R/cfaOne.R
In melissagwolf/dynamic: DFI Cutoffs for Latent Variable Models
Defines functions
print.cfaOne
cfaOne
Documented in
cfaOne
print.cfaOne
#' @title Dynamic fit index (DFI) cutoffs for one-factor CFA models
#'
#' @description This function generates DFI cutoffs for one-factor CFA models using ML estimation.
#' The default argument is a singular argument: a \code{\link{lavaan}} object from the \code{\link{cfa}} function.
#' The function can also accommodate manual entry of the model statement and sample size.
#'
#' The app-based version of this function can be found at \href{https://dynamicfit.app/}{dynamicfit.app}.
#'
#' @param model This can either be a \code{\link{lavaan}} object from the \code{\link{cfa}} function,
#' OR a model statement written in \code{\link{lavaan}} \code{\link{model.syntax}} with standardized loadings.
#' @param n If you entered a \code{\link{lavaan}} object for model, leave this blank.
#' Otherwise, enter your sample size (numeric).
#' @param plot Displays distributions of fit indices for each level of misspecification.
#' @param manual If you entered a \code{\link{lavaan}} object, keep this set to FALSE.
#' If you manually entered standardized loadings and sample size, set this to TRUE.
#' @param reps The number of replications used in your simulation. This is set to 500 by default in both the
#' R package and the corresponding Shiny App.
#' @param estimator Which estimator to use within the simulations (enter in quotes). The default is ML.
#'
#' @import dplyr lavaan simstandard ggplot2 stringr
#' @importFrom purrr map map_dfr map2
#' @importFrom tidyr unite extract
#' @importFrom patchwork plot_layout plot_annotation wrap_plots
#'
#' @author Melissa G Wolf & Daniel McNeish
#'
#' Maintainer: Melissa G Wolf <melissagordon@ucsb.edu>
#'
#' @rdname cfaOne
#'
#' @return Dynamic fit index (DFI) cutoffs for SRMR, RMSEA, and CFI.
#' @export
#'
#' @examples
#' #Lavaan object example (manual=FALSE)
#' dat <- lavaan::HolzingerSwineford1939
#' lavmod <- "F1 =~ x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9"
#' fit <- lavaan::cfa(lavmod,dat)
#' \donttest{cfaOne(fit)}
#'
#' #Manual entry example for a sample size of 300 (manual=TRUE)
#' manmod <- "F1 =~ .602*Y1 + .805*Y2 + .857*Y3 + .631*Y4 + .345*Y5 + .646*Y6"
#' \donttest{cfaOne(model=manmod,n=300,manual=TRUE)}
#'
cfaOne <- function(model,n=NULL,plot=FALSE,manual=FALSE,estimator="ML",reps=500){
#If manual, expect manual (a la Shiny app)
if(manual){
tryCatch(cleanmodel(model),
error=function(err5){
if (grepl("no method for coercing this S4 class to a vector", err5)){
stop("dynamic Error: Did you accidentally include 'manual=TRUE' with a non-manually entered lavaan object?")
}
})
n <- n
model9 <- model
tryCatch(defre(model9,n),
error=function(err4){
if (grepl("non-numeric matrix extent", err4)){
stop("dynamic Error: Did you forget to include a sample size with your manually entered model?")
}
})
}else{
#Use this to rewrite error message for when someone forgot to use manual=TRUE
#But entered in model statement and sample size
#This is hacky but works, although traceback might confuse people
#https://community.rstudio.com/t/create-custom-error-messages/39058/4
tryCatch(cfa_n(model),
error=function(err){
if (grepl("trying to get slot", err)) {
stop("dynamic Error: Did you forget to use manual=TRUE?")
}
})
#Error for when someone enters an object that doesn't exist, or a non-lavaan object
tryCatch(cfa_n(model),
error=function(err2){
if (grepl("Error in base::unlist", err2)){
stop("dynamic Error: Did you enter a lavaan object? Confirm that it is a lavaan object using class(). If you do not have a lavaan object, enter the arguments manually and select manual=TRUE.")
}
})
#Use these functions to convert to manual (input is a lavaan object)
#Probably what we should expect for people using R
#need 'n' first because otherwise model will overwrite
n <- cfa_n(model)
model9 <- cfa_lavmod(model)
}
if (unstandardized(model9)>0){
stop("dynamic Error: One of your loadings or correlations has an absolute value of 1 or above (an impossible value). Please use standardized loadings. If all of your loadings are under 1, try looking for a missing decimal somewhere in your model statement.")
