Sum Sq", "Mean Sq", "F value", "Pr(>F)")
print(desd)
ii<-0
for(i in 1:nv2) {
for(j in 1:nv3) {
ii<-ii+1
if(quali[1]==TRUE){
cat('\n',names.fat[1],' within the combination of levels ',lf2[i],' of ',names.fat[2],' and ',lf3[j],' of ',names.fat[3],"\n")
if(mcomp=='tukey'){tukey=TUKEY(resp[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
tukey=tukey$groups;colnames(tukey)=c("resp","letters")
if(transf !=1){tukey$respo=tapply(response[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
mean, na.rm=TRUE)[rownames(tukey)]}
print(tukey)}
if(mcomp=='duncan'){duncan=duncan(resp[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
duncan=duncan$groups;colnames(duncan)=c("resp","letters")
if(transf !=1){duncan$respo=tapply(response[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
mean, na.rm=TRUE)[rownames(duncan)]}
print(duncan)}
if(mcomp=='lsd'){lsd=LSD(resp[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
lsd=lsd$groups;colnames(lsd)=c("resp","letters")
if(transf !=1){lsd$respo=tapply(response[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
mean, na.rm=TRUE)[rownames(lsd)]}
print(lsd)}
if(mcomp=='sk'){
fat= fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]]
fat1=factor(fat,unique(fat))
levels(fat1)=1:length(levels(fat1))
respi=resp[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]]
nrep=table(fat1)[1]
medias=sort(tapply(respi,fat1,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
colnames(sk)=c("resp","letters")
sk=sk[as.character(unique(fat1)),]
rownames(sk)=unique(fat)
if(transf !=1){sk$respo=tapply(response[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
mean, na.rm=TRUE)[rownames(sk)]}
print(sk)}
}
if(quali[1]==FALSE){
cat('\n',names.fat[1],' within the combination of levels ',lf2[i],' of ',names.fat[2],' and ',lf3[j],' of ',names.fat[3],"\n")
polynomial(fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
resp[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],grau=grau123,
DFres= anavaF3[8,1],SSq = anavaF3[8,2],ylab=ylab,xlab=xlab,point = point)[[1]]}
}
}
cat('\n\n')
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[2], ' inside of each level of ', names.fat[1], 'and',names.fat[3])
cat(green(bold("\n------------------------------------------\n")))
m1=aov(resp~(Fator1*Fator3)/Fator2)
anova(m1)
pattern <- c(outer(levels(Fator1), levels(Fator3),
function(x,y) paste("Fator1",x,":Fator3",y,":",sep="")))
des.tab <- sapply(pattern, simplify=FALSE,
grep, x=names(coef(m1)[m1$assign==4]))
des1.tab <- summary(m1, split = list("Fator1:Fator3:Fator2" = des.tab))
desd=des1.tab[[1]][-c(1,2,3,4),]
desd=data.frame(desd[-length(rownames(desd)),])
# rownames(desd)=cbind(paste("Fator1:",rep(levels(Fator1),length(levels(Fator3))),
# "Fator3:",rep(levels(Fator3),e=length(levels(Fator1)))))
rownames(desd)=cbind(paste(names.fat[1],":",rep(levels(Fator1),length(levels(Fator3))),
names.fat[3],":",rep(levels(Fator3),e=length(levels(Fator1)))))
colnames(desd)=c("Df", "Sum Sq", "Mean Sq", "F value", "Pr(>F)")
print(desd)
ii<-0
for(k in 1:nv1) {
for(j in 1:nv3) {
ii<-ii+1
if(quali[2]==TRUE){
cat('\n\n',names.fat[2],' within the combination of levels ',lf1[k],' of ',names.fat[1],' and ',lf3[j],' of ',names.fat[3],'\n')
if(mcomp=='tukey'){tukey=TUKEY(resp[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
tukey=tukey$groups;colnames(tukey)=c("resp","letters")
if(transf !=1){tukey$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],mean, na.rm=TRUE)[rownames(tukey)]}
print(tukey)}
if(mcomp=='duncan'){duncan=duncan(resp[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
duncan=duncan$groups;colnames(duncan)=c("resp","letters")
if(transf !=1){duncan$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],mean, na.rm=TRUE)[rownames(duncan)]}
print(duncan)}
if(mcomp=='lsd'){lsd=LSD(resp[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
lsd=lsd$groups;colnames(lsd)=c("resp","letters")
if(transf !=1){lsd$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],mean, na.rm=TRUE)[rownames(lsd)]}
print(lsd)}
if(mcomp=='sk'){
fat=fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]]
fat1=factor(fat,unique(fat))
levels(fat1)=1:length(levels(fat1))
respi=resp[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]]
nrep=table(fat1)[1]
medias=sort(tapply(respi,fat1,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
colnames(sk)=c("resp","letters")
sk=sk[as.character(unique(fat1)),]
rownames(sk)=unique(fat)
if(transf !=1){sk$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],mean, na.rm=TRUE)[rownames(sk)]}
print(sk)}
}
if(quali[2]==FALSE){
cat('\n\n',names.fat[2],' within the combination of levels ',lf1[k],' of ',names.fat[1],' and ',lf3[j],' of ',names.fat[3],'\n')
polynomial(fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],
resp[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
DFres= anavaF3[8,1],SSq = anavaF3[8,2],grau=grau213,
ylab = ylab,xlab = xlab,point = point)[[1]]}
}
}
#===================================================================
#Desdobramento de FATOR 3 dentro do niveis de FATOR 1 e FATOR 2
#===================================================================
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[3], ' inside of each level of ', names.fat[1], 'and',names.fat[2])
cat(green(bold("\n------------------------------------------\n")))
m1=aov(resp~(Fator1*Fator2)/Fator3)
anova(m1)
pattern <- c(outer(levels(Fator1), levels(Fator2),
function(x,y) paste("Fator1",x,":Fator2",y,":",sep="")))
des.tab <- sapply(pattern, simplify=FALSE,
grep, x=names(coef(m1)[m1$assign==4]))
des1.tab <- summary(m1, split = list("Fator1:Fator2:Fator3" = des.tab))
desd=des1.tab[[1]][-c(1,2,3,4),]
desd=data.frame(desd[-length(rownames(desd)),])
# rownames(desd)=cbind(paste("Fator1:",rep(levels(Fator1),length(levels(Fator2))),
# "Fator2:",rep(levels(Fator2),e=length(levels(Fator1)))))
rownames(desd)=cbind(paste(names.fat[1],":",rep(levels(Fator1),length(levels(Fator2))),
names.fat[2],":",rep(levels(Fator2),e=length(levels(Fator1)))))
colnames(desd)=c("Df", "Sum Sq", "Mean Sq", "F value", "Pr(>F)")
print(desd)
ii<-0
for(k in 1:nv1) {
for(i in 1:nv2) {
ii<-ii+1
if(quali[3]==TRUE){
cat('\n\n',names.fat[3],' within the combination of levels ',lf1[k],' of ',names.fat[1],' and ',lf2[i],' of ',names.fat[2],'\n')
if(mcomp=='tukey'){tukey=TUKEY(resp[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
tukey=tukey$groups;colnames(tukey)=c("resp","letters")
if(transf !=1){tukey$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
mean, na.rm=TRUE)[rownames(tukey)]}
print(tukey)}
if(mcomp=='duncan'){duncan=duncan(resp[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
duncan=duncan$groups;colnames(duncan)=c("resp","letters")
if(transf !=1){duncan$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
mean, na.rm=TRUE)[rownames(duncan)]}
print(duncan)}
if(mcomp=='lsd'){lsd=LSD(resp[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
lsd=lsd$groups;colnames(lsd)=c("resp","letters")
if(transf !=1){lsd$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
mean, na.rm=TRUE)[rownames(lsd)]}
print(lsd)}
if(mcomp=='sk'){
fat=fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]]
fat1=factor(fat,unique(fat))
levels(fat1)=1:length(levels(fat1))
respi=resp[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]]
nrep=table(fat1)[1]
medias=sort(tapply(respi,fat1,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
# sk=sk(resp[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
# fat1,
# anavaF3$Df[8],
# anavaF3$`Sum Sq`[8],
# alpha.t)
colnames(sk)=c("resp","letters")
sk=sk[as.character(unique(fat1)),]
rownames(sk)=unique(fat)
if(transf !=1){sk$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
mean, na.rm=TRUE)[rownames(sk)]}
print(sk)}
}
if(quali[3]==FALSE){
cat('\n\n',names.fat[3],' inside of each level of ',lf1[k],' of ',names.fat[1],' and ',lf2[i],' of ',names.fat[2],'\n')
polynomial(fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
resp[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],grau=grau312,
DFres= anavaF3[8,1],SSq = anavaF3[8,2],ylab = ylab,xlab = xlab,point = point)[[1]]}
}
}
}
if(anavaF3[4,5]>alpha.f && anavaF3[5,5]>alpha.f && anavaF3[6,5]>alpha.f && anavaF3[7,5]>alpha.f){
if(anavaF3[1,5]<=alpha.f | anavaF3[2,5]<=alpha.f | anavaF3[3,5]<=alpha.f){
graficos}else{graficos=NA}}
if(anavaF3[7,5]>alpha.f && anavaF3[4,5]<=alpha.f){
graficos=list(residplot,colint1)
if(anavaF3[5,5]>alpha.f && anavaF3[6,5]>alpha.f && anavaF3[3,5]<=alpha.f){
graficos=list(residplot,colint1,grafico1)}
graficos}
if(anavaF3[7,5]>alpha.f && anavaF3[5,5]<=alpha.f){
graficos=list(residplot,colint2)
if(anavaF3[4,5]>alpha.f && anavaF3[6,5]>alpha.f && anavaF3[2,5]<=alpha.f){
graficos=list(residplot,colint2,grafico2)}
graficos}
if(anavaF3[7,5]>alpha.f && anavaF3[6,5]<=alpha.f){
graficos=list(residplot,colint3)
if(anavaF3[4,5]>alpha.f && anavaF3[5,5]>alpha.f && anavaF3[1,5]<=alpha.f){
graficos=list(residplot,colint3,grafico3)}}
if(anavaF3[7,5]>alpha.f && anavaF3[4,5]<=alpha.f && anavaF3[5,5]<=alpha.f){
graficos=list(residplot,colint1,colint2)
graficos}
if(anavaF3[7,5]>alpha.f && anavaF3[4,5]<=alpha.f && anavaF3[6,5]<=alpha.f){
graficos=list(residplot,colint1,colint3)
graficos}
if(anavaF3[7,5]>alpha.f && anavaF3[5,5]<=alpha.f && anavaF3[6,5]<=alpha.f){
graficos=list(residplot,colint2,colint3)
graficos}
if(anavaF3[7,5]<=alpha.f){graficos=list(residplot)}
graficos=graficos
}
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Defines functions FAT3DIC
Documented in FAT3DIC
#' Analysis: DIC experiments in triple factorial
#' @description Analysis of an experiment conducted in a completely randomized design in a triple factorial scheme using analysis of variance of fixed effects.
