R/bootlm.R
In matthew-quesnel/simplePsych:
library(boot)
library(broom)
library(lm.beta)
library(plyr)
library(knitr)
bootReg <- function(formula,data,indices){
d <- data[indices,]
fit <- lm(formula,data=d)
return(coef(fit))
}
semicorR <- function(x=NULL, y=NULL, cov=NULL, data=NULL){
lm1.formula <- paste(x,"~",paste(cov,collapse="+"))
yvar <- as.character(y)
resX <- residuals(lm(as.formula(lm1.formula), data=data, na.action=na.exclude))
s = as.matrix(cbind(data[y],resX))
return(cor(s[,1], s[,2], use="complete.obs"))
}
round_df <- function(df=NULL, digits=3) {
nums <- vapply(df, is.numeric, FUN.VALUE = logical(1))
df[,nums] <- round(df[,nums], digits = digits)
(df)
}
bootlm <- function(model = NULL,
output = "r",
data = NULL,
boot = 1000,
boottype="perc",
digits=3,
conf=0.95,
semicor=FALSE) {
if (is.null(data)) stop('No dataframe provided')
#if (is.null(y)) stop('No dependent variable provided')
if (is.null(model)) stop('No independent variables provided')
##Bootstrapped Linear Model
lm.model <- as.formula(model)
bootResults <- boot(statistic=bootReg, formula=lm.model, data=data, R=boot)
# if (semicor==TRUE) {
# bootResults.partcor <- boot(statistic=bootCor, formula=lm.model, data=data, R=boot)
# }
lm.model.object <- lm(lm.model,data = data)
lm.summary <- summary(lm.model.object)
totSummary.tbl <- tidy(lm.summary)
lm.D9.beta <- lm.beta(lm.model.object)
beta <- coef(lm.D9.beta, standardized = TRUE)
vars <- all.vars(formula(lm.model.object))
ci <- matrix(nrow =nrow(totSummary.tbl), ncol=5)
partcor.ci <- matrix(nrow =nrow(totSummary.tbl), ncol=5)
partcor <- vector()
boot.se <- vector()
boot.bias <- vector()
boot.p <- vector()
null.dist <- vector()
#partcor[1,1] <- NA
#colnames(partcor) <- "Part"
for(i in 1:nrow(totSummary.tbl)){
if (boottype=="perc"){
ci[i,] <- boot.ci(bootResults, type=boottype, index=i, conf=conf)$percent
if(semicor==TRUE){
#print(boot.ci(bootResults.partcor, type=boottype, index=i, conf=conf)$percent)
#partcor.ci[i,] <- boot.ci(bootResults.partcor, type=boottype, index=i, conf=conf)$percent
}
}else if(boottype=="bca"){
ci[i,] <- boot.ci(bootResults, type=boottype, index=i, conf=conf)$bca
if(semicor==TRUE){
#partcor.ci[i,] <- boot.ci(bootResults.partcor, type=boottype, index=i, conf=conf)$percent
}
}
boot.se[i] <- sqrt(var(bootResults$t[,i]))
boot.bias[i] <- mean(bootResults$t[,i]) - totSummary.tbl$estimate[i]
# The bootstrap p-value can then be approximated by
null.dist <- bootResults$t[,i] - mean(bootResults$t[,i])
bootP <- (1+sum(abs(null.dist) > abs(bootResults$t0[i])))/(1+bootResults$R)
boot.p[i] <- bootP
if(semicor==TRUE){
if(i<nrow(totSummary.tbl)){
w <- i+1
#partcor[w] <- semicorR(x=vars[w],y=vars[1],cov=vars[-c(1,w)], data=data)
}
}
}
#Remove extra information
ci<-ci[,-c(1,2,3)] #delete columns 6, 7 and 8
#partcor.ci<-partcor.ci[,-c(1,2,3)] #delete columns 6, 7 and 8
#add bias and boot se and then reorder columns and then add estimate confididence interval
totSummary.tbl <- cbind(totSummary.tbl,boot.bias,boot.se,beta)
totSummary.tbl <- totSummary.tbl[c("term","estimate","beta","std.error","boot.bias","boot.se","statistic","p.value")]
totSummary.tbl <- cbind(totSummary.tbl,ci)
#totSummary.tbl <- cbind(totSummary.tbl,ci,boot.p)
#Rename columns
totSummary.tbl <- plyr::rename(totSummary.tbl, c("term"=" ","beta"="Beta","std.error"="SE","boot.bias"="Bias","boot.se"="Boot SE","statistic"="t","p.value"="p","1"="Boot LLCI","2"="Boot ULCI"))
