Add checks for missing alpha diversity indices in multiple functions

This GitHub push updates several functions in the codebase to include checks for missing alpha diversity indices:

1. In the `generate_alpha_change_boxplot_pair` function:
   - Added a check to verify if all specified `alpha.name` values are present in `alpha.obj`.
   - If any missing alpha diversity indices are found, an error is thrown with a message listing the missing indices.

2. Similar checks for missing alpha diversity indices were added to the following functions:
   - `generate_alpha_change_test_long`
   - `generate_alpha_change_test_pair`
   - `generate_alpha_test_long`
   - `generate_alpha_test_pair`

3. In the `generate_alpha_test_single` function:
   - Updated the example code to include "ace" in the `alpha.name` parameter.
   - Modified the code to use `subset_data.obj` instead of `data.obj` when subsetting data based on `time.var` and `t.level`.
   - Added a check for missing alpha diversity indices in `alpha.obj`, similar to the other functions.
   - Updated the test list generation to use `alpha.name` instead of indexing `alpha.obj`.

These changes ensure that the functions gracefully handle cases where the specified alpha diversity indices are not available in the provided `alpha.obj`. By adding these checks, the code becomes more robust and informative, throwing an error with a clear message when missing indices are encountered.

R/generate_alpha_change_boxplot_pair.R

@@ -169,6 +169,17 @@ generate_alpha_change_boxplot_pair <-
       otu_tab <- data.obj$feature.tab
       alpha.obj <-
         mStat_calculate_alpha_diversity(x = otu_tab, alpha.name = alpha.name)
+    } else {
+      # Verify that all alpha.name are present in alpha.obj
+      if (!all(alpha.name %in% unlist(lapply(alpha.obj, function(x)
+        colnames(x))))) {
+        missing_alphas <- alpha.name[!alpha.name %in% names(alpha.obj)]
+        stop(
+          "The following alpha diversity indices are not available in alpha.obj: ",
+          paste(missing_alphas, collapse = ", "),
+          call. = FALSE
+        )
+      }
     }
 
     meta_tab <-

R/generate_alpha_change_test_long.R

@@ -109,6 +109,17 @@ generate_alpha_change_test_long <-
       }
       otu_tab <- data.obj$feature.tab
       alpha.obj <- mStat_calculate_alpha_diversity(x = otu_tab, alpha.name = alpha.name)
+    } else {
+      # Verify that all alpha.name are present in alpha.obj
+      if (!all(alpha.name %in% unlist(lapply(alpha.obj, function(x)
+        colnames(x))))) {
+        missing_alphas <- alpha.name[!alpha.name %in% names(alpha.obj)]
+        stop(
+          "The following alpha diversity indices are not available in alpha.obj: ",
+          paste(missing_alphas, collapse = ", "),
+          call. = FALSE
+        )
+      }
     }
 
     meta_tab <-

R/generate_alpha_change_test_pair.R

@@ -144,6 +144,17 @@ generate_alpha_change_test_pair <-
       }
       otu_tab <- data.obj$feature.tab
       alpha.obj <- mStat_calculate_alpha_diversity(x = otu_tab, alpha.name = alpha.name)
+    } else {
+      # Verify that all alpha.name are present in alpha.obj
+      if (!all(alpha.name %in% unlist(lapply(alpha.obj, function(x)
+        colnames(x))))) {
+        missing_alphas <- alpha.name[!alpha.name %in% names(alpha.obj)]
+        stop(
+          "The following alpha diversity indices are not available in alpha.obj: ",
+          paste(missing_alphas, collapse = ", "),
+          call. = FALSE
+        )
+      }
     }
 
     meta_tab <-

R/generate_alpha_test_long.R

@@ -105,6 +105,17 @@ generate_alpha_test_long <- function(data.obj,
     otu_tab <- data.obj$feature.tab
     alpha.obj <-
       mStat_calculate_alpha_diversity(x = otu_tab, alpha.name = alpha.name)
+  } else {
+    # Verify that all alpha.name are present in alpha.obj
+    if (!all(alpha.name %in% unlist(lapply(alpha.obj, function(x)
+      colnames(x))))) {
+      missing_alphas <- alpha.name[!alpha.name %in% names(alpha.obj)]
+      stop(
+        "The following alpha diversity indices are not available in alpha.obj: ",
+        paste(missing_alphas, collapse = ", "),
+        call. = FALSE
+      )
+    }
   }
 
   meta_tab <-

R/generate_alpha_test_pair.R

@@ -122,6 +122,17 @@ generate_alpha_test_pair <-
       otu_tab <- data.obj$feature.tab
       alpha.obj <-
         mStat_calculate_alpha_diversity(x = otu_tab, alpha.name = alpha.name)
+    } else {
+      # Verify that all alpha.name are present in alpha.obj
+      if (!all(alpha.name %in% unlist(lapply(alpha.obj, function(x)
+        colnames(x))))) {
+        missing_alphas <- alpha.name[!alpha.name %in% names(alpha.obj)]
+        stop(
+          "The following alpha diversity indices are not available in alpha.obj: ",
+          paste(missing_alphas, collapse = ", "),
+          call. = FALSE
+        )
+      }
     }
 
     meta_tab <-

R/generate_alpha_test_single.R

@@ -30,7 +30,7 @@
 #'                                              c("shannon", "observed_species"))
 #' generate_alpha_test_single(data.obj = subset_T2D.obj,
 #'                            alpha.obj = alpha.obj,
-#'                            alpha.name = c("shannon", "observed_species"),
+#'                            alpha.name = c("shannon", "observed_species", "ace"),
 #'                            time.var = "visit_number",
 #'                            t.level = NULL,
 #'                            group.var = "subject_race",
@@ -68,8 +68,10 @@ generate_alpha_test_single <-
     }
 
     if (!is.null(time.var) & !is.null(t.level)) {
-      condition <- paste(time.var, "== '", t.level, "'", sep = "")
-      data.obj <- mStat_subset_data(data.obj, condition = condition)
+      subset.ids <- rownames(data.obj$meta.dat %>%
+                               filter(!!sym(time.var) %in% c(t.level)))
+
+      subset_data.obj <- mStat_subset_data(data.obj, samIDs = subset.ids)
     }
 
     if (is.null(alpha.obj)) {
@@ -81,12 +83,23 @@ generate_alpha_test_single <-
       }
       otu_tab <- data.obj$feature.tab
       alpha.obj <- mStat_calculate_alpha_diversity(x = otu_tab, alpha.name = alpha.name)
+    } else {
+      # Verify that all alpha.name are present in alpha.obj
+      if (!all(alpha.name %in% unlist(lapply(alpha.obj, function(x)
+        colnames(x))))) {
+        missing_alphas <- alpha.name[!alpha.name %in% names(alpha.obj)]
+        stop(
+          "The following alpha diversity indices are not available in alpha.obj: ",
+          paste(missing_alphas, collapse = ", "),
+          call. = FALSE
+        )
+      }
     }
 
     # Generate tests
-    test.list <- lapply(seq_along(alpha.obj), function(i) {
+    test.list <- lapply(alpha.name, function(alpha.name) {
 
-      df <- alpha.obj[[i]]
+      df <- alpha.obj[[alpha.name]]
       # Join the alpha diversity index with metadata
       merged_df <-
         dplyr::inner_join(