#' @author Gabriel Danilo Shimizu, \email{shimizu@uel.br}
#' @author Leandro Simoes Azeredo Goncalves
#' @author Rodrigo Yudi Palhaci Marubayashi
#' @param f1 Numeric or complex vector with factor 1 levels
#' @param f2 Numeric or complex vector with factor 2 levels
#' @param f3 Numeric or complex vector with factor 3 levels
#' @param response Numerical vector containing the response of the experiment.
#' @param mcomp Multiple comparison test (Tukey (\emph{default}), LSD, Scott-Knott and Duncan)
#' @param quali Defines whether the factor is quantitative or qualitative (\emph{qualitative})
#' @param names.fat Allows labeling the factors 1, 2 and 3.
#' @param grau Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with three elements.
#' @param grau12 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 2, in the case of interaction f1 x f2 and qualitative factor 2 and quantitative factor 1.
#' @param grau21 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 1, in the case of interaction f1 x f2 and qualitative factor 1 and quantitative factor 2.
#' @param grau13 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 3, in the case of interaction f1 x f3 and qualitative factor 3 and quantitative factor 1.
#' @param grau31 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 1, in the case of interaction f1 x f3 and qualitative factor 1 and quantitative factor 3.
#' @param grau23 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 3, in the case of interaction f2 x f3 and qualitative factor 3 and quantitative factor 2.
#' @param grau32 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 2, in the case of interaction f2 x f3 and qualitative factor 2 and quantitative factor 3.
#' @param grau123 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 1, in the case of interaction f1 x f2 x f3 and quantitative factor 1.
#' @param grau213 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 2, in the case of interaction f1 x f2 x f3 and quantitative factor 2.
#' @param grau312 Polynomial degree in case of quantitative factor (\emph{default} is 1). Provide a vector with n levels of factor 3, in the case of interaction f1 x f2 x f3 and quantitative factor 3.
#' @param xlab treatments name (Accepts the \emph{expression}() function)
#' @param ylab Variable response name (Accepts the \emph{expression}() function)
#' @param xlab.factor Provide a vector with two observations referring to the x-axis name of factors 1, 2 and 3, respectively, when there is an isolated effect of the factors. This argument uses `parse`.
#' @param alpha.t Significance level of the multiple comparison test (\emph{default} is 0.05)
#' @param alpha.f Level of significance of the F test (\emph{default} is 0.05)
#' @param norm Error normality test (\emph{default} is Shapiro-Wilk)
#' @param transf Applies data transformation (\emph{default} is 1; for log consider 0; `angular` for angular transformation)
#' @param constant Add a constant for transformation (enter value)
#' @param sup Number of units above the standard deviation or average bar on the graph
#' @param geom Graph type (columns or segments)
#' @param fill Defines chart color (to generate different colors for different treatments, define fill = "trat")
#' @param angulo x-axis scale text rotation
#' @param textsize Font size
#' @param labelsize Label Size
#' @param dec Number of cells
#' @param family Font family
#' @param theme ggplot2 theme (\emph{default} is theme_classic())
#' @param addmean Plot the average value on the graph (\emph{default} is TRUE)
#' @param errorbar Plot the standard deviation bar on the graph (In the case of a segment and column graph) - \emph{default} is TRUE
#' @param point This function defines whether the point must have all points ("all"), mean ("mean"), standard deviation (\emph{default} - "mean_sd") or mean with standard error ("mean_se") if quali= FALSE. For quali=TRUE, `mean_sd` and `mean_se` change which information will be displayed in the error bar.
#' @param angle.label label angle
#' @note The order of the chart follows the alphabetical pattern. Please use `scale_x_discrete` from package ggplot2, `limits` argument to reorder x-axis. The bars of the column and segment graphs are standard deviation.
#' @return The analysis of variance table, the Shapiro-Wilk error normality test, the Bartlett homogeneity test of variances, the Durbin-Watson error independence test, multiple comparison test (Tukey, LSD, Scott-Knott or Duncan) or adjustment of regression models up to grade 3 polynomial, in the case of quantitative treatments. The column chart for qualitative treatments is also returned.For significant triple interaction only, no graph is returned.
#' @note The function does not perform multiple regression in the case of two or more quantitative factors. The bars of the column and segment graphs are standard deviation.
#' @note In the final output when transformation (transf argument) is different from 1, the columns resp and respo in the mean test are returned, indicating transformed and non-transformed mean, respectively.
#' @references
#'
#' Principles and procedures of statistics a biometrical approach Steel, Torry and Dickey. Third Edition 1997
#'
#' Multiple comparisons theory and methods. Departament of statistics the Ohio State University. USA, 1996. Jason C. Hsu. Chapman Hall/CRC.
#'
#' Practical Nonparametrics Statistics. W.J. Conover, 1999
#'
#' Ramalho M.A.P., Ferreira D.F., Oliveira A.C. 2000. Experimentacao em Genetica e Melhoramento de Plantas. Editora UFLA.
#'
#' Scott R.J., Knott M. 1974. A cluster analysis method for grouping mans in the analysis of variance. Biometrics, 30, 507-512.
#'
#' Ferreira, E. B., Cavalcanti, P. P., and Nogueira, D. A. (2014). ExpDes: an R package for ANOVA and experimental designs. Applied Mathematics, 5(19), 2952.
#'
#' Mendiburu, F., and de Mendiburu, M. F. (2019). Package ‘agricolae’. R Package, Version, 1-2.
#'
#' @keywords DIC
#' @keywords Factorial
#' @export
#' @examples
#' library(AgroR)
#' data(enxofre)
#' with(enxofre, FAT3DIC(f1, f2, f3, resp))
######################################################################################
## Analise de variancia para experimentos em DIC
######################################################################################
FAT3DIC=function(f1,
f2,
f3,
response,
norm="sw",
alpha.t=0.05,
alpha.f=0.05,
quali=c(TRUE,TRUE,TRUE),
mcomp='tukey',
grau=c(NA,NA,NA),
grau12=NA, # F1/F2
grau13=NA, # F1/F3
grau23=NA, # F2/F3
grau21=NA, # F2/F1
grau31=NA, # F3/F1
grau32=NA, # F3/F2
grau123=NA,
grau213=NA,
grau312=NA,
transf=1,
constant=0,
names.fat=c("F1","F2","F3"),
ylab="Response",
xlab="",
xlab.factor=c("F1","F2","F3"),
sup=NA,
fill="lightblue",
theme=theme_classic(),
angulo=0,
family="sans",
addmean=TRUE,
errorbar=TRUE,
dec=3,
geom="bar",
textsize=12,
labelsize=4,
point="mean_sd",
angle.label=0) {
if(is.na(sup==TRUE)){sup=0.2*mean(response)}
if(angle.label==0){hjust=0.5}else{hjust=0}
if(transf==1){resp=response+constant}else{if(transf!="angular"){resp=((response+constant)^transf-1)/transf}}
# if(transf==1){resp=response+constant}else{resp=((response+constant)^transf-1)/transf}
if(transf==0){resp=log(response+constant)}
if(transf==0.5){resp=sqrt(response+constant)}
if(transf==-0.5){resp=1/sqrt(response+constant)}
if(transf==-1){resp=1/(response+constant)}
if(transf=="angular"){resp=asin(sqrt((response+constant)/100))}
ordempadronizado=data.frame(f1,f2,f3,response,resp)
resp1=resp
organiz=data.frame(f1,f2,f3,response,resp)
organiz=organiz[order(organiz$f3),]
organiz=organiz[order(organiz$f2),]
organiz=organiz[order(organiz$f1),]
f1=organiz$f1
f2=organiz$f2
f3=organiz$f3
response=organiz$response
resp=organiz$resp
fator1=f1
fator2=f2
fator3=f3
fator1a=fator1
fator2a=fator2
fator3a=fator3
requireNamespace("crayon")
requireNamespace("ggplot2")
requireNamespace("nortest")
fatores<-data.frame(fator1,fator2,fator3)
Fator1<-factor(fator1,levels=unique(fator1));
Fator2<-factor(fator2,levels=unique(fator2));
Fator3<-factor(fator3,levels=unique(fator3))
nv1<-length(summary(Fator1)); nv2<-length(summary(Fator2)); nv3<-length(summary(Fator3))
J<-(length(resp))/(nv1*nv2*nv3)
lf1<-levels(Fator1); lf2<-levels(Fator2); lf3<-levels(Fator3)
anava<-aov(resp~Fator1*Fator2*Fator3)
anavaF3<-anova(anava)
anovaF3=anavaF3
colnames(anovaF3)=c("GL","SQ","QM","Fcal","p-value")
anavares<-aov(resp~as.factor(f1)*
as.factor(f2)*
as.factor(f3),data = ordempadronizado)
respad=anavares$residuals/sqrt(anavaF3$`Mean Sq`[8])
out=respad[respad>3 | respad<(-3)]
out=names(out)
out=if(length(out)==0)("No discrepant point")else{out}
Ids=ifelse(respad>3 | respad<(-3), "darkblue","black")
residplot=ggplot(data=data.frame(respad,Ids),aes(y=respad,x=1:length(respad)))+
geom_point(shape=21,color="gray",fill="gray",size=3)+
labs(x="",y="Standardized residuals")+
geom_text(x=1:length(respad),label=1:length(respad),color=Ids,size=labelsize)+