#totSummary.tbl <- plyr::rename(totSummary.tbl, c("term"=" ","beta"="Beta","std.error"="SE","boot.bias"="Bias","boot.se"="Boot SE","statistic"="t","p.value"="p","1"="Boot LLCI","2"="Boot ULCI","boot.p"="Bootstrap p"))
# if(semicor==TRUE){
# #add , semi-partial correlation and it's confidence interval
# #partcor.ci[1,1] <- NA
# #partcor.ci[1,2] <- NA
# totSummary.tbl <- cbind(totSummary.tbl,partcor)
# #totSummary.tbl <- cbind(totSummary.tbl,partcor.ci)
#
# #totSummary.tbl <- rename(totSummary.tbl, c("partcor"="semipartial r","1"= "semipartial LLCI","2"="semipartial ULCI"))
# totSummary.tbl <- plyr::rename(totSummary.tbl, c("partcor"="semipartial r"))
# }
if (boottype=="perc"){
print.boottype <- "Percentile"
}else if (boottype=="bca"){
print.boottype <- "BCa"
}
if(output=="r"){
#round results to 4 digits
totSummary.tbl <- totSummary.tbl[-1]
totSummary.tbl <- round_df(totSummary.tbl,digits)
#Print Header
cat(paste("Bootstrapped Regression Model \n \n Model = ", as.character(model), "\n Outcome = ", vars[1],"\n IVs = ",paste(vars[2:length(vars)], collapse = ", "),"\n Observations = ",nrow(data),"\n Bootstrap Type = ", print.boottype,"\n Bootstrap Samples = ",boot,"\n Confidence Interval = ", as.character(conf), "\n \n",sep=""))
#Print output
print(totSummary.tbl, na.print = "")
#Print Model Parameters
f.sig = pf(lm.summary$fstatistic[1], lm.summary$fstatistic[2],lm.summary$fstatistic[3], lower.tail = FALSE)
model.params <- paste("F(",lm.summary$fstatistic[2],",",lm.summary$fstatistic[3],") = ",round(lm.summary$fstatistic[1],3), ", p= ",round(f.sig,3) , ", R^2: ",round(lm.summary$r.squared,3), ", Adjusted R^2: ",round(lm.summary$adj.r.squared,3),sep="")
cat("\n",model.params,"\n\n")
}else if(output=="html"){
totSummary.tbl <- round_df(totSummary.tbl,digits)
#Model Parameters
f.sig = pf(lm.summary$fstatistic[1], lm.summary$fstatistic[2],lm.summary$fstatistic[3], lower.tail = FALSE)
model.params <- paste("F(",lm.summary$fstatistic[2],",",lm.summary$fstatistic[3],") = ",round(lm.summary$fstatistic[1],3), ", p= ",round(f.sig,3) , ", R^2: ",round(lm.summary$r.squared,3), ", Adjusted R^2: ",round(lm.summary$adj.r.squared,3),sep="")
#Print Header
header <- paste("<p><b>Bootstrapped Regression Model</b> <br /><br /> <b>Model:</b> ", as.character(model), "<br /> <b>Outcome =</b> ", vars[1],"<br /> <b>IVs =</b> ",paste(vars[2:length(vars)], collapse = ", "),"<br /> <b>Observations=</b> ",nrow(data),"<br /> <b>Bootstrap Type:</b> ", print.boottype,"<br /> <b>Bootstrap Samples=</b> ",boot,"<br /> <b>Confidence Interval =</b> ", conf, "<br /></p>",sep="")
cat(header)
#Print output
APAhtmlTable(totSummary.tbl,round = FALSE, tidy=FALSE,tableTitle="Bootstrapped Regression results",genNote=model.params)
}
}
APAhtmlTable <- function(df=NULL,
round=TRUE,
tidy=TRUE,
digits=3,
genNote=NULL,
font="Times New Roman",
fontSize=12, tableNum=NULL,
tableTitle=NULL,
headerBold=FALSE,
headerAlign="center",
leftColAlign="left",
contentAlign="center",
header=NULL){
# for (df1 in df){
# #df1 <- tidy(df1)
# print(df1)
# }
#Set font options
fontWeight <- ifelse(headerBold==TRUE,"font-weight:bold;","font-weight:normal;")
if ((!headerAlign=="left") & (!headerAlign=="right") & (!headerAlign=="center")) stop("Invalid headerAlign set. Options include 'left', 'center', 'right'.")