}
if (number_factor(model9)>1){
stop("dynamic Error: You entered a multi-factor model. Use cfaHB instead.")
}
if (defre(model9,n)==0){
stop("dynamic Error: It is impossible to add misspecifications to a just identified model.")
}
if ( nrow(one_num(model9)) < (number_factor(model9)-1)){
stop("dynamic Error: There are not enough free items to produce all misspecification levels.")
}
if (estimator=="MLR"){
stop("dynamic Error: the cfaOne function generates data from multivariate normal distributions, so the MLR estimator is equivalent to the ML estimator. Either change the estimator to ML or use the nnorOne function if you wish to derive cutoffs that are sensitive to non-normality")
}
if (startsWith(estimator,"U")|startsWith(estimator,"W")){
message("dynamic Warning: Cutoffs are interpretable if normality is reasonble to assume. The ULS and WLS families of estimators are often used for non-normal data, so if you are trying to derive cutoffs that will be sensitive to non-normality, the nnorOne function may provide more accurate cuttofs. Treating items as categorical is supported with the catOne function.")
}
#Create list to store outputs (table and plot)
res <- list()
#Output fit indices if someone used manual=F
#Will ignore in print statement if manual=T
#Exclamation point is how we indicate if manual = T (because default is F)
if(!manual){
fitted <- round(lavaan::fitmeasures(model,c("chisq","df","pvalue","srmr","rmsea","cfi")),3)
fitted_m <- as.matrix(fitted)
fitted_t <- t(fitted_m)
fitted_t <- as.data.frame(fitted_t)
colnames(fitted_t) <- c("Chi-Square"," df","p-value"," SRMR"," RMSEA"," CFI")
rownames(fitted_t) <- c("")
res$fit <- fitted_t
}
#Run simulation
results <- one_df(model9,n,estimator, reps)
#Save the data and make it exportable
res$data <- fit_data(results)
misspec_sum <- purrr::map(results,~dplyr::reframe(.,SRMR_M=stats::quantile(SRMR_M, c(seq(0.05,1,0.01))),
RMSEA_M=stats::quantile(RMSEA_M, c(seq(0.05,1,0.01))),
CFI_M=stats::quantile(CFI_M, c(seq(0.95,0,-0.01)))))
#For the true model, compute the cutoffs (these will all be the same - just need in list form)
true_sum <- purrr::map(results,~dplyr::reframe(.,SRMR_T=stats::quantile(SRMR_T, c(.95)),
RMSEA_T=stats::quantile(RMSEA_T, c(.95)),
CFI_T=stats::quantile(CFI_T, c(.05))))
fit<-list()
S<-list()
R<-list()
C<-list()
final<-list()
for (i in 1:length(misspec_sum))
{
fit[[i]]<-cbind(misspec_sum[[i]], true_sum[[i]])
fit[[i]]$Power<-seq(.95, 0.0, -.01)
fit[[i]]$S<-ifelse(fit[[i]]$SRMR_M >= fit[[i]]$SRMR_T, 1, 0)
fit[[i]]$R<-ifelse(fit[[i]]$RMSEA_M >= fit[[i]]$RMSEA_T, 1, 0)
fit[[i]]$C<-ifelse(fit[[i]]$CFI_M <= fit[[i]]$CFI_T, 1, 0)
S[[i]]<-subset(fit[[i]], subset=(!duplicated(fit[[i]][('S')])|fit[[i]][('Power')]==0), select=c("SRMR_M","Power","S")) %>% filter(S==1|Power==0)
R[[i]]<-subset(fit[[i]], subset=(!duplicated(fit[[i]][('R')])|fit[[i]][('Power')]==0), select=c("RMSEA_M","Power","R")) %>% filter(R==1|Power==0)
C[[i]]<-subset(fit[[i]], subset=(!duplicated(fit[[i]][('C')])|fit[[i]][('Power')]==0), select=c("CFI_M","Power","C")) %>% filter(C==1|Power==0)
colnames(S[[i]])<-c("SRMR","PowerS")
