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#'@method plot gimmep
#'@export
plot.gimmep <- function(x, file = NULL, subgroup = NULL, ...){
if (is.null(file) & is.null(subgroup)) {
cat("Please specify a file id for individual plots. Otherwise, summary plot is presented.")
plot(x$group_plot_paths)
invisible(x$group_plot_paths)
} else if (is.null(subgroup)){
a <- x$plots[[file]]
plot(a)
invisible(a)
} else if (is.null(file)){
## insert code here to grab subgroup plot
a <- x$sub_plots_paths[[subgroup]]
if (!is.list(a)){
cat("Subgroup", subgroup, "contains one individual. No subgroup plot provided.")
} else {
plot(a)
invisible(a)
}
}
}
#'@method print gimmep
#'@export
print.gimmep <- function(x, file = NULL, subgroup = NULL,
mean = FALSE, estimates = FALSE, fitMeasures = FALSE, ...){
if (!is.null(file)){
if (estimates == TRUE){
ind <- x$path_se_est[x$path_se_est$file %in% file, ]
ind <- ind[, !names(ind) %in% c("subgroup")]
ind[ ,4:6] <- round(ind[ ,4:6], digits = 3)
cat("Coefficients for", file, "\n")
print(ind, row.names = F)
invisible(ind)
} else if (estimates == FALSE){
ind <- x$path_est_mats[[file]]
colnames(ind) <- x$varnames
# changed to reflect possibility of different # of lagged vars
# rownames(ind) <- x$varnames[(x$n_rois +1):(x$n_rois*2)]
rownames(ind) <- x$varnames[(x$n_lagged+1):(x$n_vars_total)]
ind <- round(ind, digits = 2)
#ind_lag <- ind[ , 1:x$n_lagged]
ind_lag <- ind[ , 1:x$n_lagged]
#ind_con <- ind[ , (x$n_lagged+1):(x$n_rois*2)]
ind_con <- ind[ , (x$n_lagged+1):(x$n_vars_total)]
cat("\n")
cat("Lagged Matrix for", file, "\n")
print(ind_lag)
cat("\n")
cat("Contemporaneous Matrix for", file, "\n")
print(ind_con)
invisible(ind)
}
if (fitMeasures == TRUE){
allfit <- x$fit[, !names(x$fit) %in% c("modularity")]
ind <- allfit[allfit$file %in% file, ]
cat("Fit for file", file, "\n")
print.data.frame(ind, row.names = F)
}
}
if (!is.null(subgroup)){
if (mean == TRUE){
# subidx <- x$fit[,c("file", "subgroup")]
# STL I'm not sure if this is what you meant:
subidx <- x$fit[,c("file", "sub_membership")]
files <- subidx[subidx$sub_membership == subgroup, ]$file
subfiles <- x$path_est_mats[files]
if (length(files) == 1){
cat("Subgroup", subgroup, "contains one individual. No average subgroup matrix provided.")
} else {
s <- apply(simplify2array(subfiles), 1:2, mean, na.rm = TRUE)
colnames(s) <- x$varnames
#rownames(s) <- x$varnames[(x$n_rois +1):(x$n_rois*2)]
rownames(s) <- x$varnames[(x$n_lagged +1):(x$n_vars_total)]
s <- round(s, digits = 2)
#s <- s[(x$n_rois+1):(x$n_rois*2), ] #kmg did not comment this out 5/3/2018
# s_lag <- s[ , 1:x$n_rois] #commented this out kmg
s_lag <- s[ , 1:x$n_lagged]
s_con <- s[ , (x$n_lagged+1):(x$n_vars_total)]
cat("\n")
cat("Lagged Average Matrix for Subgroup", subgroup, "\n")
print(s_lag)
cat("\n")
cat("Contemporaneous Average Matrix for Subgroup", subgroup, "\n")
print(s_con)
invisible(s)
}
} else if (mean == FALSE & estimates == TRUE){
# INSERT ESTIMATES FOR THAT SUBGROUP
subest <- x$path_se_est
subest <- subest[subest$subgroup == subgroup, ]
subest[ ,4:6] <- round(subest[ ,4:6], digits = 3)
cat("Coefficients for individuals in subgroup", subgroup, "\n")
print(subest, row.names = F)
invisible(subest)
} else if (mean == FALSE & estimates == FALSE){
sub <- x$path_counts_sub[[subgroup]]
if (is.null(sub)){
cat("Subgroup", subgroup, "contains one individual. No subgroup matrix provided.")