if ((!leftColAlign=="left") & (!leftColAlign=="right") & (!leftColAlign=="center")) stop("Invalid leftColAlign set. Options include 'left', 'center', 'right'.")
if ((!contentAlign=="left") & (!contentAlign=="right") & (!contentAlign=="center")) stop("Invalid contentAlign set. Options include 'left', 'center', 'right'.")
#Check header length
#if((!is.null(header)) && (!length(header)==(ncol(df)+1))) stop("Number of header columns provided does not match number of columns in dataframe")
#Convert object to dataFrame
if(tidy==TRUE){
df <- tidy(df)
}
#Round digits in data frame
if(round==TRUE){
df <- round_df(df,digits)
}
#Convert dataframe to characters and replace NAs with blanks
df[, ] <- lapply(df[, ], as.character)
df[is.na(df)] <- ""
#Populate table header with column names
if (is.null(header)){
toprow.names <- as.list(colnames(df))
toprow <- paste(as.character(toprow.names),collapse = paste("</th><th style='border-bottom:solid 1px #000000;border-top:solid 1px #000000;padding-right: 10px;text-align: ", headerAlign,";", as.character(fontWeight),"'>",sep=""),sep="")
}else{
toprow.names <- as.list(header)
toprow <- paste(as.character(toprow.names),collapse = paste("</th><th style='border-bottom:solid 1px #000000;border-top:solid 1px #000000;padding-right: 10px;text-align: ", headerAlign,";", as.character(fontWeight),"'>",sep=""),sep="")
}
#Add start table tag
tbl.summary <- paste("<br/><table style='border-collapse: collapse;font-family: ", font ,";font-size:", fontSize ,"pt'>",sep="")
#Add Table Number if not Null
if(!is.null(tableNum)){
tbl.summary <- paste(tbl.summary, "<tr><td colspan=", ncol(df) ," style='line-height: 2;'>Table", as.character(tableNum),"</td></tr>",sep="")
}
#Add Table Title if not Null
if(!is.null(tableTitle)){
tbl.summary <- paste(tbl.summary, "<tr><td colspan='", ncol(df) ,"', style='font-style:italic;line-height: 2;'>", as.character(tableTitle),"</td></tr>",sep="")
}
#ADD header row
tbl.summary <- paste(tbl.summary, "<tr><th style='border-bottom:solid 1px #000000;border-top:solid 1px #000000;padding-right: 10px;text-align: ", leftColAlign,";", fontWeight,"'>",toprow,"</th></tr>")
#Add content rows
for (i in 1:nrow(df)){
cell.style <- ifelse(i==nrow(df),paste("padding-right: 10px;text-align: ", contentAlign,";border-bottom:solid 1px #000000;"),paste("padding-right: 10px;text-align: ", contentAlign,";"))
firstcell.style <- ifelse(i==nrow(df),paste("padding-right: 10px;border-bottom:solid 1px #000000;text-align: ", leftColAlign,";"),paste("padding-right: 10px;text-align: ", leftColAlign,";"))
cell.content <- paste(df[i,],collapse = paste("</td><td style='", cell.style,"'>",sep=""),sep="")
tbl.summary <- paste(tbl.summary,"<tr><td style='", firstcell.style,"'>", as.character(cell.content),"</td></tr>",sep="")
}
#Add general not if not Null
if(!is.null(genNote)){
tbl.summary <- paste(tbl.summary,"<tr><td colspan='", ncol(df) ,"'><i>Note.</i> ", genNote ,"</td></tr>",sep="")
}
#Add closing table tag
tbl.summary <- paste(tbl.summary,"</table><br />",sep="")
#Print Final table
#cat(tbl.summary)
asis_output(tbl.summary)
}
matthew-quesnel/simplePsych documentation built on May 17, 2019, 12:02 p.m.