scale_x_continuous(breaks=1:length(respad))+
theme_classic()+theme(axis.text.y = element_text(size=textsize),
axis.text.x = element_blank())+
geom_hline(yintercept = c(0,-3,3),lty=c(1,2,2),color="red",size=1)
# print(residplot)
#Teste de normalidade
norm1<-shapiro.test(anava$residuals)
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Normality of errors")))
cat(green(bold("\n------------------------------------------\n")))
print(norm1)
message(if(norm1$p.value>0.05){
black("As the calculated p-value is greater than the 5% significance level, hypothesis H0 is not rejected. Therefore, errors can be considered normal")}
else {"As the calculated p-value is less than the 5% significance level, H0 is rejected. Therefore, errors do not follow a normal distribution"})
homog1=bartlett.test(anava$residuals~paste(Fator1,Fator2,Fator3))
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Homogeneity of Variances")))
cat(green(bold("\n------------------------------------------\n")))
print(homog1)
message(if(homog1$p.value[1]>0.05){
black("As the calculated p-value is greater than the 5% significance level, hypothesis H0 is not rejected. Therefore, the variances can be considered homogeneous")}
else {"As the calculated p-value is less than the 5% significance level, H0 is rejected. Therefore, the variances are not homogeneous"})
indep=dwtest(anava)
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Independence from errors")))
cat(green(bold("\n------------------------------------------\n")))
print(indep)
message(if(indep$p.value>0.05){
black("As the calculated p-value is greater than the 5% significance level, hypothesis H0 is not rejected. Therefore, errors can be considered independent")}
else {"As the calculated p-value is less than the 5% significance level, H0 is rejected. Therefore, errors are not independent"})
cat("\n")
cat(green(bold("\n-----------------------------------------------------------------\n")))
cat(green(bold("Additional Information")))
cat(green(bold("\n-----------------------------------------------------------------\n")))
cat(paste("\nCV (%) = ",round(sqrt(anavaF3$`Mean Sq`[8])/mean(resp,na.rm=TRUE)*100,2)))
cat(paste("\nMean = ",round(mean(response,na.rm=TRUE),4)))
cat(paste("\nMedian = ",round(median(response,na.rm=TRUE),4)))
cat("\nPossible outliers = ", out)
cat("\n")
cat(green(bold("\n------------------------------------------\n")))
cat(green(italic("Analysis of Variance")))
cat(green(bold("\n------------------------------------------\n")))
anava1=as.matrix(data.frame(anovaF3))
colnames(anava1)=c("Df","Sum Sq","Mean.Sq","F value","Pr(F)" )
rownames(anava1)=c(names.fat[1],
names.fat[2],
names.fat[3],
paste(names.fat[1],"x",names.fat[2]),
paste(names.fat[1],"x",names.fat[3]),
paste(names.fat[2],"x",names.fat[3]),
paste(names.fat[1],"x",names.fat[2],"x",names.fat[3]),
"Residuals")
print(anava1,na.print = "")
cat("\n")
if(transf==1 && norm1$p.value<0.05 | transf==1 && indep$p.value<0.05 | transf==1 &&homog1$p.value<0.05){
message("\n Your analysis is not valid, suggests using a non-parametric test and try to transform the data\n")}else{}
if(transf != 1 && norm1$p.value<0.05 | transf!=1 && indep$p.value<0.05 | transf!=1 && homog1$p.value<0.05){
message("\n Your analysis is not valid, suggests using the function FATDIC.art\n")}else{}
message(if(transf !=1){blue("\nNOTE: resp = transformed means; respO = averages without transforming\n")})
if(anavaF3[4,5]>alpha.f && anavaF3[5,5]>alpha.f && anavaF3[6,5]>alpha.f && anavaF3[7,5]>alpha.f) {
graficos=list(1,2,3)
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold('Non-significant interaction: analyzing the simple effects')))
cat(green(bold("\n------------------------------------------\n")))
fatores<-data.frame('fator 1'=fator1,'fator 2' = fator2,'fator 3' = fator3)
for(i in 1:3){
if(quali[i]==TRUE && anavaF3[i,5]<=alpha.f) {
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
cat(green(bold("\n------------------------------------------\n")))
if(mcomp=='tukey'){letra=TUKEY(resp,fatores[,i],anavaF3[8,1],anavaF3[8,3],alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="sk"){
nrep=table(fatores[,i])[1]
medias=sort(tapply(resp,fatores[i],mean, na.rm=TRUE),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3[8,1],
nrep = nrep,
QME = anavaF3[8,3],
alpha = alpha.t)
letra1=data.frame(resp=medias,groups=sk)
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="duncan"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- duncan(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="lsd"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- LSD(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
teste=if(mcomp=="tukey"){"Tukey HSD"}else{
if(mcomp=="sk"){"Scott-Knott"}else{
if(mcomp=="lsd"){"LSD-Fischer"}else{
if(mcomp=="duncan"){"Duncan"}}}}
cat(green(italic(paste("Multiple Comparison Test:",teste,"\n"))))
print(letra1)
cat(green(bold("\n------------------------------------------\n")))
#=====================================================
if(point=="mean_sd"){desvio=tapply(response, c(fatores[i]), sd, na.rm=TRUE)[rownames(letra1)]}
if(point=="mean_se"){desvio=(tapply(response, c(fatores[i]), sd, na.rm=TRUE)/
sqrt(tapply(response, c(fatores[i]), length)))[rownames(letra1)]}
dadosm=data.frame(letra1,
media=tapply(response, c(fatores[i]), mean, na.rm=TRUE)[rownames(letra1)],
desvio=desvio)
dadosm$trats=factor(rownames(dadosm),
levels = unique(unlist(fatores[i])))
dadosm$limite=dadosm$media+dadosm$desvio
dadosm=dadosm[as.character(unique(unlist(fatores[i]))),]
if(addmean==TRUE){dadosm$letra=paste(format(dadosm$media,digits = dec),dadosm$groups)}
if(addmean==FALSE){dadosm$letra=dadosm$groups}
media=dadosm$media
desvio=dadosm$desvio
trats=dadosm$trats
letra=dadosm$letra
if(geom=="bar"){grafico=ggplot(dadosm,
aes(x=trats,
y=media))
if(fill=="trat"){grafico=grafico+
geom_col(aes(fill=trats),
color=1)}else{grafico=grafico+
geom_col(aes(fill=trats),
fill=fill,color=1)}
if(errorbar==TRUE){grafico=grafico+
geom_text(aes(y=media+sup+
if(sup<0){-desvio}else{desvio},
label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==FALSE){grafico=grafico+
geom_text(aes(y=media+sup,label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==TRUE){grafico=grafico+
geom_errorbar(data=dadosm,
aes(ymin=media-desvio,
ymax=media+desvio,color=1),
color="black",width=0.3)}
grafico=grafico+
theme+
ylab(ylab)+
xlab(parse(text = xlab.factor[i]))+
theme(text = element_text(size=textsize,color="black", family = family),
axis.text = element_text(size=textsize,color="black", family = family),
axis.title = element_text(size=textsize,color="black", family = family),
legend.position = "none")
print(grafico)}
# ================================
# grafico de segmentos
# ================================
if(geom=="point"){grafico=ggplot(dadosm,
aes(x=trats,
y=media))
if(fill=="trat"){grafico=grafico+
geom_point(aes(color=trats))}
else{grafico=grafico+
geom_point(aes(color=trats),color=fill,size=4)}
if(errorbar==TRUE){grafico=grafico+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==FALSE){grafico=grafico+
geom_text(aes(y=media+sup,label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==TRUE){grafico=grafico+
geom_errorbar(data=dadosm,
aes(ymin=media-desvio,
ymax=media+desvio,color=1),
color="black",width=0.3)}
grafico=grafico+theme+
ylab(ylab)+
xlab(parse(text = xlab.factor[i]))+
theme(text = element_text(size=textsize,color="black", family = family),
axis.text = element_text(size=textsize,color="black", family = family),
axis.title = element_text(size=textsize,color="black", family = family),
legend.position = "none")
print(grafico)}
}
if(anavaF3[i,5]>alpha.f) {
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
cat(green(bold("\n------------------------------------------\n")))
mean.table<-mean_stat(response,fatores[,i],mean)
colnames(mean.table)<-c('Levels','Mean')
print(mean.table)
grafico=NA}
if(quali[i]==FALSE && anavaF3[i,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
cat(green(bold("\n------------------------------------------\n")))
dose=as.numeric(as.vector(unlist(fatores[,i])))
grafico=polynomial(dose,resp,grau = grau[i],
DFres= anavaF3[8,1],SSq = anavaF3[8,2],ylab = ylab,xlab = parse(text = xlab.factor[i]),point = point)[[1]]
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial\" command\n"))
cat(green(bold("\n------------------------------------------")))}
cat('\n')
graficos[[1]]=residplot
graficos[[i+1]]=grafico
}
}
if(anavaF3[7,5]>alpha.f && anavaF3[4,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Interaction",paste(names.fat[1],'*',names.fat[2],sep='')," significant: unfolding the interaction")))
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[1], ' inside of each level of ', names.fat[2])
cat(green(bold("\n------------------------------------------\n")))
des<-aov(resp~Fator2/Fator1+Fator3+Fator2+Fator2:Fator3+Fator1:Fator2:Fator3)
l<-vector('list',nv2)
names(l)<-names(summary(Fator2))
v<-numeric(0)