colnames(R[[i]])<-c("RMSEA","PowerR")
colnames(C[[i]])<-c("CFI","PowerC")
final[[i]]<-cbind(S[[i]][1,],R[[i]][1,],C[[i]][1,])
final[[i]]<-final[[i]][c("SRMR","PowerS","RMSEA","PowerR","CFI","PowerC")]
}
L0<-data.frame(cbind(true_sum[[1]]$SRMR_T,.95,true_sum[[1]]$RMSEA_T,0.95,true_sum[[1]]$CFI_T,0.95))%>%
`colnames<-`(c("SRMR","PowerS","RMSEA","PowerR","CFI","PowerC"))
if(length(misspec_sum)==3) {
Fit<-round(rbind(L0,final[[1]],final[[2]],final[[3]]),3)
}
if(length(misspec_sum)==2) {
Fit<-round(rbind(L0,final[[1]],final[[2]]),3)
}
if(length(misspec_sum)==1) {
Fit<-round(rbind(L0,final[[1]]),3)
}
fit1<-unlist(Fit)%>% matrix(nrow=(length(misspec_sum)+1), ncol=6) %>%
`colnames<-`(c("SRMR","PowerS","RMSEA","PowerR","CFI","PowerC"))
PS<-paste(round(100*fit1[,2], 2), "%", sep="")
PR<-paste(round(100*fit1[,4], 2), "%", sep="")
PC<-paste(round(100*fit1[,6], 2), "%", sep="")
for (j in 2:(length(misspec_sum)+1)) {
if(fit1[j,2]<.50){fit1[j,1]<-"NONE"}
if(fit1[j,4]<.50){fit1[j,3]<-"NONE"}
if(fit1[j,6]<.50){fit1[j,5]<-"NONE"}
}
fit1[,2]<-PS
fit1[,4]<-PR
fit1[,6]<-PC
pp<-c(rep("--",(length(misspec_sum)+1)))
pp0<-c(rep("",(length(misspec_sum)+1)))
SS<-noquote(matrix(rbind(fit1[,1],fit1[,2],pp0),ncol=1))
RR<-noquote(matrix(rbind(fit1[,3],fit1[,4],pp0),ncol=1))
CC<-noquote(matrix(rbind(fit1[,5],fit1[,6],pp0),ncol=1))
Table<-noquote(cbind(SS,RR,CC) %>%
`colnames<-`(c("SRMR","RMSEA","CFI")))
if(length(misspec_sum)==3) {
rownames(Table)<-c("Level-0","Specificity", "","Level-1", "Sensitivity","", "Level-2", "Sensitivity","", "Level-3", "Sensitivity","")
}
if(length(misspec_sum)==2) {
rownames(Table)<-c("Level-0","Specificity", "","Level-1", "Sensitivity","", "Level-2", "Sensitivity","")
}
if(length(misspec_sum)==1) {
rownames(Table)<-c("Level-0","Specificity", "","Level-1", "Sensitivity","")
}
Table<-Table[1:(nrow(Table)-1),]
#Put into list
res$cutoffs <- Table
#If user selects plot = T
if(plot){
#For each list element (misspecification) compute the cutoffs
#misspec_sum <- purrr::map(results,~dplyr::reframe(.,SRMR_M=stats::quantile(SRMR_M, c(.05,.1)),
# RMSEA_M=stats::quantile(RMSEA_M, c(.05,.1)),
# CFI_M=stats::quantile(CFI_M, c(.95,.9))))
#For the true model, compute the cutoffs (these will all be the same - just need in list form)
#true_sum <- purrr::map(results,~dplyr::reframe(.,SRMR_T=stats::quantile(SRMR_T, c(.95,.9)),
# RMSEA_T=stats::quantile(RMSEA_T, c(.95,.9)),
# CFI_T=stats::quantile(CFI_T, c(.05,.1))))
#Select just those variables and rename columns to be the same
Misspec_dat <- purrr::map(results,~dplyr::select(.,SRMR_M:Type_M) %>%
`colnames<-`(c("SRMR","RMSEA","CFI","Model")))
#Select just those variables and rename columns to be the same
True_dat <- purrr::map(results,~dplyr::select(.,SRMR_T:Type_T) %>%
`colnames<-`(c("SRMR","RMSEA","CFI","Model")))
#For each element in the list, bind the misspecified cutoffs to the true cutoffs
#rbind doesn't work well with lists (needs do.call statement)
plot <- base::lapply(base::seq(base::length(Misspec_dat)),function(x) dplyr::bind_rows(Misspec_dat[x],True_dat[x]))
#Plot SRMR. Need map2 and data=.x (can't remember why).