R Package Documentation
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library(boot)
library(broom)
library(lm.beta)
library(plyr)
library(knitr)
bootReg <- function(formula,data,indices){
d <- data[indices,]
fit <- lm(formula,data=d)
return(coef(fit))
}
semicorR <- function(x=NULL, y=NULL, cov=NULL, data=NULL){
lm1.formula <- paste(x,"~",paste(cov,collapse="+"))
yvar <- as.character(y)
resX <- residuals(lm(as.formula(lm1.formula), data=data, na.action=na.exclude))
s = as.matrix(cbind(data[y],resX))
return(cor(s[,1], s[,2], use="complete.obs"))
}
round_df <- function(df=NULL, digits=3) {
nums <- vapply(df, is.numeric, FUN.VALUE = logical(1))
df[,nums] <- round(df[,nums], digits = digits)
(df)
}
bootlm <- function(model = NULL,
output = "r",
data = NULL,
boot = 1000,
boottype="perc",
digits=3,
conf=0.95,
semicor=FALSE) {
if (is.null(data)) stop('No dataframe provided')
#if (is.null(y)) stop('No dependent variable provided')
if (is.null(model)) stop('No independent variables provided')
##Bootstrapped Linear Model
lm.model <- as.formula(model)
bootResults <- boot(statistic=bootReg, formula=lm.model, data=data, R=boot)
# if (semicor==TRUE) {
# bootResults.partcor <- boot(statistic=bootCor, formula=lm.model, data=data, R=boot)
# }
lm.model.object <- lm(lm.model,data = data)
lm.summary <- summary(lm.model.object)
totSummary.tbl <- tidy(lm.summary)
lm.D9.beta <- lm.beta(lm.model.object)
beta <- coef(lm.D9.beta, standardized = TRUE)
vars <- all.vars(formula(lm.model.object))
ci <- matrix(nrow =nrow(totSummary.tbl), ncol=5)
partcor.ci <- matrix(nrow =nrow(totSummary.tbl), ncol=5)
partcor <- vector()
boot.se <- vector()
boot.bias <- vector()
boot.p <- vector()
null.dist <- vector()
#partcor[1,1] <- NA
#colnames(partcor) <- "Part"
for(i in 1:nrow(totSummary.tbl)){
if (boottype=="perc"){
ci[i,] <- boot.ci(bootResults, type=boottype, index=i, conf=conf)$percent
if(semicor==TRUE){
#print(boot.ci(bootResults.partcor, type=boottype, index=i, conf=conf)$percent)
#partcor.ci[i,] <- boot.ci(bootResults.partcor, type=boottype, index=i, conf=conf)$percent
}
}else if(boottype=="bca"){
ci[i,] <- boot.ci(bootResults, type=boottype, index=i, conf=conf)$bca
if(semicor==TRUE){
#partcor.ci[i,] <- boot.ci(bootResults.partcor, type=boottype, index=i, conf=conf)$percent
}
}
boot.se[i] <- sqrt(var(bootResults$t[,i]))
boot.bias[i] <- mean(bootResults$t[,i]) - totSummary.tbl$estimate[i]
# The bootstrap p-value can then be approximated by
null.dist <- bootResults$t[,i] - mean(bootResults$t[,i])
bootP <- (1+sum(abs(null.dist) > abs(bootResults$t0[i])))/(1+bootResults$R)
boot.p[i] <- bootP
if(semicor==TRUE){
if(i<nrow(totSummary.tbl)){
w <- i+1
#partcor[w] <- semicorR(x=vars[w],y=vars[1],cov=vars[-c(1,w)], data=data)
}
}
}
#Remove extra information
ci<-ci[,-c(1,2,3)] #delete columns 6, 7 and 8
#partcor.ci<-partcor.ci[,-c(1,2,3)] #delete columns 6, 7 and 8
#add bias and boot se and then reorder columns and then add estimate confididence interval
totSummary.tbl <- cbind(totSummary.tbl,boot.bias,boot.se,beta)
totSummary.tbl <- totSummary.tbl[c("term","estimate","beta","std.error","boot.bias","boot.se","statistic","p.value")]
totSummary.tbl <- cbind(totSummary.tbl,ci)
#totSummary.tbl <- cbind(totSummary.tbl,ci,boot.p)
#Rename columns
totSummary.tbl <- plyr::rename(totSummary.tbl, c("term"=" ","beta"="Beta","std.error"="SE","boot.bias"="Bias","boot.se"="Boot SE","statistic"="t","p.value"="p","1"="Boot LLCI","2"="Boot ULCI"))