} else {
#sub_lag <- sub[ , 1:x$n_rois]
#sub_con <- sub[ , (x$n_rois+1):(x$n_rois*2)]
sub_lag <- sub[ , 1:x$n_lagged]
sub_con <- sub[ , (x$n_lagged+1):(x$n_vars_total)]
cat("\n")
cat("Lagged Count Matrix for Subgroup", subgroup, "\n")
print(sub_lag)
cat("\n")
cat("Contemporaneous Count Matrix for Subgroup", subgroup, "\n")
print(sub_con)
invisible(sub)
}
}
if (fitMeasures == TRUE){
# RETURN FITMEASURES FOR MEMBERS OF THAT SUBGROUP
allfit <- x$fit[, !names(x$fit) %in% c("modularity")]
allfit[allfit$subgroup == subgroup, ]
cat("Fit for individuals in subgroup", subgroup, "\n")
print.data.frame(allfit, row.names = F)
}
}
if (is.null(file) & is.null(subgroup)) {
if (mean == FALSE & estimates == FALSE){
cat("Please specify a file id for individual coefficient matrix. ", "\n",
"Otherwise, a summary count matrix is presented below.", "\n")
all <- x$path_counts
#all_lag <- all[ , 1:x$n_rois]
all_lag <- all[ , 1:x$n_lagged]
#all_con <- all[ , (x$n_rois+1):(x$n_rois*2)]
all_con <- all[ , (x$n_lagged+1):(x$n_vars_total)]
cat("\n")
cat("Lagged Count Matrix for Sample", "\n")
print(all_lag)
cat("\n")
cat("Contemporaneous Count Matrix for Sample", "\n")
print(all_con)
invisible(all)
} else if (mean == FALSE & estimates == TRUE){
print(x$path_se_est)
invisible(x$path_se_est)
}
if (mean == TRUE){
cat("Please specify a file id for individual coefficient matrix. ", "\n",
"Otherwise, a summary average matrix is presented below.", "\n")
all2 <- apply(simplify2array(x$path_est_mats), 1:2, mean, na.rm = TRUE)
colnames(all2) <- x$varnames
#rownames(all2) <- x$varnames[(x$n_rois +1):(x$n_rois*2)]
rownames(all2) <- x$varnames[(x$n_lagged +1):(x$n_vars_total)]
all2 <- round(all2, digits = 2)
#all2_lag <- all2[ , 1:x$n_rois]
all2_lag <- all2[ , 1:x$n_lagged]
all2_con <- all2[ , (x$n_lagged+1):(x$n_vars_total)]
cat("\n")
cat("Lagged Average Matrix for Sample", "\n")
print(all2_lag)
cat("\n")
cat("Contemporaneous Average Matrix for Sample", "\n")
print(all2_con)
}
if (fitMeasures == TRUE){
allfit <- x$fit[, !names(x$fit) %in% c("modularity")]
cat("Fit for sample", "\n")
print.data.frame(allfit, row.names = F)
invisible(allfit)
}
}
}
# else if (length(file) > 1){
# ind <- x$a[file]
# for (i in 1:length(file)){
# w <- ind[[i]]
# colnames(w) <- x$b
# rownames(w) <- x$b
# w <- round(w, digits = 2)
# w_lag <- w[(x$c+1):(x$c*2), 1:x$c]
# w_con <- w[(x$c+1):(x$c*2), (x$c+1):(x$c*2)]
# cat("\n")
# cat("Lagged Coefficient Matrix for", file[i], "\n")
# print(w_lag)
# cat("\n")
# cat("Contemporaneous Coefficient Matrix for", file[i], "\n")
# print(w_con)
# }
# invisible(w)
# }
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