SRMR_plot <- purrr::map2(plot,misspec_sum,~ggplot(data=.x,aes(x=SRMR,fill=Model))+
geom_histogram(position="identity",
alpha=.5, bins=30)+
scale_fill_manual(values=c("#E9798C","#66C2F5"))+
geom_vline(aes(xintercept=.y$SRMR_M[1],
linetype="misspec_sum$SRMR_M[1]",color="misspec_sum$SRMR_M[1]"),
size=.6)+
geom_vline(aes(xintercept=.08,
linetype=".08",color=".08"),
size=.75)+
scale_color_manual(name="Cutoff Values",
labels=c("Hu & Benter Cutoff","Dynamic Cutoff"),
values=c("misspec_sum$SRMR_M[1]"="black",
".08"="black"))+
scale_linetype_manual(name="Cutoff Values",
labels=c("Hu & Benter Cutoff","Dynamic Cutoff"),
values=c("misspec_sum$SRMR_M[1]"="longdash",
".08"="dotted"))+
theme(axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
panel.background = element_blank(),
axis.line = element_line(color="black"),
legend.position = "none",
legend.title = element_blank(),
legend.box = "vertical"))
#Plot RMSEA. Need map2 and data=.x (can't remember why).
RMSEA_plot <- purrr::map2(plot,misspec_sum,~ggplot(data=.x,aes(x=RMSEA,fill=Model))+
geom_histogram(position="identity",
alpha=.5, bins=30)+
scale_fill_manual(values=c("#E9798C","#66C2F5"))+
geom_vline(aes(xintercept=.y$RMSEA_M[1],
linetype="misspec_sum$RMSEA_M[1]",color="misspec_sum$RMSEA_M[1]"),
size=.6)+
geom_vline(aes(xintercept=.06,
linetype=".06",color=".06"),
size=.75)+
scale_color_manual(name="Cutoff Values",
labels=c("Hu & Benter Cutoff","Dynamic Cutoff"),
values=c("misspec_sum$RMSEA_M[1]"="black",
".06"="black"))+
scale_linetype_manual(name="Cutoff Values",
labels=c("Hu & Benter Cutoff","Dynamic Cutoff"),
values=c("misspec_sum$RMSEA_M[1]"="longdash",
".06"="dotted"))+
theme(axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
panel.background = element_blank(),
axis.line = element_line(color="black"),
legend.position = "none",
legend.title = element_blank(),
legend.box = "vertical"))
#Plot CFI. Need map2 and data=.x (can't remember why).
CFI_plot <- purrr::map2(plot,misspec_sum,~ggplot(data=.x,aes(x=CFI,fill=Model))+
geom_histogram(position="identity",
alpha=.5, bins=30)+
scale_fill_manual(values=c("#E9798C","#66C2F5"))+
geom_vline(aes(xintercept=.y$CFI_M[1],
linetype="misspec_sum$CFI_M[1]",color="misspec_sum$CFI_M[1]"),
size=.6)+
geom_vline(aes(xintercept=.95,
linetype=".95",color=".95"),
size=.75)+
scale_color_manual(name="Cutoff Values",
labels=c("Hu & Benter Cutoff","Dynamic Cutoff"),
values=c("misspec_sum$CFI_M[1]"="black",
".95"="black"))+
scale_linetype_manual(name="Cutoff Values",
labels=c("Hu & Benter Cutoff","Dynamic Cutoff"),
values=c("misspec_sum$CFI_M[1]"="longdash",
".95"="dotted"))+
theme(axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
panel.background = element_blank(),
axis.line = element_line(color="black"),
legend.position = "none",
legend.title = element_blank(),
legend.box = "vertical"))
#Create a list with the plots combined for each severity level
plots_combo <- base::lapply(base::seq(base::length(plot)),function(x) c(SRMR_plot[x],RMSEA_plot[x],CFI_plot[x]))
#Add a collective legend and title with the level indicator
plots <- base::lapply(base::seq(base::length(plots_combo)), function(x) patchwork::wrap_plots(plots_combo[[x]])+
plot_layout(guides = "collect")+
plot_annotation(title=paste("Level", x))
& theme(legend.position = 'bottom'))
#Put into list
res$plots <- plots
}
#Create object (necessary for subsequent print statement)
class(res) <- 'cfaOne'
return(res)
}
#' @method print cfaOne
#' @param x cfaOne object
#' @param ... other print parameters
#' @rdname cfaOne
#' @export
#Print suppression/organization statement for list
#Needs same name as class, not function name
#Need to add ... param or will get error message in CMD check
print.cfaOne <- function(x,...){
#Automatically return fit cutoffs
base::cat("Your DFI cutoffs: \n")
base::print(x$cutoffs)
#Only print fit indices from lavaan object if someone submits a lavaan object
if(!is.null(x$fit)){
base::cat("\n")
base::cat("Empirical fit indices: \n")
base::print(x$fit)
}
if(!is.null(x$plots)){
base::cat("\n The distributions for each level are in the Plots tab \n")
base::print(x$plots)
}
#Hides this function
base::invisible()
}
melissagwolf/dynamic documentation built on June 29, 2024, 6:24 p.m.