#totSummary.tbl <- plyr::rename(totSummary.tbl, c("term"=" ","beta"="Beta","std.error"="SE","boot.bias"="Bias","boot.se"="Boot SE","statistic"="t","p.value"="p","1"="Boot LLCI","2"="Boot ULCI","boot.p"="Bootstrap p"))
# if(semicor==TRUE){
# #add , semi-partial correlation and it's confidence interval
# #partcor.ci[1,1] <- NA
# #partcor.ci[1,2] <- NA
# totSummary.tbl <- cbind(totSummary.tbl,partcor)
# #totSummary.tbl <- cbind(totSummary.tbl,partcor.ci)
#
# #totSummary.tbl <- rename(totSummary.tbl, c("partcor"="semipartial r","1"= "semipartial LLCI","2"="semipartial ULCI"))
# totSummary.tbl <- plyr::rename(totSummary.tbl, c("partcor"="semipartial r"))
# }
if (boottype=="perc"){
print.boottype <- "Percentile"
}else if (boottype=="bca"){
print.boottype <- "BCa"
}
if(output=="r"){
#round results to 4 digits
totSummary.tbl <- totSummary.tbl[-1]
totSummary.tbl <- round_df(totSummary.tbl,digits)
#Print Header
cat(paste("Bootstrapped Regression Model \n \n Model = ", as.character(model), "\n Outcome = ", vars[1],"\n IVs = ",paste(vars[2:length(vars)], collapse = ", "),"\n Observations = ",nrow(data),"\n Bootstrap Type = ", print.boottype,"\n Bootstrap Samples = ",boot,"\n Confidence Interval = ", as.character(conf), "\n \n",sep=""))
#Print output
print(totSummary.tbl, na.print = "")
#Print Model Parameters
f.sig = pf(lm.summary$fstatistic[1], lm.summary$fstatistic[2],lm.summary$fstatistic[3], lower.tail = FALSE)
model.params <- paste("F(",lm.summary$fstatistic[2],",",lm.summary$fstatistic[3],") = ",round(lm.summary$fstatistic[1],3), ", p= ",round(f.sig,3) , ", R^2: ",round(lm.summary$r.squared,3), ", Adjusted R^2: ",round(lm.summary$adj.r.squared,3),sep="")
cat("\n",model.params,"\n\n")
}else if(output=="html"){
totSummary.tbl <- round_df(totSummary.tbl,digits)
#Model Parameters
f.sig = pf(lm.summary$fstatistic[1], lm.summary$fstatistic[2],lm.summary$fstatistic[3], lower.tail = FALSE)
model.params <- paste("F(",lm.summary$fstatistic[2],",",lm.summary$fstatistic[3],") = ",round(lm.summary$fstatistic[1],3), ", p= ",round(f.sig,3) , ", R^2: ",round(lm.summary$r.squared,3), ", Adjusted R^2: ",round(lm.summary$adj.r.squared,3),sep="")
#Print Header
header <- paste("<p><b>Bootstrapped Regression Model</b> <br /><br /> <b>Model:</b> ", as.character(model), "<br /> <b>Outcome =</b> ", vars[1],"<br /> <b>IVs =</b> ",paste(vars[2:length(vars)], collapse = ", "),"<br /> <b>Observations=</b> ",nrow(data),"<br /> <b>Bootstrap Type:</b> ", print.boottype,"<br /> <b>Bootstrap Samples=</b> ",boot,"<br /> <b>Confidence Interval =</b> ", conf, "<br /></p>",sep="")
cat(header)
#Print output
APAhtmlTable(totSummary.tbl,round = FALSE, tidy=FALSE,tableTitle="Bootstrapped Regression results",genNote=model.params)
}
}
APAhtmlTable <- function(df=NULL,
round=TRUE,
tidy=TRUE,
digits=3,
genNote=NULL,
font="Times New Roman",
fontSize=12, tableNum=NULL,
tableTitle=NULL,
headerBold=FALSE,
headerAlign="center",
leftColAlign="left",
contentAlign="center",
header=NULL){
# for (df1 in df){
# #df1 <- tidy(df1)
# print(df1)
# }
#Set font options
fontWeight <- ifelse(headerBold==TRUE,"font-weight:bold;","font-weight:normal;")
if ((!headerAlign=="left") & (!headerAlign=="right") & (!headerAlign=="center")) stop("Invalid headerAlign set. Options include 'left', 'center', 'right'.")
