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prepare_results_CA.R
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prepare_results_CA.R
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##' @rdname prepare_results
##' @aliases prepare_results.CA
##'
##' @seealso \code{\link[FactoMineR]{CA}}
##' @import dplyr
##' @importFrom tidyr pivot_longer
##' @importFrom utils head
##' @export
prepare_results.CA <- function(obj) {
if (!inherits(obj, "CA")) stop("obj must be of class CA")
if (!is.array(obj$row$coord) || !is.array(obj$col$coord)) stop("obj must have at least two dimensions on rows or columns")
## Axes names and inertia
axes <- seq_len(ncol(obj$col$coord))
names(axes) <- paste("Axis", axes, paste0("(", head(round(obj$eig[, 2], 2), length(axes)),"%)"))
## Eigenvalues
eig <- data.frame(dim = seq_len(nrow(obj$eig)), percent = obj$eig[,2])
## Variables coordinates
## Columns
vars <- data.frame(obj$col$coord)
vars$name <- rownames(vars)
vars$pos <- "Column"
# Counts
col.mods <- rownames(obj$col$coord)
counts.cols <- sapply(obj$call$Xtot[, col.mods, drop = FALSE], sum, na.rm = TRUE)
vars$Count <- counts.cols
## Rows
tmp <- data.frame(obj$row$coord)
tmp$name <- rownames(tmp)
tmp$pos <- "Row"
# Counts
row.mods <- rownames(obj$row$coord)
if (!is.null(obj$call$quali.sup) || !is.null(obj$call$quanti.sup)) {
tmp_call <- obj$call$Xtot[, -c(obj$call$quali.sup, obj$call$quanti.sup)]
} else {
tmp_call <- obj$call$Xtot
}
counts.rows <- sapply(data.frame(t(tmp_call))[, make.names(row.mods), drop = FALSE], sum, na.rm = TRUE)
tmp$Count <- counts.rows
vars <- rbind(vars, tmp)
vars$Type <- "Active"
vars$Class <- "Qualitative"
## Supplementary rows coordinates
if (!is.null(obj$row.sup)) {
tmp <- data.frame(obj$row.sup$coord)
tmp$name <- rownames(tmp)
## Counts
row.mods <- rownames(obj$row.sup$coord)
counts.rows <- sapply(data.frame(t(tmp_call), check.names = FALSE)[, row.mods, drop = FALSE], sum, na.rm = TRUE)
tmp$Count <- counts.rows
tmp$pos <- "Row"
tmp$Type <- "Supplementary level"
tmp$Class <- "Qualitative"
vars <- rbind(vars, tmp)
}
## Supplementary columns coordinates
if (!is.null(obj$col.sup)) {
tmp <- tmp <- data.frame(obj$col.sup$coord)
tmp$name <- rownames(tmp)
## Counts
col.mods <- rownames(obj$col.sup$coord)
counts.cols <- sapply(obj$call$Xtot[, col.mods, drop = FALSE], sum, na.rm = TRUE)
tmp$Count <- counts.cols
tmp$pos <- "Column"
tmp$Type <- "Supplementary level"
tmp$Class <- "Qualitative"
vars <- rbind(vars, tmp)
}
## Supplementary variables coordinates
if (!is.null(obj$quali.sup)) {
vars.quali.sup <- data.frame(obj$quali.sup$coord)
vars.quali.sup$name <- rownames(vars.quali.sup)
vars.quali.sup$Type <- "Supplementary variable"
vars.quali.sup$Class <- "Qualitative"
# quali.sup.mods <- rownames(obj$quali.sup$coord)
# counts <- sapply(counts.tab[,quali.sup.mods, drop = FALSE], sum)
# vars.quali.sup$Count <- counts
vars.quali.sup$Count <- NA
vars.quali.sup$pos <- "Supplementary variable"
vars <- rbind(vars, vars.quali.sup)
}
vars <- vars %>% pivot_longer(names_to = "Axis", values_to = "Coord", starts_with("Dim.")) %>%
mutate(Axis = gsub("Dim.", "", Axis, fixed = TRUE),
Coord = round(Coord, 3))
## Contributions
tmp_row <- data.frame(obj$row$contrib)
tmp_row <- tmp_row %>% mutate(name = rownames(tmp_row),
pos = "Row",
Type = "Active",
Class = "Qualitative")
tmp_col <- data.frame(obj$col$contrib)
tmp_col <- tmp_col %>% mutate(name = rownames(tmp_col),
pos = "Column",
Type = "Active",
Class = "Qualitative")
tmp <- tmp_col %>% bind_rows(tmp_row) %>%
pivot_longer(names_to = "Axis", values_to = "Contrib", starts_with("Dim.")) %>%
mutate(Axis = gsub("Dim.", "", Axis, fixed = TRUE),
Contrib = round(Contrib, 3))
vars <- vars %>% left_join(tmp, by = c("name", "pos", "Type", "Class", "Axis"))
## Cos2
tmp_col <- data.frame(obj$col$cos2) %>%
mutate(name = rownames(obj$col$cos2),
pos = "Column")
tmp_row <- data.frame(obj$row$cos2) %>%
mutate(name = rownames(obj$row$cos2),
pos = "Row")
tmp <- tmp_col %>% bind_rows(tmp_row) %>%
mutate(Type = "Active",
Class = "Qualitative")
## Supplementary rows cos2
if (!is.null(obj$row.sup)) {
tmp_row_sup <- data.frame(obj$row.sup$cos2) %>%
mutate(name = rownames(obj$row.sup$cos2),
pos = "Row",
Type = "Supplementary level",
Class = "Qualitative")
tmp <- tmp %>% bind_rows(tmp_row_sup)
}
## Supplementary columns cos2
if (!is.null(obj$col.sup)) {
tmp_col_sup <- data.frame(obj$col.sup$cos2) %>%
mutate(name = rownames(obj$col.sup$cos2),
pos = "Column",
Type = "Supplementary level",
Class = "Qualitative")
tmp <- tmp %>% bind_rows(tmp_col_sup)
}
## Supplementary variables cos2
if (!is.null(obj$quali.sup)) {
tmp_sup <- data.frame(obj$quali.sup$cos2)
tmp_sup$name <- rownames(tmp_sup)
tmp_sup$pos <- "Supplementary variable"
tmp_sup$Type <- "Supplementary variable"
tmp_sup$Class <- "Qualitative"
tmp <- tmp %>% bind_rows(tmp_sup)
}
tmp <- tmp %>% pivot_longer(names_to = "Axis", values_to = "Cos2", starts_with("Dim.")) %>%
mutate(Axis = gsub("Dim.", "", Axis, fixed = TRUE),
Cos2 = round(Cos2, 3))
vars <- vars %>% left_join(tmp, by = c("name", "pos", "Type", "Class", "Axis")) %>%
rename(Level = name, Position = pos)
return(list(vars = vars, eig = eig, axes = axes))
}