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Defines functions print.cfaOne cfaOne
Documented in cfaOne print.cfaOne
#' @title Dynamic fit index (DFI) cutoffs for one-factor CFA models
#'
#' @description This function generates DFI cutoffs for one-factor CFA models using ML estimation.
#' The default argument is a singular argument: a \code{\link{lavaan}} object from the \code{\link{cfa}} function.
#' The function can also accommodate manual entry of the model statement and sample size.
#'
#' The app-based version of this function can be found at \href{https://dynamicfit.app/}{dynamicfit.app}.
#'
#' @param model This can either be a \code{\link{lavaan}} object from the \code{\link{cfa}} function,
#' OR a model statement written in \code{\link{lavaan}} \code{\link{model.syntax}} with standardized loadings.
#' @param n If you entered a \code{\link{lavaan}} object for model, leave this blank.
#' Otherwise, enter your sample size (numeric).
#' @param plot Displays distributions of fit indices for each level of misspecification.
#' @param manual If you entered a \code{\link{lavaan}} object, keep this set to FALSE.
#' If you manually entered standardized loadings and sample size, set this to TRUE.
#' @param reps The number of replications used in your simulation. This is set to 500 by default in both the
#' R package and the corresponding Shiny App.
#' @param estimator Which estimator to use within the simulations (enter in quotes). The default is ML.
#'
#' @import dplyr lavaan simstandard ggplot2 stringr
#' @importFrom purrr map map_dfr map2
#' @importFrom tidyr unite extract
#' @importFrom patchwork plot_layout plot_annotation wrap_plots
#'
#' @author Melissa G Wolf & Daniel McNeish
#'
#' Maintainer: Melissa G Wolf <melissagordon@ucsb.edu>
#'
#' @rdname cfaOne
#'
#' @return Dynamic fit index (DFI) cutoffs for SRMR, RMSEA, and CFI.
#' @export
#'
#' @examples
#' #Lavaan object example (manual=FALSE)
#' dat <- lavaan::HolzingerSwineford1939
#' lavmod <- "F1 =~ x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9"
#' fit <- lavaan::cfa(lavmod,dat)
#' \donttest{cfaOne(fit)}
#'
#' #Manual entry example for a sample size of 300 (manual=TRUE)
#' manmod <- "F1 =~ .602*Y1 + .805*Y2 + .857*Y3 + .631*Y4 + .345*Y5 + .646*Y6"
#' \donttest{cfaOne(model=manmod,n=300,manual=TRUE)}
#'
cfaOne <- function(model,n=NULL,plot=FALSE,manual=FALSE,estimator="ML",reps=500){
#If manual, expect manual (a la Shiny app)
if(manual){
tryCatch(cleanmodel(model),
error=function(err5){
if (grepl("no method for coercing this S4 class to a vector", err5)){
stop("dynamic Error: Did you accidentally include 'manual=TRUE' with a non-manually entered lavaan object?")
}
})
n <- n
model9 <- model
tryCatch(defre(model9,n),
error=function(err4){
if (grepl("non-numeric matrix extent", err4)){
stop("dynamic Error: Did you forget to include a sample size with your manually entered model?")
}
})
}else{
#Use this to rewrite error message for when someone forgot to use manual=TRUE
#But entered in model statement and sample size
#This is hacky but works, although traceback might confuse people
#https://community.rstudio.com/t/create-custom-error-messages/39058/4
tryCatch(cfa_n(model),
error=function(err){
if (grepl("trying to get slot", err)) {
stop("dynamic Error: Did you forget to use manual=TRUE?")
}
})
#Error for when someone enters an object that doesn't exist, or a non-lavaan object
tryCatch(cfa_n(model),
error=function(err2){
if (grepl("Error in base::unlist", err2)){
stop("dynamic Error: Did you enter a lavaan object? Confirm that it is a lavaan object using class(). If you do not have a lavaan object, enter the arguments manually and select manual=TRUE.")
}
})
#Use these functions to convert to manual (input is a lavaan object)
#Probably what we should expect for people using R
#need 'n' first because otherwise model will overwrite
n <- cfa_n(model)
model9 <- cfa_lavmod(model)
}
if (unstandardized(model9)>0){
stop("dynamic Error: One of your loadings or correlations has an absolute value of 1 or above (an impossible value). Please use standardized loadings. If all of your loadings are under 1, try looking for a missing decimal somewhere in your model statement.")
}
if (number_factor(model9)>1){
stop("dynamic Error: You entered a multi-factor model. Use cfaHB instead.")
