Error in exp(spurious_coefficients) : non-numeric argument to mathema…

…tical function

Fixes #999

R/format.R

@@ -312,7 +312,7 @@ format.compare_parameters <- function(x,
     # since we merged all models together, and we only have model-specific
     # columns for estimates, CI etc. but not for Effects and Component, we
     # extract "valid" rows via non-NA values in the coefficient column
-    coef_column <- which(colnames(cols) %in% c(.all_coefficient_types(), "Coefficient"))
+    coef_column <- which(colnames(cols) %in% c(.all_coefficient_types, "Coefficient"))
     valid_rows <- which(!is.na(cols[[coef_column]]))
     # check if we have mixed models with random variance parameters
     # in such cases, we don't need the group-column, but we rather
@@ -919,11 +919,13 @@ format.parameters_sem <- function(x,
 
 
 .print_footer_exp <- function(x) {
+  # we need this to check whether we have extremely large cofficients
   if (isTRUE(getOption("parameters_exponentiate", TRUE))) {
     msg <- NULL
-    # we need this to check whether we have extremely large cofficients
-    if (all(c("Coefficient", "Parameter") %in% colnames(x))) {
-      spurious_coefficients <- abs(x$Coefficient[!.in_intercepts(x$Parameter)])
+    # try to find out the name of the coefficient column
+    coef_column <- intersect(colnames(x), .all_coefficient_names)
+    if (length(coef_column) && "Parameter" %in% colnames(x)) {
+      spurious_coefficients <- abs(x[[coef_column[1]]][!.in_intercepts(x$Parameter)])
     } else {
       spurious_coefficients <- NULL
     }
@@ -932,7 +934,9 @@ format.parameters_sem <- function(x,
       if (isTRUE(.additional_arguments(x, "log_link", FALSE))) {
         msg <- "The model has a log- or logit-link. Consider using `exponentiate = TRUE` to interpret coefficients as ratios." # nolint
         # we only check for exp(coef), so exp() here soince coefficients are on logit-scale
-        spurious_coefficients <- exp(spurious_coefficients)
+        if (!is.null(spurious_coefficients)) {
+          spurious_coefficients <- exp(spurious_coefficients)
+        }
       } else if (isTRUE(.additional_arguments(x, "log_response", FALSE))) {
         msg <- "The model has a log-transformed response variable. Consider using `exponentiate = TRUE` to interpret coefficients as ratios." # nolint
         # don't show warning about complete separation

R/utils_format.R

@@ -295,15 +295,15 @@
   }
 
   # fix coefficient column name for random effects
-  if (!is.null(x$Effects) && all(x$Effects == "random") && any(colnames(x) %in% .all_coefficient_types())) {
-    colnames(x)[colnames(x) %in% .all_coefficient_types()] <- "Coefficient"
+  if (!is.null(x$Effects) && all(x$Effects == "random") && any(colnames(x) %in% .all_coefficient_types)) {
+    colnames(x)[colnames(x) %in% .all_coefficient_types] <- "Coefficient"
   }
 
   # fix coefficient column name for mixed count and zi pars
   if (!is.null(x$Component) &&
     sum(c("conditional", "zero_inflated", "dispersion") %in% x$Component) >= 2 &&
-    any(colnames(x) %in% .all_coefficient_types())) {
-    colnames(x)[colnames(x) %in% .all_coefficient_types()] <- "Coefficient"
+    any(colnames(x) %in% .all_coefficient_types)) {
+    colnames(x)[colnames(x) %in% .all_coefficient_types] <- "Coefficient"
   }
 
   # random pars with level? combine into parameter column
@@ -468,13 +468,14 @@
 # components into different tables, we change the column name for those "tables"
 # that contain the random effects or zero-inflation parameters
 
-.all_coefficient_types <- function() {
-  c(
-    "Odds Ratio", "Risk Ratio", "Prevalence Ratio", "IRR", "Log-Odds",
-    "Log-Mean", "Log-Ratio", "Log-Prevalence", "Probability", "Marginal Means",
-    "Estimated Counts", "Ratio"
-  )
-}
+.all_coefficient_types <- c(
+  "Odds Ratio", "Risk Ratio", "Prevalence Ratio", "IRR", "Log-Odds",
+  "Log-Mean", "Log-Ratio", "Log-Prevalence", "Probability", "Marginal Means",
+  "Estimated Counts", "Ratio"
+)
+
+
+.all_coefficient_names <- c("Coefficient", "Std_Coefficient", "Estimate", "Median", "Mean", "MAP")
 
 
 .format_stan_parameters <- function(out) {
@@ -1087,8 +1088,8 @@
     }
 
     # rename columns for random part
-    if (grepl("random", type, fixed = TRUE) && any(colnames(tables[[type]]) %in% .all_coefficient_types())) {
-      colnames(tables[[type]])[colnames(tables[[type]]) %in% .all_coefficient_types()] <- "Coefficient"
+    if (grepl("random", type, fixed = TRUE) && any(colnames(tables[[type]]) %in% .all_coefficient_types)) {
+      colnames(tables[[type]])[colnames(tables[[type]]) %in% .all_coefficient_types] <- "Coefficient"
     }
 
     if (grepl("random", type, fixed = TRUE) && isTRUE(ran_pars)) {