for(j in 1:nv2) {
for(i in 0:(nv1-2)) v<-cbind(v,i*nv2+j)
l[[j]]<-v
v<-numeric(0)}
des1<-summary(des,split=list('Fator2:Fator1'=l))[[1]]
des1a=des1[-c(1,2,3,length(des1[,1]),length(des1[,1])-1,length(des1[,1])-2),]
#============================
rn<-numeric(0)
for (j in 1:nv2) {
rn <- c(rn, paste(paste(names.fat[1], ":", names.fat[2],
sep = ""), lf2[j]))
}
rownames(des1a)=rn
#============================
print(des1a)
if(quali[1]==TRUE & quali[2]==TRUE){
if (mcomp == "tukey"){
tukeygrafico=c()
ordem=c()
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
tukeygrafico[[i]]=tukey$groups[levels(trati),2]
ordem[[i]]=rownames(tukey$groups[levels(trati),])
}
letra=unlist(tukeygrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "duncan"){
duncangrafico=c()
ordem=c()
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
duncangrafico[[i]]=duncan$groups[levels(trati),2]
ordem[[i]]=rownames(duncan$groups[levels(trati),])
}
letra=unlist(duncangrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "lsd"){
lsdgrafico=c()
ordem=c()
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator2 == lf2[i]],trati,
mean, na.rm=TRUE)[rownames(lsd$groups)]}
lsdgrafico[[i]]=lsd$groups[levels(trati),2]
ordem[[i]]=rownames(lsd$groups[levels(trati),])
}
letra=unlist(lsdgrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "sk"){
skgrafico=c()
ordem=c()
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !="1"){sk$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(sk)]}
skgrafico[[i]]=sk[levels(trati),2]
ordem[[i]]=rownames(sk[levels(trati),])
}
letra=unlist(skgrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}}
# Desdobramento de F2 dentro de F1
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[2], " inside of the level of ",names.fat[1])
cat(green(bold("\n------------------------------------------\n")))
# Desdobramento de F1 dentro de F2
des<-aov(resp~Fator1/Fator2+Fator3+Fator1+Fator1:Fator3+Fator1:Fator2:Fator3)
l<-vector('list',nv1)
names(l)<-names(summary(Fator1))
v<-numeric(0)
for(j in 1:nv1) {
for(i in 0:(nv2-2)) v<-cbind(v,i*nv1+j)
l[[j]]<-v
v<-numeric(0)}
des1<-summary(des,split=list('Fator1:Fator2'=l))[[1]]
des1a=des1[-c(1,2,3,length(des1[,1]),length(des1[,1])-1,length(des1[,1])-2),]
#============================
rn<-numeric(0)
for (j in 1:nv1) {
rn <- c(rn, paste(paste(names.fat[2], ":", names.fat[1],
sep = ""), lf1[j]))
}
rownames(des1a)=rn
#============================
print(des1a)
if(quali[1]==TRUE & quali[2]==TRUE){
if (mcomp == "tukey"){
tukeygrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator1 == lf1[i]],
trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
tukeygrafico1[[i]]=tukey$groups[levels(trati),2]
}
letra1=unlist(tukeygrafico1)
letra1=toupper(letra1)}
if (mcomp == "duncan"){
duncangrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
duncangrafico1[[i]]=duncan$groups[levels(trati),2]
}
letra1=unlist(duncangrafico1)
letra1=toupper(letra1)}
if (mcomp == "lsd"){
lsdgrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator1 == lf1[i]],
trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
lsdgrafico1[[i]]=lsd$groups[levels(trati),2]
}
letra1=unlist(lsdgrafico1)
letra1=toupper(letra1)}
if (mcomp == "sk"){
skgrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
# sk=sk(respi,trati,anavaF3$Df[8],anavaF3$`Sum Sq`[8],alpha.t)
if(transf !=1){sk$respo=tapply(response[Fator1 == lf1[i]],trati,
mean, na.rm=TRUE)[rownames(sk)]}
skgrafico1[[i]]=sk[levels(trati),2]
}
letra1=unlist(skgrafico1)
letra1=toupper(letra1)}}
if(quali[1] & quali[2]==TRUE){
f1=rep(levels(Fator1),e=length(levels(Fator2)))
f2=rep(unique(as.character(Fator2)),length(levels(Fator1)))
media=tapply(response,paste(Fator1,Fator2), mean, na.rm=TRUE)[unique(paste(f1,f2))]
# desvio=tapply(response,paste(Fator1,Fator2), sd, na.rm=TRUE)[unique(paste(f1,f2))]
if(point=="mean_sd"){desvio=tapply(response,paste(Fator1,Fator2), sd, na.rm=TRUE)}
if(point=="mean_se"){desvio=tapply(response,paste(Fator1,Fator2), sd, na.rm=TRUE)/
sqrt(tapply(response,paste(Fator1,Fator2), length))}
desvio=desvio[unique(paste(f1,f2))]
f1=factor(f1,levels = unique(f1))
f2=factor(f2,levels = unique(f2))
graph=data.frame(f1=f1,
f2=f2,
media,
desvio,
letra,
letra1,
numero=format(media,digits = dec))
numero=paste(graph$numero,graph$letra,graph$letra1,sep="")
graph$numero=numero
colint=ggplot(graph,
aes(x=f2,
y=media,
fill=f1))+
ylab(ylab)+xlab(xlab)+
theme+
geom_col(position = "dodge",color="black")+
labs(fill=names.fat[1])+
geom_errorbar(aes(ymin=media-desvio,
ymax=media+desvio),
width=0.3,position = position_dodge(width=0.9))+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=numero),
position = position_dodge(width=0.9),angle=angle.label, hjust=hjust,size=labelsize)+
theme(text=element_text(size=textsize,family=family),
axis.text = element_text(size=textsize,color="black",family=family),
axis.title = element_text(size=textsize,color="black",family=family))
colint1=colint
print(colint)
letras=paste(graph$letra,
graph$letra1,
sep="")
matriz=data.frame(t(matrix(paste(format(graph$media,digits = dec),letras),ncol = length(levels(Fator1)))))
rownames(matriz)=levels(Fator1)
colnames(matriz)=levels(Fator2)
cat(green(bold("\n-----------------------------------------------------------------\n")))
cat(green(bold("Final table")))
cat(green(bold("\n-----------------------------------------------------------------\n")))
print(matriz)
message(black("\nAverages followed by the same lowercase letter in the column and \nuppercase in the row do not differ by the",mcomp,"(p<",alpha.t,")"))
}
if(quali[1]==FALSE | quali[2]==FALSE){
if(quali[1]==FALSE){
if (mcomp == "tukey"){
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator1 == lf1[i]],
trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(tukey$groups)}}
if (mcomp == "duncan"){
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(duncan$groups)}}
if (mcomp == "lsd"){
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator1 == lf1[i]],
trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(lsd$groups)}}
if (mcomp == "sk"){
for (i in 1:nv1) {
trati=fatores[, 2][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator1 == lf1[i]],trati,
mean, na.rm=TRUE)[rownames(sk)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(sk)}}
}
if(quali[1]==FALSE){
Fator1=fator1a
colint1=polynomial2(Fator1,
response,
Fator2,
grau = grau12,
ylab=ylab,
xlab=xlab,
theme=theme,
DFres= anavaF3[8,1],SSq = anavaF3[8,2])}
if(quali[2]==FALSE){
if (mcomp == "tukey"){
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(tukey$groups)
}}
if (mcomp == "duncan"){
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(duncan$groups)
}}
if (mcomp == "lsd"){
lsdgrafico=c()
ordem=c()
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator2 == lf2[i]],trati,
mean, na.rm=TRUE)[rownames(lsd$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(lsd$groups)}}
if (mcomp == "sk"){
for (i in 1:nv2) {
trati=fatores[, 1][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !="1"){sk$respo=tapply(response[Fator2 == lf2[i]],
trati,mean, na.rm=TRUE)[rownames(sk)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(sk)
}}
}
if(quali[2]==FALSE){
Fator2=fator2a#as.numeric(as.character(Fator2))
colint1=polynomial2(Fator2,
response,
Fator1,
grau = grau21,
ylab=ylab,
xlab=xlab,
theme=theme,
DFres= anavaF3[8,1],SSq = anavaF3[8,2])}
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial2\" command\n"))
}
if(anavaF3[5,5]>alpha.f && anavaF3[6,5]>alpha.f) {
i<-3
{
if(quali[i]==TRUE && anavaF3[i,5]<=alpha.f) {
cat(green(bold("\n------------------------------------------\n")))
cat(green(italic('Analyzing the simple effects of the factor ',names.fat[3])))
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
if(mcomp=='tukey'){letra=TUKEY(resp,fatores[,i],anavaF3[8,1],anavaF3[8,3],alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="sk"){
ad=data.frame(Fator1,Fator2,Fator3)
nrep=table(fatores[,i])[1]
medias=sort(tapply(resp,fatores[i],mean, na.rm=TRUE),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3[8,1],
nrep = nrep,
QME = anavaF3[8,3],
alpha = alpha.t)
letra1=data.frame(resp=medias,groups=sk)
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="duncan"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- duncan(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="lsd"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- LSD(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
print(letra1)
cat(green(bold("\n-----------------------------------------------------------------")))
if(point=="mean_sd"){desvio=tapply(response, c(fatores[i]), sd, na.rm=TRUE)[rownames(letra1)]}
if(point=="mean_se"){desvio=(tapply(response, c(fatores[i]), sd, na.rm=TRUE)/
sqrt(tapply(response, c(fatores[i]), length)))[rownames(letra1)]}
dadosm=data.frame(letra1,
media=tapply(response, c(fatores[i]), mean, na.rm=TRUE)[rownames(letra1)],
desvio=desvio)
dadosm$Tratamentos=factor(rownames(dadosm),levels = unique(unlist(fatores[i])))