}
if (defre(model9,n)==0){
stop("dynamic Error: It is impossible to add misspecifications to a just identified model.")
}
if ( nrow(one_num(model9)) < (number_factor(model9)-1)){
stop("dynamic Error: There are not enough free items to produce all misspecification levels.")
}
if (estimator=="MLR"){
stop("dynamic Error: the cfaOne function generates data from multivariate normal distributions, so the MLR estimator is equivalent to the ML estimator. Either change the estimator to ML or use the nnorOne function if you wish to derive cutoffs that are sensitive to non-normality")
}
if (startsWith(estimator,"U")|startsWith(estimator,"W")){
message("dynamic Warning: Cutoffs are interpretable if normality is reasonble to assume. The ULS and WLS families of estimators are often used for non-normal data, so if you are trying to derive cutoffs that will be sensitive to non-normality, the nnorOne function may provide more accurate cuttofs. Treating items as categorical is supported with the catOne function.")
}
#Create list to store outputs (table and plot)
res <- list()
#Output fit indices if someone used manual=F
#Will ignore in print statement if manual=T
#Exclamation point is how we indicate if manual = T (because default is F)
if(!manual){
fitted <- round(lavaan::fitmeasures(model,c("chisq","df","pvalue","srmr","rmsea","cfi")),3)
fitted_m <- as.matrix(fitted)
fitted_t <- t(fitted_m)
fitted_t <- as.data.frame(fitted_t)
colnames(fitted_t) <- c("Chi-Square"," df","p-value"," SRMR"," RMSEA"," CFI")
rownames(fitted_t) <- c("")
res$fit <- fitted_t
}
#Run simulation
results <- one_df(model9,n,estimator, reps)
#Save the data and make it exportable
res$data <- fit_data(results)
misspec_sum <- purrr::map(results,~dplyr::reframe(.,SRMR_M=stats::quantile(SRMR_M, c(seq(0.05,1,0.01))),
RMSEA_M=stats::quantile(RMSEA_M, c(seq(0.05,1,0.01))),
CFI_M=stats::quantile(CFI_M, c(seq(0.95,0,-0.01)))))
#For the true model, compute the cutoffs (these will all be the same - just need in list form)
true_sum <- purrr::map(results,~dplyr::reframe(.,SRMR_T=stats::quantile(SRMR_T, c(.95)),
RMSEA_T=stats::quantile(RMSEA_T, c(.95)),
CFI_T=stats::quantile(CFI_T, c(.05))))
fit<-list()
S<-list()
R<-list()
C<-list()
final<-list()
for (i in 1:length(misspec_sum))
{
fit[[i]]<-cbind(misspec_sum[[i]], true_sum[[i]])
fit[[i]]$Power<-seq(.95, 0.0, -.01)
fit[[i]]$S<-ifelse(fit[[i]]$SRMR_M >= fit[[i]]$SRMR_T, 1, 0)
fit[[i]]$R<-ifelse(fit[[i]]$RMSEA_M >= fit[[i]]$RMSEA_T, 1, 0)
fit[[i]]$C<-ifelse(fit[[i]]$CFI_M <= fit[[i]]$CFI_T, 1, 0)
S[[i]]<-subset(fit[[i]], subset=(!duplicated(fit[[i]][('S')])|fit[[i]][('Power')]==0), select=c("SRMR_M","Power","S")) %>% filter(S==1|Power==0)
R[[i]]<-subset(fit[[i]], subset=(!duplicated(fit[[i]][('R')])|fit[[i]][('Power')]==0), select=c("RMSEA_M","Power","R")) %>% filter(R==1|Power==0)
C[[i]]<-subset(fit[[i]], subset=(!duplicated(fit[[i]][('C')])|fit[[i]][('Power')]==0), select=c("CFI_M","Power","C")) %>% filter(C==1|Power==0)
colnames(S[[i]])<-c("SRMR","PowerS")
colnames(R[[i]])<-c("RMSEA","PowerR")
