fix/feat: Updating github + github.io to latest development version

Author: retostauffer

NEWS.md

@@ -16,9 +16,12 @@
     from one or multiple XLSX files written by `annex_write_stats()` (beta).
 * Removing ventilation type 'Exhaust air' added in 0.2-8
 * `annex_stats()` will return `NA`s for 'Mean' and 'Sd' in case the number of
-    valid observations (`N - NAs`) are less than 30. `annex_validate()` will
-    test that.
-* `annes_validate()` now also throws an error if `Sd < 0` (see condition above).
+    valid observations (`N - NAs`) are less than 30.
+* `annex_stats()` will return `NA`s for `interval_*` if `N - NAs == 1` (we have
+    exactely one valid observation).
+* `annex_validate()` validates for the two conditions above.
+* `annex_validate()` now also throws an error if `Sd < 0` (see condition above).
+* Series of additional tests added.
 
 # annex 0.2-8
 

R/stats.R

@@ -346,8 +346,7 @@ annex_stats <- function(object, format = "wide", ..., probs = NULL) {
     # cells in the final xlsx file (`annex_write_stats()`)
     idx <- which(res$N - res$NAs < annex:::minsamplesize)
     if (length(idx) > 0) {
-        cols <- names(res)[grepl("^(Mean|Sd)$", names(res))]
-        res[idx, cols] <- NA
+        res[idx, c("Mean", "Sd")] <- NA
     }
 
     # Reshape to long format if required

R/validate.R

@@ -157,13 +157,29 @@ annex_validate_sheet_STAT <- function(file, user, quiet, ...) {
     # Checking user
     if (nrow(data) == 0) stop(red $ bold("No data in sheet 'STAT'"))
 
+    # NAs > N
+    idx <- data$N <= data$NAs
+    if (any(idx)) {
+        stop(red $ bold("Found ", sum(idx), " rows where N <= NAs (all or more than all missing)",
+                        " in sheet 'STAT',\n", get_row_info(idx), sep = ""))
+    }
+
     # Missing values
     for (col in required_cols) {
-        if (grepl("^(Nestim|N|NAs)$", col)) {
-            idx <- is.na(data[[col]] | data[[col]] < 0)
+        if (grepl("^(N|NAs)$", col)) {
+            tau <- if (col == "N") 1 else 0
+            idx <- is.na(data[[col]] | data[[col]] < tau)
             if (any(idx))
-                stop(red $ bold("Found ", sum(idx), " missing or negative values ",
-                                "(empty cells) in column '", col,
+                stop(red $ bold("Found ", sum(idx), " missing values (empty cells) or ",
+                                "values <", tau, "in column '", col,
+                                "' in sheet 'STAT',\n", get_row_info(idx), sep = ""))
+        # If interval-based columns (interval_* and Nestim): must be NA if
+        # N - NAs == 1, else must be filled and positive.
+        } else if (grepl("^(interval_.*|Nestim)$", col)) {
+            idx <- (data$N - data$NAs == 1 & !is.na(data[[col]]))
+            if (any(idx))
+                stop(red $ bold("Found ", sum(idx), " non-missing values ",
+                                "in column where `N-NAs == 1` '", col,
                                 "' in sheet 'STAT',\n", get_row_info(idx), sep = ""))
         } else {
             idx <- is.na(data[[col]])

docs/articles/lookupfunctions.html

@@ -12,7 +12,7 @@ articles:
   unitconversion: unitconversion.html
   visualization: visualization.html
   write_and_validate: write_and_validate.html
-last_built: 2023-12-17T19:02Z
+last_built: 2023-12-22T06:11Z
 urls:
   reference: https://some.example-url.com/reference
   article: https://some.example-url.com/articles