@@ -1,7 +1,6 @@

 on:

   push:

     branches:

-      - RELEASE_3_13

       - master

 name: pkgdown

@@ -1258,7 +1258,9 @@ cumulative_count_union <- function(x,

 #' default_stats()

 default_stats <- function() {

     list(

-        diversity = vegan::diversity,

+        shannon = ~ vegan::diversity(.x, index = "shannon"),

+        simpson = ~ vegan::diversity(.x, index = "simpson"),

+        invsimpson = ~ vegan::diversity(.x, index = "invsimpson"),

         sum = ~ sum(.x, na.rm = TRUE),

         count = length,

         describe = ~ tibble::as_tibble(psych::describe(.x))

@@ -254,6 +254,7 @@ import_association_file <- function(path,

     filter_for = NULL,

     import_iss = FALSE,

     export_widget_path = NULL,

+    convert_tp = TRUE,

     ...) {

     # Check parameters

     stopifnot(is.character(path) & length(path) == 1)

@@ -310,55 +311,45 @@ import_association_file <- function(path,

         missing_dates

     )))

     ## Fix timepoints

-    if (!"TimepointMonths" %in% colnames(as_file)) {

-        as_file <- as_file %>%

-            tibble::add_column(TimepointMonths = NA_real_)

-    }

-    if (!"TimepointYears" %in% colnames(as_file)) {

+    if (convert_tp) {

+        if (!"TimepointMonths" %in% colnames(as_file)) {

+            as_file <- as_file %>%

+                tibble::add_column(TimepointMonths = NA_real_)

+        }

+        if (!"TimepointYears" %in% colnames(as_file)) {

+            as_file <- as_file %>%

+                tibble::add_column(TimepointYears = NA_real_)

+        }

         as_file <- as_file %>%

-            tibble::add_column(TimepointYears = NA_real_)

-    }

-    as_file <- as_file %>%

-        dplyr::mutate(

-            TimepointMonths = dplyr::if_else(

-                condition = is.na(.data$TimepointMonths),

-                false = .data$TimepointMonths,

-                true = dplyr::if_else(

-                    condition = as.numeric(.data$TimePoint) == 0,

-                    true = 0,

-                    false = dplyr::if_else(

-                        condition = as.numeric(.data$TimePoint) > 0 &

-                            as.numeric(.data$TimePoint) < 30,

-                        true = ceiling(as.numeric(.data$TimePoint) / 30),

-                        false = round(as.numeric(.data$TimePoint) / 30)

-                    )

-                )

-            ),

-            TimepointYears = dplyr::if_else(

-                condition = is.na(.data$TimepointYears),

-                false = .data$TimepointYears,

-                true = dplyr::if_else(

-                    condition = as.numeric(.data$TimePoint) == 0,

-                    true = 0,

-                    false = dplyr::if_else(

-                        condition = as.numeric(.data$TimePoint) > 0 &

-                            as.numeric(.data$TimePoint) < 360,

-                        true = ceiling(as.numeric(.data$TimePoint) / 360),

-                        false = round(as.numeric(.data$TimePoint) / 360)

+            dplyr::mutate(

+                TimepointMonths = dplyr::if_else(

+                        condition = as.numeric(.data$TimePoint) == 0,

+                        true = 0,

+                        false = dplyr::if_else(

+                            condition = as.numeric(.data$TimePoint) > 0 &

+                                as.numeric(.data$TimePoint) < 30,

+                            true = ceiling(as.numeric(.data$TimePoint) / 30),

+                            false = round(as.numeric(.data$TimePoint) / 30)

+                        )

+                    ),

+                TimepointYears = dplyr::if_else(

+                        condition = as.numeric(.data$TimePoint) == 0,

+                        true = 0,

+                        false = ceiling(as.numeric(.data$TimePoint) / 360)

                     )

-                )

+                ) %>%

+            dplyr::mutate(

+                TimepointMonths = stringr::str_pad(

+                    as.character(.data$TimepointMonths),

+                    pad = "0", side = "left", width = 2

+                ),

+                TimepointYears = stringr::str_pad(

+                    as.character(.data$TimepointYears),

+                    pad = "0", side = "left", width = 2

+                ),

             )

-        ) %>%

-        dplyr::mutate(

-            TimepointMonths = stringr::str_pad(

-                as.character(.data$TimepointMonths),

-                pad = "0", side = "left", width = 2

-            ),

-            TimepointYears = stringr::str_pad(

-                as.character(.data$TimepointYears),

-                pad = "0", side = "left", width = 2

-            ),

-        )

+    }

+

     widget <- if (something_to_report) {

         summary_report <- .summary_af_import_msg(

             pars_prob = parsing_problems, dates_prob = date_problems,

@@ -95,9 +95,16 @@ generate_Vispa2_launch_AF <- function(association_file, project, pool, path) {

     }

     files <- purrr::map2(project, pool, function(x, y) {

         selected_cols <- association_file %>%

-            dplyr::select(dplyr::all_of(reduced_AF_columns())) %>%

+            dplyr::select(dplyr::all_of(reduced_AF_columns()),

+                          .data$concatenatePoolIDSeqRun) %>%

             dplyr::filter(.data$ProjectID == x, .data$PoolID == y) %>%

-            dplyr::mutate(TagID2 = .data$TagID, .before = .data$TagID)

+            dplyr::mutate(TagID2 = .data$TagID, .before = .data$TagID) %>%

+            dplyr::mutate(PoolName = dplyr::if_else(

+                !is.na(.data$concatenatePoolIDSeqRun),

+                .data$concatenatePoolIDSeqRun,

+                .data$PoolID

+                )) %>%

+            dplyr::select(-.data$PoolID, -.data$concatenatePoolIDSeqRun)

     }) %>% purrr::set_names(paste0(project, "-", pool, "_AF.tsv"))

     purrr::walk2(files, names(files), function(x, y) {

         complete_path <- fs::path(path, y)