colnames(C[[i]])<-c("CFI","PowerC")
final[[i]]<-cbind(S[[i]][1,],R[[i]][1,],C[[i]][1,])
final[[i]]<-final[[i]][c("SRMR","PowerS","RMSEA","PowerR","CFI","PowerC")]
}
L0<-data.frame(cbind(true_sum[[1]]$SRMR_T,.95,true_sum[[1]]$RMSEA_T,0.95,true_sum[[1]]$CFI_T,0.95))%>%
`colnames<-`(c("SRMR","PowerS","RMSEA","PowerR","CFI","PowerC"))
if(length(misspec_sum)==3) {
Fit<-round(rbind(L0,final[[1]],final[[2]],final[[3]]),3)
}
if(length(misspec_sum)==2) {
Fit<-round(rbind(L0,final[[1]],final[[2]]),3)
}
if(length(misspec_sum)==1) {
Fit<-round(rbind(L0,final[[1]]),3)
}
fit1<-unlist(Fit)%>% matrix(nrow=(length(misspec_sum)+1), ncol=6) %>%
`colnames<-`(c("SRMR","PowerS","RMSEA","PowerR","CFI","PowerC"))
PS<-paste(round(100*fit1[,2], 2), "%", sep="")
PR<-paste(round(100*fit1[,4], 2), "%", sep="")
PC<-paste(round(100*fit1[,6], 2), "%", sep="")
for (j in 2:(length(misspec_sum)+1)) {
if(fit1[j,2]<.50){fit1[j,1]<-"NONE"}
if(fit1[j,4]<.50){fit1[j,3]<-"NONE"}
if(fit1[j,6]<.50){fit1[j,5]<-"NONE"}
}
fit1[,2]<-PS
fit1[,4]<-PR
fit1[,6]<-PC
pp<-c(rep("--",(length(misspec_sum)+1)))
pp0<-c(rep("",(length(misspec_sum)+1)))
SS<-noquote(matrix(rbind(fit1[,1],fit1[,2],pp0),ncol=1))
RR<-noquote(matrix(rbind(fit1[,3],fit1[,4],pp0),ncol=1))
CC<-noquote(matrix(rbind(fit1[,5],fit1[,6],pp0),ncol=1))
Table<-noquote(cbind(SS,RR,CC) %>%
`colnames<-`(c("SRMR","RMSEA","CFI")))
if(length(misspec_sum)==3) {
rownames(Table)<-c("Level-0","Specificity", "","Level-1", "Sensitivity","", "Level-2", "Sensitivity","", "Level-3", "Sensitivity","")
}
if(length(misspec_sum)==2) {
rownames(Table)<-c("Level-0","Specificity", "","Level-1", "Sensitivity","", "Level-2", "Sensitivity","")
}
if(length(misspec_sum)==1) {
rownames(Table)<-c("Level-0","Specificity", "","Level-1", "Sensitivity","")
}
Table<-Table[1:(nrow(Table)-1),]
#Put into list
res$cutoffs <- Table
#If user selects plot = T
if(plot){
#For each list element (misspecification) compute the cutoffs
#misspec_sum <- purrr::map(results,~dplyr::reframe(.,SRMR_M=stats::quantile(SRMR_M, c(.05,.1)),
# RMSEA_M=stats::quantile(RMSEA_M, c(.05,.1)),
# CFI_M=stats::quantile(CFI_M, c(.95,.9))))
#For the true model, compute the cutoffs (these will all be the same - just need in list form)
#true_sum <- purrr::map(results,~dplyr::reframe(.,SRMR_T=stats::quantile(SRMR_T, c(.95,.9)),
# RMSEA_T=stats::quantile(RMSEA_T, c(.95,.9)),
# CFI_T=stats::quantile(CFI_T, c(.05,.1))))
#Select just those variables and rename columns to be the same
Misspec_dat <- purrr::map(results,~dplyr::select(.,SRMR_M:Type_M) %>%
`colnames<-`(c("SRMR","RMSEA","CFI","Model")))
#Select just those variables and rename columns to be the same
True_dat <- purrr::map(results,~dplyr::select(.,SRMR_T:Type_T) %>%
`colnames<-`(c("SRMR","RMSEA","CFI","Model")))
#For each element in the list, bind the misspecified cutoffs to the true cutoffs
#rbind doesn't work well with lists (needs do.call statement)
plot <- base::lapply(base::seq(base::length(Misspec_dat)),function(x) dplyr::bind_rows(Misspec_dat[x],True_dat[x]))
#Plot SRMR. Need map2 and data=.x (can't remember why).
