v2.1.0.9010

- refactor: Add summation of duplicate taxa in taxa translate in Shiny
leppott · Aug 6, 2024 · 665b577 · 665b577
1 parent 0d1b498
commit 665b577
Show file tree

Hide file tree

Showing 6 changed files with 64 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: BCGcalc
 Type: Package
 Title: Biological Condition Gradient, calculator
-Version: 2.1.0.9008
+Version: 2.1.0.9010
 Authors@R: c(
   person("Erik W.", "Leppo", email="Erik.Leppo@tetratech.com", role=c("aut","cre")), 
   person("Jen", "Stamp", email="Jen.Stamp@tetratech.com", role="ctb"),

diff --git a/NEWS b/NEWS
@@ -1,11 +1,24 @@
 BCGcalc-NEWS
 ================
 <Erik.Leppo@tetratech.com>
-2024-07-24 21:12:35.715856
+2024-08-06 11:28:24.889548
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-07-24 21:12:35.737282
+    #> Last Update: 2024-08-06 11:28:24.909271
+
+# BCGcalc 2.1.0.9010 (2024-08-06)
+
+- refactor: Add summation of duplicate taxa in taxa translate in Shiny
+
+# BCGcalc 2.1.0.9009 (2024-07-30)
+
+- refactor: Merge Pull Request 92
+
+# BCGcalc 2.1.0.9008 (2024-07-29)
+
+- refactor: Update Rules.xlsx for MN_BCG metric descriptions and index
+  regions
 
 # BCGcalc 2.1.0.9007 (2024-07-24)
 

diff --git a/NEWS.md b/NEWS.md
@@ -1,11 +1,24 @@
 BCGcalc-NEWS
 ================
 <Erik.Leppo@tetratech.com>
-2024-07-24 21:12:35.715856
+2024-08-06 11:28:24.889548
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-07-24 21:12:35.737282
+    #> Last Update: 2024-08-06 11:28:24.909271
+
+# BCGcalc 2.1.0.9010 (2024-08-06)
+
+- refactor: Add summation of duplicate taxa in taxa translate in Shiny
+
+# BCGcalc 2.1.0.9009 (2024-07-30)
+
+- refactor: Merge Pull Request 92
+
+# BCGcalc 2.1.0.9008 (2024-07-29)
+
+- refactor: Update Rules.xlsx for MN_BCG metric descriptions and index
+  regions
 
 # BCGcalc 2.1.0.9007 (2024-07-24)
 

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -21,6 +21,14 @@ knitr::opts_chunk$set(
 cat(paste0("Last Update: ",Sys.time()))
 ```
 
+# BCGcalc 2.1.0.9010 (2024-08-06)
+
+* refactor: Add summation of duplicate taxa in taxa translate in Shiny
+
+# BCGcalc 2.1.0.9009 (2024-07-30)
+
+* refactor: Merge Pull Request 92
+
 # BCGcalc 2.1.0.9008 (2024-07-29)
 
 * refactor: Update Rules.xlsx for MN_BCG metric descriptions and index regions

diff --git a/inst/shiny-examples/BCGcalc/global.R b/inst/shiny-examples/BCGcalc/global.R
@@ -1,7 +1,7 @@
 # Shiny Global File
 
 # Version ----
-pkg_version <- "2.1.0.9008"
+pkg_version <- "2.1.0.9010"
 
 # Packages----
 # nolint start

diff --git a/inst/shiny-examples/BCGcalc/server.R b/inst/shiny-examples/BCGcalc/server.R
@@ -618,6 +618,30 @@ shinyServer(function(input, output) {
                                                             , "Match_Official"
                                                             , sel_user_groupby)]
         df_ttrm <- df_ttrm[, col_keep_ttrm]
+
+        ### COMBINE same TaxaID and sum N_Taxa----
+        # 20240806 from MNcalc
+        boo_combine_taxa <- TRUE
+        if (boo_combine_taxa) {
+          # use 'known' values with tidyverse then change back
+          #
+          # name field to known value
+          col_ttrm_ntaxa <- "ttrm_ntaxa"
+          df_ttrm[, col_ttrm_ntaxa] <- df_ttrm[, sel_user_ntaxa]
+          col_non_ntaxa <- names(df_ttrm)[!names(df_ttrm) %in% sel_user_ntaxa]
+          # drop ntaxa
+          df_ttrm <- df_ttrm[, col_non_ntaxa]
+          # columns by (for summarize)
+          col_by <- col_non_ntaxa[!col_non_ntaxa %in% col_ttrm_ntaxa]
+          # sum
+          df_ttrm <- dplyr::summarise(df_ttrm
+                                      , .by = dplyr::all_of(col_by)
+                                      , sum_ntaxa = sum(ttrm_ntaxa, na.rm = TRUE)
+          )
+          # rename 'known' ntaxa back to 'user' value
+          names(df_ttrm)[names(df_ttrm) == "sum_ntaxa"] <- sel_user_ntaxa
+        }## boo_combine_taxa
+
         # merge with attributes
         df_merge_attr <- merge(df_ttrm
                                , df_taxoff_attr