dadosm$limite=dadosm$media+dadosm$desvio
dadosm=dadosm[as.character(unique(unlist(fatores[i]))),]
if(addmean==TRUE){dadosm$letra=paste(format(dadosm$media,digits = dec),dadosm$groups)}
if(addmean==FALSE){dadosm$letra=dadosm$groups}
media=dadosm$media
desvio=dadosm$desvio
Tratamentos=dadosm$Tratamentos
letra=dadosm$letra
grafico=ggplot(dadosm,
aes(x=Tratamentos,y=media))
if(fill=="trat"){grafico=grafico+
geom_col(aes(fill=Tratamentos),color=1)}
else{grafico=grafico+
geom_col(aes(fill=Tratamentos),fill=fill,color=1)}
if(errorbar==TRUE){grafico=grafico+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=letra),
family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==FALSE){grafico=grafico+
geom_text(aes(y=media+sup,label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==TRUE){grafico=grafico+
geom_errorbar(data=dadosm,
aes(ymin=media-desvio,
ymax=media+desvio,color=1),
color="black",width=0.3)
grafico1=grafico+theme+
ylab(ylab)+
xlab(parse(text = xlab.factor[3]))+
theme(text = element_text(size=textsize,color="black", family = family),
axis.text = element_text(size=textsize,color="black", family = family),
axis.title = element_text(size=textsize,color="black", family = family),
legend.position = "none")
print(grafico1)}
}
if(quali[i]==FALSE && anavaF3[i,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat('Analyzing the simple effects of the factor ',names.fat[3])
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
grafico1=polynomial(fatores[,i], resp,grau=grau[i],
DFres= anavaF3[8,1],SSq = anavaF3[8,2],ylab = ylab,xlab = parse(text = xlab.factor[3]),point = point)[[1]]
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial\" command"))}
}
}
}
if(anavaF3[7,5]>alpha.f && anavaF3[5,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Interaction",paste(names.fat[1],'*',names.fat[3],sep='')," significant: unfolding the interaction")))
cat(green(bold("\n------------------------------------------\n")))
#Desdobramento de FATOR 1 dentro do niveis de FATOR 3
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[1], ' inside of each level of ', names.fat[3])
cat(green(bold("\n------------------------------------------\n")))
des<-aov(resp~Fator3/Fator1+Fator2+Fator3+Fator2:Fator3+Fator1:Fator2:Fator3)
l<-vector('list',nv3)
names(l)<-names(summary(Fator3))
v<-numeric(0)
for(j in 1:nv3) {
for(i in 0:(nv1-2)) v<-cbind(v,i*nv3+j)
l[[j]]<-v
v<-numeric(0)
}
des1<-summary(des,split=list('Fator3:Fator1'=l))[[1]]
des1a=des1[-c(1,2,3,length(des1[,1]),length(des1[,1])-1,length(des1[,1])-2),]
#============================
rn<-numeric(0)
for (j in 1:nv3) {
rn <- c(rn, paste(paste(names.fat[1], ":", names.fat[3],
sep = ""), lf3[j]))
}
rownames(des1a)=rn
#============================
print(des1a)
if(quali[1]==TRUE & quali[3]==TRUE){
if (mcomp == "tukey"){
tukeygrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator3 == lf3[i]],
trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
tukeygrafico[[i]]=tukey$groups[levels(trati),2]
ordem[[i]]=rownames(tukey$groups[levels(trati),])
}
letra=unlist(tukeygrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "duncan"){
duncangrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator3 == lf3[i]],
trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
duncangrafico[[i]]=duncan$groups[levels(trati),2]
ordem[[i]]=rownames(duncan$groups[levels(trati),])
}
letra=unlist(duncangrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "lsd"){
lsdgrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator3 == lf3[i]],trati,
mean, na.rm=TRUE)[rownames(lsd$groups)]}
lsdgrafico[[i]]=lsd$groups[levels(trati),2]
ordem[[i]]=rownames(lsd$groups[levels(trati),])
}
letra=unlist(lsdgrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "sk"){
skgrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
skgrafico[[i]]=sk[levels(trati),2]
ordem[[i]]=rownames(sk[levels(trati),])
}
letra=unlist(skgrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}}
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[3], " inside of the level of ",names.fat[1])
cat(green(bold("\n------------------------------------------\n")))
des<-aov(resp~Fator1/Fator3+Fator1+Fator2+Fator2:Fator1+Fator1:Fator2:Fator3)
l<-vector('list',nv1)
names(l)<-names(summary(Fator1))
v<-numeric(0)
for(j in 1:nv1) {
for(i in 0:(nv3-2)) v<-cbind(v,i*nv1+j)
l[[j]]<-v
v<-numeric(0)
}
des1<-summary(des,split=list('Fator1:Fator3'=l))[[1]]
des1a=des1[-c(1,2,3,length(des1[,1]),length(des1[,1])-1,length(des1[,1])-2),]
#============================
rn<-numeric(0)
for (j in 1:nv1) {
rn <- c(rn, paste(paste(names.fat[3], ":", names.fat[1],
sep = ""), lf1[j]))
}
rownames(des1a)=rn
#============================
print(des1a)
if(quali[1]==TRUE & quali[3]==TRUE){
if (mcomp == "tukey"){
tukeygrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
tukeygrafico1[[i]]=tukey$groups[levels(trati),2]
}
letra1=unlist(tukeygrafico1)
letra1=toupper(letra1)}
if (mcomp == "duncan"){
duncangrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
duncangrafico1[[i]]=duncan$groups[levels(trati),2]
}
letra1=unlist(duncangrafico1)
letra1=toupper(letra1)}
if (mcomp == "lsd"){
lsdgrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
mod=aov(respi~trati)
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
lsdgrafico1[[i]]=lsd$groups[levels(trati),2]
}
letra1=unlist(lsdgrafico1)
letra1=toupper(letra1)}
if (mcomp == "sk"){
skgrafico1=c()
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
mod=aov(respi~trati)
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
skgrafico1[[i]]=sk[levels(trati),2]
}
letra1=unlist(skgrafico1)
letra1=toupper(letra1)}}
if(quali[1]==TRUE & quali[3]==TRUE){
f1=rep(levels(Fator1),e=length(levels(Fator3)))
f3=rep(unique(as.character(Fator3)),length(levels(Fator1)))
media=tapply(response,paste(Fator1,Fator3), mean, na.rm=TRUE)[unique(paste(f1,f3))]
# desvio=tapply(response,paste(Fator1,Fator3), sd, na.rm=TRUE)[unique(paste(f1,f3))]
if(point=="mean_sd"){desvio=tapply(response,paste(Fator1,Fator3), sd, na.rm=TRUE)}
if(point=="mean_se"){desvio=tapply(response,paste(Fator1,Fator3), sd, na.rm=TRUE)/
sqrt(tapply(response,paste(Fator1,Fator3), length))}
desvio=desvio[unique(paste(f1,f3))]
f1=factor(f1,levels = unique(f1))
f3=factor(f3,levels = unique(f3))
graph=data.frame(f1=f1,
f3=f3,
media,
desvio,
letra,letra1,
numero=format(media,digits = dec))
numero=paste(graph$numero,graph$letra,graph$letra1,sep="")
graph$numero=numero
colint=ggplot(graph,
aes(x=f3,
y=media,
fill=f1))+
geom_col(position = "dodge",color="black")+
ylab(ylab)+xlab(xlab)+
theme+
labs(fill=names.fat[1])+
geom_errorbar(aes(ymin=media-desvio,
ymax=media+desvio),
width=0.3,position = position_dodge(width=0.9))+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=numero),
position = position_dodge(width=0.9),angle=angle.label, hjust=hjust,size=labelsize)+
theme(text=element_text(size=textsize,family=family),
axis.text = element_text(size=textsize,color="black",family=family),
axis.title = element_text(size=textsize,color="black",family=family))
colint2=colint
print(colint)
letras=paste(graph$letra,graph$letra1,sep="")
matriz=data.frame(t(matrix(paste(format(graph$media,digits = dec),letras),ncol = length(levels(Fator1)))))
rownames(matriz)=levels(Fator1)
colnames(matriz)=levels(Fator3)
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Final table")))
cat(green(bold("\n------------------------------------------\n")))
print(matriz)
message(black("\n\nAverages followed by the same lowercase letter in the column and \nuppercase in the row do not differ by the",mcomp,"(p<",alpha.t,")"))
}
if(quali[1]==FALSE | quali[3]==FALSE){
if(quali[1]==FALSE){
if (mcomp == "tukey"){
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(tukey$groups)}}
if (mcomp == "duncan"){
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(duncan$groups)}}
if (mcomp == "lsd"){
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(lsd$groups)}}
if (mcomp == "sk"){
for (i in 1:nv1) {
trati=fatores[, 3][Fator1 == lf1[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator1 == lf1[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator1 == lf1[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf1[i],"of F1")
cat("\n----------------------\n")
print(sk)}}
}
if(quali[1]==FALSE){
Fator1=fator1a#as.numeric(as.character(Fator1))
colint2=polynomial2(Fator1,
response,
Fator3,
grau = grau13,
ylab=ylab,
xlab=xlab,
theme=theme,
DFres= anavaF3[8,1],SSq = anavaF3[8,2])}
if(quali[3]==FALSE){
if (mcomp == "tukey"){
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator3 == lf3[i]],
trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(tukey$groups)}}
if (mcomp == "duncan"){
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator3 == lf3[i]],
trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(duncan$groups)}}
if (mcomp == "lsd"){
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator3 == lf3[i]],trati,
mean, na.rm=TRUE)[rownames(lsd$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(lsd$groups)}}