SRMR_plot <- purrr::map2(plot,misspec_sum,~ggplot(data=.x,aes(x=SRMR,fill=Model))+
geom_histogram(position="identity",
alpha=.5, bins=30)+
scale_fill_manual(values=c("#E9798C","#66C2F5"))+
geom_vline(aes(xintercept=.y$SRMR_M[1],
linetype="misspec_sum$SRMR_M[1]",color="misspec_sum$SRMR_M[1]"),
size=.6)+
geom_vline(aes(xintercept=.08,
linetype=".08",color=".08"),
size=.75)+
scale_color_manual(name="Cutoff Values",
labels=c("Hu & Benter Cutoff","Dynamic Cutoff"),
values=c("misspec_sum$SRMR_M[1]"="black",
".08"="black"))+
scale_linetype_manual(name="Cutoff Values",
labels=c("Hu & Benter Cutoff","Dynamic Cutoff"),
values=c("misspec_sum$SRMR_M[1]"="longdash",
".08"="dotted"))+
theme(axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
panel.background = element_blank(),
axis.line = element_line(color="black"),
legend.position = "none",
legend.title = element_blank(),
legend.box = "vertical"))
#Plot RMSEA. Need map2 and data=.x (can't remember why).
RMSEA_plot <- purrr::map2(plot,misspec_sum,~ggplot(data=.x,aes(x=RMSEA,fill=Model))+
geom_histogram(position="identity",
alpha=.5, bins=30)+
scale_fill_manual(values=c("#E9798C","#66C2F5"))+
geom_vline(aes(xintercept=.y$RMSEA_M[1],
linetype="misspec_sum$RMSEA_M[1]",color="misspec_sum$RMSEA_M[1]"),
size=.6)+
geom_vline(aes(xintercept=.06,
linetype=".06",color=".06"),
size=.75)+
scale_color_manual(name="Cutoff Values",
labels=c("Hu & Benter Cutoff","Dynamic Cutoff"),
values=c("misspec_sum$RMSEA_M[1]"="black",
".06"="black"))+
scale_linetype_manual(name="Cutoff Values",
labels=c("Hu & Benter Cutoff","Dynamic Cutoff"),
values=c("misspec_sum$RMSEA_M[1]"="longdash",
".06"="dotted"))+
theme(axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
panel.background = element_blank(),
axis.line = element_line(color="black"),
legend.position = "none",
legend.title = element_blank(),
legend.box = "vertical"))
#Plot CFI. Need map2 and data=.x (can't remember why).
CFI_plot <- purrr::map2(plot,misspec_sum,~ggplot(data=.x,aes(x=CFI,fill=Model))+
geom_histogram(position="identity",
alpha=.5, bins=30)+
scale_fill_manual(values=c("#E9798C","#66C2F5"))+
geom_vline(aes(xintercept=.y$CFI_M[1],
linetype="misspec_sum$CFI_M[1]",color="misspec_sum$CFI_M[1]"),
size=.6)+
geom_vline(aes(xintercept=.95,
linetype=".95",color=".95"),
size=.75)+
scale_color_manual(name="Cutoff Values",
labels=c("Hu & Benter Cutoff","Dynamic Cutoff"),
values=c("misspec_sum$CFI_M[1]"="black",
".95"="black"))+
scale_linetype_manual(name="Cutoff Values",
labels=c("Hu & Benter Cutoff","Dynamic Cutoff"),
values=c("misspec_sum$CFI_M[1]"="longdash",
".95"="dotted"))+
theme(axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
panel.background = element_blank(),
axis.line = element_line(color="black"),
legend.position = "none",
legend.title = element_blank(),
legend.box = "vertical"))
#Create a list with the plots combined for each severity level
plots_combo <- base::lapply(base::seq(base::length(plot)),function(x) c(SRMR_plot[x],RMSEA_plot[x],CFI_plot[x]))
#Add a collective legend and title with the level indicator
plots <- base::lapply(base::seq(base::length(plots_combo)), function(x) patchwork::wrap_plots(plots_combo[[x]])+
plot_layout(guides = "collect")+
plot_annotation(title=paste("Level", x))
& theme(legend.position = 'bottom'))
#Put into list
res$plots <- plots
}
#Create object (necessary for subsequent print statement)
class(res) <- 'cfaOne'
return(res)
}
#' @method print cfaOne
#' @param x cfaOne object
#' @param ... other print parameters
#' @rdname cfaOne
#' @export
#Print suppression/organization statement for list
#Needs same name as class, not function name
#Need to add ... param or will get error message in CMD check
print.cfaOne <- function(x,...){
#Automatically return fit cutoffs
base::cat("Your DFI cutoffs: \n")
base::print(x$cutoffs)
#Only print fit indices from lavaan object if someone submits a lavaan object
if(!is.null(x$fit)){
base::cat("\n")
base::cat("Empirical fit indices: \n")
base::print(x$fit)
}
if(!is.null(x$plots)){
base::cat("\n The distributions for each level are in the Plots tab \n")
base::print(x$plots)
}
#Hides this function
base::invisible()
}
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