if ((!leftColAlign=="left") & (!leftColAlign=="right") & (!leftColAlign=="center")) stop("Invalid leftColAlign set. Options include 'left', 'center', 'right'.")
if ((!contentAlign=="left") & (!contentAlign=="right") & (!contentAlign=="center")) stop("Invalid contentAlign set. Options include 'left', 'center', 'right'.")
#Check header length
#if((!is.null(header)) && (!length(header)==(ncol(df)+1))) stop("Number of header columns provided does not match number of columns in dataframe")
#Convert object to dataFrame
if(tidy==TRUE){
df <- tidy(df)
}
#Round digits in data frame
if(round==TRUE){
df <- round_df(df,digits)
}
#Convert dataframe to characters and replace NAs with blanks
df[, ] <- lapply(df[, ], as.character)
df[is.na(df)] <- ""
#Populate table header with column names
if (is.null(header)){
toprow.names <- as.list(colnames(df))
toprow <- paste(as.character(toprow.names),collapse = paste("</th><th style='border-bottom:solid 1px #000000;border-top:solid 1px #000000;padding-right: 10px;text-align: ", headerAlign,";", as.character(fontWeight),"'>",sep=""),sep="")
}else{
toprow.names <- as.list(header)
toprow <- paste(as.character(toprow.names),collapse = paste("</th><th style='border-bottom:solid 1px #000000;border-top:solid 1px #000000;padding-right: 10px;text-align: ", headerAlign,";", as.character(fontWeight),"'>",sep=""),sep="")
}
#Add start table tag
tbl.summary <- paste("<br/><table style='border-collapse: collapse;font-family: ", font ,";font-size:", fontSize ,"pt'>",sep="")
#Add Table Number if not Null
if(!is.null(tableNum)){
tbl.summary <- paste(tbl.summary, "<tr><td colspan=", ncol(df) ," style='line-height: 2;'>Table", as.character(tableNum),"</td></tr>",sep="")
}
#Add Table Title if not Null
if(!is.null(tableTitle)){
tbl.summary <- paste(tbl.summary, "<tr><td colspan='", ncol(df) ,"', style='font-style:italic;line-height: 2;'>", as.character(tableTitle),"</td></tr>",sep="")
}
#ADD header row
tbl.summary <- paste(tbl.summary, "<tr><th style='border-bottom:solid 1px #000000;border-top:solid 1px #000000;padding-right: 10px;text-align: ", leftColAlign,";", fontWeight,"'>",toprow,"</th></tr>")
#Add content rows
for (i in 1:nrow(df)){
cell.style <- ifelse(i==nrow(df),paste("padding-right: 10px;text-align: ", contentAlign,";border-bottom:solid 1px #000000;"),paste("padding-right: 10px;text-align: ", contentAlign,";"))
firstcell.style <- ifelse(i==nrow(df),paste("padding-right: 10px;border-bottom:solid 1px #000000;text-align: ", leftColAlign,";"),paste("padding-right: 10px;text-align: ", leftColAlign,";"))
cell.content <- paste(df[i,],collapse = paste("</td><td style='", cell.style,"'>",sep=""),sep="")
tbl.summary <- paste(tbl.summary,"<tr><td style='", firstcell.style,"'>", as.character(cell.content),"</td></tr>",sep="")
}
#Add general not if not Null
if(!is.null(genNote)){
tbl.summary <- paste(tbl.summary,"<tr><td colspan='", ncol(df) ,"'><i>Note.</i> ", genNote ,"</td></tr>",sep="")
}
#Add closing table tag
tbl.summary <- paste(tbl.summary,"</table><br />",sep="")
#Print Final table
#cat(tbl.summary)
asis_output(tbl.summary)
}
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