if (mcomp == "sk"){
for (i in 1:nv3) {
trati=fatores[, 1][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
cat("\n----------------------\n")
cat("Multiple comparison of F1 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(sk)}}}
if(quali[3]==FALSE){
Fator3=fator3a#as.numeric(as.character(Fator3))
colint2=polynomial2(Fator3,
response,
Fator1,
grau = grau31,
ylab=ylab,
xlab=xlab,
theme=theme,
DFres= anavaF3[8,1],SSq = anavaF3[8,2])}
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial2\" command\n"))
}
#Checar o Fator2
if(anavaF3[4,5]>alpha.f && anavaF3[6,5]>alpha.f) {
i<-2
{
if(quali[i]==TRUE && anavaF3[i,5]<=alpha.f) {
cat(green(bold("\n------------------------------------------\n")))
cat(green(italic('Analyzing the simple effects of the factor ',names.fat[2])))
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
if(mcomp=='tukey'){letra=TUKEY(resp,fatores[,i],anavaF3[8,1],anavaF3[8,3],alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="sk"){
ad=data.frame(Fator1,Fator2,Fator3)
nrep=table(fatores[,i])[1]
medias=sort(tapply(resp,fatores[i],mean, na.rm=TRUE),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3[8,1],
nrep = nrep,
QME = anavaF3[8,3],
alpha = alpha.t)
letra1=data.frame(resp=medias,groups=sk)
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="duncan"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- duncan(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="lsd"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- LSD(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
print(letra1)
cat(green(bold("\n-----------------------------------------------------------------")))
if(point=="mean_sd"){desvio=tapply(response, c(fatores[i]), sd, na.rm=TRUE)[rownames(letra1)]}
if(point=="mean_se"){desvio=(tapply(response, c(fatores[i]), sd, na.rm=TRUE)/
sqrt(tapply(response, c(fatores[i]), length)))[rownames(letra1)]}
dadosm=data.frame(letra1,
media=tapply(response, c(fatores[i]), mean, na.rm=TRUE)[rownames(letra1)],
desvio=desvio)
dadosm$Tratamentos=factor(rownames(dadosm),levels = unique(unlist(fatores[i])))
dadosm$limite=dadosm$media+dadosm$desvio
dadosm=dadosm[as.character(unique(unlist(fatores[i]))),]
if(addmean==TRUE){dadosm$letra=paste(format(dadosm$media,digits = dec),dadosm$groups)}
if(addmean==FALSE){dadosm$letra=dadosm$groups}
media=dadosm$media
desvio=dadosm$desvio
Tratamentos=dadosm$Tratamentos
letra=dadosm$letra
grafico=ggplot(dadosm,
aes(x=Tratamentos,
y=media))
if(fill=="trat"){grafico=grafico+
geom_col(aes(fill=Tratamentos),color=1)}
else{grafico=grafico+
geom_col(aes(fill=Tratamentos),fill=fill,color=1)}
if(errorbar==TRUE){grafico=grafico+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==FALSE){grafico=grafico+
geom_text(aes(y=media+sup,label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==TRUE){grafico=grafico+
geom_errorbar(data=dadosm,aes(ymin=media-desvio,
ymax=media+desvio,color=1),
color="black",width=0.3)
grafico2=grafico+theme+
ylab(ylab)+
xlab(parse(text = xlab.factor[2]))+
theme(text = element_text(size=textsize,color="black", family = family),
axis.text = element_text(size=textsize,color="black", family = family),
axis.title = element_text(size=textsize,color="black", family = family),
legend.position = "none")
print(grafico2)}
}
if(quali[i]==FALSE && anavaF3[i,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat('Analyzing the simple effects of the factor ',names.fat[2])
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
grafico2=polynomial(fatores[,i], resp,grau=grau[i],
DFres= anavaF3[8,1],SSq = anavaF3[8,2],ylab = ylab,xlab = parse(text = xlab.factor[2]),point = point)[[1]]
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial\" command"))
}
cat('\n')
}
}
}
if(anavaF3[7,5]>alpha.f && anavaF3[6,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("\nInteraction",paste(names.fat[2],'*',names.fat[3],sep='')," significant: unfolding the interaction\n")))
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[2], ' inside of each level of ', names.fat[3])
cat(green(bold("\n------------------------------------------\n")))
des<-aov(resp~Fator3/Fator2+Fator1+Fator3+Fator1:Fator3+Fator1:Fator2:Fator3)
l<-vector('list',nv3)
names(l)<-names(summary(Fator3))
v<-numeric(0)
for(j in 1:nv3) {
for(i in 0:(nv2-2)) v<-cbind(v,i*nv3+j)
l[[j]]<-v
v<-numeric(0)
}
des1<-summary(des,split=list('Fator3:Fator2'=l))[[1]]
des1a=des1[-c(1,2,3,length(des1[,1]),length(des1[,1])-1,length(des1[,1])-2),]
#============================
rn<-numeric(0)
for (j in 1:nv3) {
rn <- c(rn, paste(paste(names.fat[2], ":", names.fat[3],
sep = ""), lf3[j]))
}
rownames(des1a)=rn
#============================
print(des1a)
cat(green(bold("\n------------------------------------------\n")))
if(quali[2]==TRUE & quali[3]==TRUE){
if (mcomp == "tukey"){
tukeygrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
mod=aov(respi~trati)
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
tukeygrafico[[i]]=tukey$groups[levels(trati),2]
ordem[[i]]=rownames(tukey$groups[levels(trati),])
}
letra=unlist(tukeygrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "duncan"){
duncangrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
duncangrafico[[i]]=duncan$groups[levels(trati),2]
ordem[[i]]=rownames(duncan$groups[levels(trati),])
}
letra=unlist(duncangrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "lsd"){
lsdgrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
lsdgrafico[[i]]=lsd$groups[levels(trati),2]
ordem[[i]]=rownames(lsd$groups[levels(trati),])
}
letra=unlist(lsdgrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}
if (mcomp == "sk"){
skgrafico=c()
ordem=c()
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
skgrafico[[i]]=sk[levels(trati),2]
ordem[[i]]=rownames(sk[levels(trati),])
}
letra=unlist(skgrafico)
datag=data.frame(letra,ordem=unlist(ordem))
datag$ordem=factor(datag$ordem,levels = unique(datag$ordem))
datag=datag[order(datag$ordem),]
letra=datag$letra}}
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[3], " inside of the level of ",names.fat[2])
cat(green(bold("\n------------------------------------------\n")))
des<-aov(resp~Fator2/Fator3+Fator1+Fator2+Fator1:Fator2+Fator1:Fator2:Fator3)
l<-vector('list',nv2)
names(l)<-names(summary(Fator2))
v<-numeric(0)
for(j in 1:nv2) {
for(i in 0:(nv3-2)) v<-cbind(v,i*nv2+j)
l[[j]]<-v
v<-numeric(0)
}
des1<-summary(des,split=list('Fator2:Fator3'=l))[[1]]
des1a=des1[-c(1,2,3,length(des1[,1]),length(des1[,1])-1,length(des1[,1])-2),]
#============================
rn<-numeric(0)
for (j in 1:nv2) {
rn <- c(rn, paste(paste(names.fat[3], ":", names.fat[2],
sep = ""), lf2[j]))
}
rownames(des1a)=rn
#============================
print(des1a)
if(quali[2]==TRUE & quali[3]==TRUE){
if (mcomp == "tukey"){
tukeygrafico1=c()
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
mod=aov(respi~trati)
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
tukeygrafico1[[i]]=tukey$groups[levels(trati),2]
}
letra1=unlist(tukeygrafico1)
letra1=toupper(letra1)}
if (mcomp == "duncan"){
duncangrafico1=c()
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
duncangrafico1[[i]]=duncan$groups[levels(trati),2]
}
letra1=unlist(duncangrafico1)
letra1=toupper(letra1)}
if (mcomp == "lsd"){
lsdgrafico1=c()
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
lsdgrafico1[[i]]=lsd$groups[levels(trati),2]
}
letra1=unlist(lsdgrafico1)
letra1=toupper(letra1)}
if (mcomp == "sk"){
skgrafico1=c()
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
if(transf !=1){sk$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
skgrafico1[[i]]=sk[levels(trati),2]
}
letra1=unlist(skgrafico1)
letra1=toupper(letra1)}}
if(quali[2]==TRUE & quali[3]==TRUE){
f2=rep(levels(Fator2),e=length(levels(Fator3)))
f3=rep(unique(as.character(Fator3)),length(levels(Fator2)))
media=tapply(response,paste(Fator2,Fator3), mean, na.rm=TRUE)[unique(paste(f2,f3))]
# desvio=tapply(response,paste(Fator2,Fator3), sd, na.rm=TRUE)[unique(paste(f2,f3))]
if(point=="mean_sd"){desvio=tapply(response,paste(Fator2,Fator3), sd, na.rm=TRUE)}
if(point=="mean_se"){desvio=tapply(response,paste(Fator2,Fator3), sd, na.rm=TRUE)/
sqrt(tapply(response,paste(Fator2,Fator3), length))}
desvio=desvio[unique(paste(f2,f3))]
f2=factor(f2,levels = unique(f2))
f3=factor(f3,levels = unique(f3))
graph=data.frame(f2=f2,
f3=f3,
media,
desvio,
letra,letra1,
numero=format(media,digits = dec))
numero=paste(graph$numero,graph$letra,graph$letra1,sep="")
graph$numero=numero
colint=ggplot(graph,
aes(x=f3,
y=media,
fill=f2))+
geom_col(position = "dodge",color="black")+
ylab(ylab)+xlab(xlab)+
theme+
labs(fill=names.fat[2])+
geom_errorbar(aes(ymin=media-desvio,
ymax=media+desvio),
width=0.3,position = position_dodge(width=0.9))+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=numero),
position = position_dodge(width=0.9),angle=angle.label, hjust=hjust,size=labelsize)+
theme(text=element_text(size=textsize,family=family),
axis.text = element_text(size=textsize,color="black",family=family),
axis.title = element_text(size=textsize,color="black",family=family))
colint3=colint
print(colint)
letras=paste(graph$letra,graph$letra1,sep="")
matriz=data.frame(t(matrix(paste(format(graph$media,digits = dec),letras),ncol = length(levels(Fator2)))))
rownames(matriz)=levels(Fator2)
colnames(matriz)=levels(Fator3)
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Final table")))
cat(green(bold("\n------------------------------------------\n")))
print(matriz)
message(black("\n\nAverages followed by the same lowercase letter in the column and \nuppercase in the row do not differ by the",mcomp,"(p<",alpha.t,")"))
}
if(quali[2]==FALSE | quali[3]==FALSE){
if(quali[2]==FALSE){
if (mcomp == "tukey"){
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
mod=aov(respi~trati)
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(tukey$groups)}}
if (mcomp == "duncan"){
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(duncan$groups)}}
if (mcomp == "lsd"){
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(lsd$groups)}}
if (mcomp == "sk"){
for (i in 1:nv2) {
trati=fatores[, 3][Fator2 == lf2[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator2 == lf2[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
# sk=sk(respi,trati,anavaF3$Df[8],anavaF3$`Sum Sq`[8],alpha.t)
if(transf !=1){sk$respo=tapply(response[Fator2 == lf2[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
cat("\n----------------------\n")
cat("Multiple comparison of F3 within level",lf2[i],"of F2")
cat("\n----------------------\n")
print(sk)}}
}
if(quali[2]==FALSE){
Fator2=fator2a#as.numeric(as.character(Fator2))
colint3=polynomial2(Fator2,
response,
Fator3,
grau = grau23,
ylab=ylab,
xlab=xlab,
theme=theme,
DFres= anavaF3[8,1],SSq = anavaF3[8,2])}
if(quali[3]==FALSE){
if (mcomp == "tukey"){
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
mod=aov(respi~trati)
tukey=TUKEY(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){tukey$groups$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(tukey$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(tukey$groups)}}
if (mcomp == "duncan"){
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
duncan=duncan(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){duncan$groups$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(duncan$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(duncan$groups)}}
if (mcomp == "lsd"){
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
lsd=LSD(respi,trati,anavaF3$Df[8],anavaF3$`Mean Sq`[8],alpha.t)
if(transf !=1){lsd$groups$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(lsd$groups)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(lsd$groups)}}
if (mcomp == "sk"){
for (i in 1:nv3) {
trati=fatores[, 2][Fator3 == lf3[i]]
trati=factor(trati,levels = unique(trati))
respi=resp[Fator3 == lf3[i]]
nrep=table(trati)[1]
medias=sort(tapply(respi,trati,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
# sk=sk(respi,trati,anavaF3$Df[8],anavaF3$`Sum Sq`[8],alpha.t)
if(transf !=1){sk$respo=tapply(response[Fator3 == lf3[i]],trati,mean, na.rm=TRUE)[rownames(sk)]}
cat("\n----------------------\n")
cat("Multiple comparison of F2 within level",lf3[i],"of F3")
cat("\n----------------------\n")
print(sk)}}
}
if(quali[3]==FALSE){
Fator3=fator3a#as.numeric(as.character(Fator3))
colint3=polynomial2(Fator3,
response,
Fator2,
grau = grau32,
ylab=ylab,
xlab=xlab,
theme=theme,
DFres= anavaF3[8,1],SSq = anavaF3[8,2])}
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial2\" command"))
}
if(anavaF3[4,5]>alpha.f && anavaF3[5,5]>alpha.f) {
i<-1
{
if(quali[i]==TRUE && anavaF3[i,5]<=alpha.f) {
cat(green(bold("\n------------------------------------------\n")))
cat(green(italic('Analyzing the simple effects of the factor ',names.fat[2])))
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
if(mcomp=='tukey'){letra=TUKEY(resp,fatores[,i],anavaF3[8,1],anavaF3[8,3],alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="sk"){
ad=data.frame(Fator1,Fator2,Fator3)
nrep=table(fatores[,i])[1]
medias=sort(tapply(resp,fatores[i],mean, na.rm=TRUE),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3[8,1],
nrep = nrep,
QME = anavaF3[8,3],
alpha = alpha.t)
letra1=data.frame(resp=medias,groups=sk)
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="duncan"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- duncan(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
if(mcomp=="lsd"){
ad=data.frame(Fator1,Fator2,Fator3)
letra <- LSD(anava, colnames(ad[i]), alpha=alpha.t)
letra1 <- letra$groups; colnames(letra1)=c("resp","groups")
if(transf !=1){letra1$respo=tapply(response,fatores[,i],mean, na.rm=TRUE)[rownames(letra1)]}}
print(letra1)
cat(green(bold("\n------------------------------------------\n")))
if(point=="mean_sd"){desvio=tapply(response, c(fatores[i]), sd, na.rm=TRUE)[rownames(letra1)]}
if(point=="mean_se"){desvio=(tapply(response, c(fatores[i]), sd, na.rm=TRUE)/
sqrt(tapply(response, c(fatores[i]), length)))[rownames(letra1)]}
dadosm=data.frame(letra1,
media=tapply(response, c(fatores[i]), mean, na.rm=TRUE)[rownames(letra1)],
desvio=desvio)
dadosm$Tratamentos=factor(rownames(dadosm),levels = unique(unlist(fatores[i])))
dadosm$limite=dadosm$media+dadosm$desvio
dadosm=dadosm[as.character(unique(unlist(fatores[i]))),]
if(addmean==TRUE){dadosm$letra=paste(format(dadosm$media,digits = dec),dadosm$groups)}
if(addmean==FALSE){dadosm$letra=dadosm$groups}
media=dadosm$media
desvio=dadosm$desvio
Tratamentos=dadosm$Tratamentos
letra=dadosm$letra
grafico=ggplot(dadosm,
aes(x=Tratamentos,
y=media))
if(fill=="trat"){grafico=grafico+
geom_col(aes(fill=Tratamentos),color=1)}
else{grafico=grafico+
geom_col(aes(fill=Tratamentos),fill=fill,color=1)}
if(errorbar==TRUE){grafico=grafico+
geom_text(aes(y=media+sup+if(sup<0){-desvio}else{desvio},
label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==FALSE){grafico=grafico+
geom_text(aes(y=media+sup,label=letra),family=family,angle=angle.label, hjust=hjust,size=labelsize)}
if(errorbar==TRUE){grafico=grafico+
geom_errorbar(data=dadosm,aes(ymin=media-desvio,
ymax=media+desvio,color=1),
color="black",width=0.3)
grafico3=grafico+theme+
ylab(ylab)+
xlab(parse(text = xlab.factor[1]))+
theme(text = element_text(size=textsize,color="black", family = family),
axis.text = element_text(size=textsize,color="black", family = family),
axis.title = element_text(size=textsize,color="black", family = family),
legend.position = "none")
print(grafico3)}
}
if(quali[i]==FALSE && anavaF3[i,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat('Analyzing the simple effects of the factor ',names.fat[2])
cat(green(bold("\n------------------------------------------\n")))
cat(names.fat[i])
grafico3=polynomial(fatores[,i], resp,grau=grau[i],
DFres= anavaF3[8,1],SSq = anavaF3[8,2],ylab = ylab,xlab=parse(text = xlab.factor[1]),point = point)[[1]]
print(grafico3)
cat(green("\nTo edit graphical parameters, I suggest analyzing using the \"polynomial\" command"))
}
cat('\n')
}
}
}
if(anavaF3[7,5]<=alpha.f){
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("Interaction",paste(names.fat[1],'*',names.fat[2],'*',names.fat[3],sep='')," significant: unfolding the interaction")))
cat(green(bold("\n------------------------------------------\n")))
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[1], ' inside of each level of ', names.fat[2], 'and',names.fat[3])
cat(green(bold("\n------------------------------------------\n")))
m1=aov(resp~(Fator2*Fator3)/Fator1)
anova(m1)
pattern <- c(outer(levels(Fator2), levels(Fator3),
function(x,y) paste("Fator2",x,":Fator3",y,":",sep="")))
des.tab <- sapply(pattern, simplify=FALSE,
grep, x=names(coef(m1)[m1$assign==4]))
des1.tab <- summary(m1, split = list("Fator2:Fator3:Fator1" = des.tab))
desd=des1.tab[[1]][-c(1,2,3,4),]
desd=data.frame(desd[-length(rownames(desd)),])
# rownames(desd)=cbind(paste("Fator2:",rep(levels(Fator2),length(levels(Fator3))),
# "Fator3:",rep(levels(Fator3),e=length(levels(Fator2)))))
#
rownames(desd)=cbind(paste(names.fat[2],":",rep(levels(Fator2),length(levels(Fator3))),
names.fat[3],":",rep(levels(Fator3),e=length(levels(Fator2)))))
colnames(desd)=c("Df", "Sum Sq", "Mean Sq", "F value", "Pr(>F)")
print(desd)
ii<-0
for(i in 1:nv2) {
for(j in 1:nv3) {
ii<-ii+1
if(quali[1]==TRUE){
cat('\n',names.fat[1],' within the combination of levels ',lf2[i],' of ',names.fat[2],' and ',lf3[j],' of ',names.fat[3],"\n")
if(mcomp=='tukey'){tukey=TUKEY(resp[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
tukey=tukey$groups;colnames(tukey)=c("resp","letters")
if(transf !=1){tukey$respo=tapply(response[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
mean, na.rm=TRUE)[rownames(tukey)]}
print(tukey)}
if(mcomp=='duncan'){duncan=duncan(resp[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
duncan=duncan$groups;colnames(duncan)=c("resp","letters")
if(transf !=1){duncan$respo=tapply(response[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
mean, na.rm=TRUE)[rownames(duncan)]}
print(duncan)}
if(mcomp=='lsd'){lsd=LSD(resp[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
lsd=lsd$groups;colnames(lsd)=c("resp","letters")
if(transf !=1){lsd$respo=tapply(response[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
mean, na.rm=TRUE)[rownames(lsd)]}
print(lsd)}
if(mcomp=='sk'){
fat= fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]]
fat1=factor(fat,unique(fat))
levels(fat1)=1:length(levels(fat1))
respi=resp[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]]
nrep=table(fat1)[1]
medias=sort(tapply(respi,fat1,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
colnames(sk)=c("resp","letters")
sk=sk[as.character(unique(fat1)),]
rownames(sk)=unique(fat)
if(transf !=1){sk$respo=tapply(response[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],
fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
mean, na.rm=TRUE)[rownames(sk)]}
print(sk)}
}
if(quali[1]==FALSE){
cat('\n',names.fat[1],' within the combination of levels ',lf2[i],' of ',names.fat[2],' and ',lf3[j],' of ',names.fat[3],"\n")
polynomial(fatores[,1][Fator2==lf2[i] & Fator3==lf3[j]],
resp[fatores[,2]==lf2[i] & fatores[,3]==lf3[j]],grau=grau123,
DFres= anavaF3[8,1],SSq = anavaF3[8,2],ylab=ylab,xlab=xlab,point = point)[[1]]}
}
}
cat('\n\n')
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[2], ' inside of each level of ', names.fat[1], 'and',names.fat[3])
cat(green(bold("\n------------------------------------------\n")))
m1=aov(resp~(Fator1*Fator3)/Fator2)
anova(m1)
pattern <- c(outer(levels(Fator1), levels(Fator3),
function(x,y) paste("Fator1",x,":Fator3",y,":",sep="")))
des.tab <- sapply(pattern, simplify=FALSE,
grep, x=names(coef(m1)[m1$assign==4]))
des1.tab <- summary(m1, split = list("Fator1:Fator3:Fator2" = des.tab))
desd=des1.tab[[1]][-c(1,2,3,4),]
desd=data.frame(desd[-length(rownames(desd)),])
# rownames(desd)=cbind(paste("Fator1:",rep(levels(Fator1),length(levels(Fator3))),
# "Fator3:",rep(levels(Fator3),e=length(levels(Fator1)))))
rownames(desd)=cbind(paste(names.fat[1],":",rep(levels(Fator1),length(levels(Fator3))),
names.fat[3],":",rep(levels(Fator3),e=length(levels(Fator1)))))
colnames(desd)=c("Df", "Sum Sq", "Mean Sq", "F value", "Pr(>F)")
print(desd)
ii<-0
for(k in 1:nv1) {
for(j in 1:nv3) {
ii<-ii+1
if(quali[2]==TRUE){
cat('\n\n',names.fat[2],' within the combination of levels ',lf1[k],' of ',names.fat[1],' and ',lf3[j],' of ',names.fat[3],'\n')
if(mcomp=='tukey'){tukey=TUKEY(resp[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
tukey=tukey$groups;colnames(tukey)=c("resp","letters")
if(transf !=1){tukey$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],mean, na.rm=TRUE)[rownames(tukey)]}
print(tukey)}
if(mcomp=='duncan'){duncan=duncan(resp[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
duncan=duncan$groups;colnames(duncan)=c("resp","letters")
if(transf !=1){duncan$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],mean, na.rm=TRUE)[rownames(duncan)]}
print(duncan)}
if(mcomp=='lsd'){lsd=LSD(resp[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
lsd=lsd$groups;colnames(lsd)=c("resp","letters")
if(transf !=1){lsd$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],mean, na.rm=TRUE)[rownames(lsd)]}
print(lsd)}
if(mcomp=='sk'){
fat=fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]]
fat1=factor(fat,unique(fat))
levels(fat1)=1:length(levels(fat1))
respi=resp[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]]
nrep=table(fat1)[1]
medias=sort(tapply(respi,fat1,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
colnames(sk)=c("resp","letters")
sk=sk[as.character(unique(fat1)),]
rownames(sk)=unique(fat)
if(transf !=1){sk$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],mean, na.rm=TRUE)[rownames(sk)]}
print(sk)}
}
if(quali[2]==FALSE){
cat('\n\n',names.fat[2],' within the combination of levels ',lf1[k],' of ',names.fat[1],' and ',lf3[j],' of ',names.fat[3],'\n')
polynomial(fatores[,2][Fator1==lf1[k] & fatores[,3]==lf3[j]],
resp[fatores[,1]==lf1[k] & fatores[,3]==lf3[j]],
DFres= anavaF3[8,1],SSq = anavaF3[8,2],grau=grau213,
ylab = ylab,xlab = xlab,point = point)[[1]]}
}
}
#===================================================================
#Desdobramento de FATOR 3 dentro do niveis de FATOR 1 e FATOR 2
#===================================================================
cat(green(bold("\n------------------------------------------\n")))
cat("Analyzing ", names.fat[3], ' inside of each level of ', names.fat[1], 'and',names.fat[2])
cat(green(bold("\n------------------------------------------\n")))
m1=aov(resp~(Fator1*Fator2)/Fator3)
anova(m1)
pattern <- c(outer(levels(Fator1), levels(Fator2),
function(x,y) paste("Fator1",x,":Fator2",y,":",sep="")))
des.tab <- sapply(pattern, simplify=FALSE,
grep, x=names(coef(m1)[m1$assign==4]))
des1.tab <- summary(m1, split = list("Fator1:Fator2:Fator3" = des.tab))
desd=des1.tab[[1]][-c(1,2,3,4),]
desd=data.frame(desd[-length(rownames(desd)),])
# rownames(desd)=cbind(paste("Fator1:",rep(levels(Fator1),length(levels(Fator2))),
# "Fator2:",rep(levels(Fator2),e=length(levels(Fator1)))))
rownames(desd)=cbind(paste(names.fat[1],":",rep(levels(Fator1),length(levels(Fator2))),
names.fat[2],":",rep(levels(Fator2),e=length(levels(Fator1)))))
colnames(desd)=c("Df", "Sum Sq", "Mean Sq", "F value", "Pr(>F)")
print(desd)
ii<-0
for(k in 1:nv1) {
for(i in 1:nv2) {
ii<-ii+1
if(quali[3]==TRUE){
cat('\n\n',names.fat[3],' within the combination of levels ',lf1[k],' of ',names.fat[1],' and ',lf2[i],' of ',names.fat[2],'\n')
if(mcomp=='tukey'){tukey=TUKEY(resp[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
tukey=tukey$groups;colnames(tukey)=c("resp","letters")
if(transf !=1){tukey$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
mean, na.rm=TRUE)[rownames(tukey)]}
print(tukey)}
if(mcomp=='duncan'){duncan=duncan(resp[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
duncan=duncan$groups;colnames(duncan)=c("resp","letters")
if(transf !=1){duncan$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
mean, na.rm=TRUE)[rownames(duncan)]}
print(duncan)}
if(mcomp=='lsd'){lsd=LSD(resp[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
anavaF3[8,1],
anavaF3[8,3],
alpha.t)
lsd=lsd$groups;colnames(lsd)=c("resp","letters")
if(transf !=1){lsd$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
mean, na.rm=TRUE)[rownames(lsd)]}
print(lsd)}
if(mcomp=='sk'){
fat=fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]]
fat1=factor(fat,unique(fat))
levels(fat1)=1:length(levels(fat1))
respi=resp[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]]
nrep=table(fat1)[1]
medias=sort(tapply(respi,fat1,mean),decreasing = TRUE)
sk=scottknott(means = medias,
df1 = anavaF3$Df[8],
nrep = nrep,
QME = anavaF3$`Mean Sq`[8],
alpha = alpha.t)
sk=data.frame(respi=medias,groups=sk)
# sk=sk(resp[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
# fat1,
# anavaF3$Df[8],
# anavaF3$`Sum Sq`[8],
# alpha.t)
colnames(sk)=c("resp","letters")
sk=sk[as.character(unique(fat1)),]
rownames(sk)=unique(fat)
if(transf !=1){sk$respo=tapply(response[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
mean, na.rm=TRUE)[rownames(sk)]}
print(sk)}
}
if(quali[3]==FALSE){
cat('\n\n',names.fat[3],' inside of each level of ',lf1[k],' of ',names.fat[1],' and ',lf2[i],' of ',names.fat[2],'\n')
polynomial(fatores[,3][fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],
resp[fatores[,1]==lf1[k] & fatores[,2]==lf2[i]],grau=grau312,
DFres= anavaF3[8,1],SSq = anavaF3[8,2],ylab = ylab,xlab = xlab,point = point)[[1]]}
}
}
}
if(anavaF3[4,5]>alpha.f && anavaF3[5,5]>alpha.f && anavaF3[6,5]>alpha.f && anavaF3[7,5]>alpha.f){
if(anavaF3[1,5]<=alpha.f | anavaF3[2,5]<=alpha.f | anavaF3[3,5]<=alpha.f){
graficos}else{graficos=NA}}
if(anavaF3[7,5]>alpha.f && anavaF3[4,5]<=alpha.f){
graficos=list(residplot,colint1)
if(anavaF3[5,5]>alpha.f && anavaF3[6,5]>alpha.f && anavaF3[3,5]<=alpha.f){
graficos=list(residplot,colint1,grafico1)}
graficos}
if(anavaF3[7,5]>alpha.f && anavaF3[5,5]<=alpha.f){
graficos=list(residplot,colint2)
if(anavaF3[4,5]>alpha.f && anavaF3[6,5]>alpha.f && anavaF3[2,5]<=alpha.f){
graficos=list(residplot,colint2,grafico2)}
graficos}
if(anavaF3[7,5]>alpha.f && anavaF3[6,5]<=alpha.f){
graficos=list(residplot,colint3)
if(anavaF3[4,5]>alpha.f && anavaF3[5,5]>alpha.f && anavaF3[1,5]<=alpha.f){
graficos=list(residplot,colint3,grafico3)}}
if(anavaF3[7,5]>alpha.f && anavaF3[4,5]<=alpha.f && anavaF3[5,5]<=alpha.f){
graficos=list(residplot,colint1,colint2)
graficos}
if(anavaF3[7,5]>alpha.f && anavaF3[4,5]<=alpha.f && anavaF3[6,5]<=alpha.f){
graficos=list(residplot,colint1,colint3)
graficos}
if(anavaF3[7,5]>alpha.f && anavaF3[5,5]<=alpha.f && anavaF3[6,5]<=alpha.f){
graficos=list(residplot,colint2,colint3)
graficos}
if(anavaF3[7,5]<=alpha.f){graficos=list(residplot)}
graficos=graficos
}
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