v2.0.0.9128

* refactor: Modify Shiny single report + Add taxatrans table + Verify sorting of tables by user selections + Add summary color thresholds + Color summary color thresholds + Set column widths + update formulas on NOTES
leppott · Dec 20, 2023 · 832bb59 · 832bb59
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: BCGcalc
 Type: Package
 Title: Biological Condition Gradient, calculator
-Version: 2.0.0.9127
+Version: 2.0.0.9128
 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 +1,21 @@
 BCGcalc-NEWS
 ================
 <Erik.Leppo@tetratech.com>
-2023-12-19 11:18:29.25482
+2023-12-20 17:45:57.183284
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2023-12-19 11:18:29.284286
+    #> Last Update: 2023-12-20 17:45:57.221885
+
+# BCGcalc 2.0.0.9128 (2023-12-20)
+
+- refactor: Modify Shiny single report
+  - Add taxatrans table
+  - Verify sorting of tables by user selections
+  - Add summary color thresholds
+  - Color summary color thresholds
+  - Set column widths
+  - update formulas on NOTES
 
 # BCGcalc 2.0.0.9127 (2023-12-19)
 

diff --git a/NEWS.md b/NEWS.md
@@ -1,11 +1,21 @@
 BCGcalc-NEWS
 ================
 <Erik.Leppo@tetratech.com>
-2023-12-19 11:18:29.25482
+2023-12-20 17:45:57.183284
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2023-12-19 11:18:29.284286
+    #> Last Update: 2023-12-20 17:45:57.221885
+
+# BCGcalc 2.0.0.9128 (2023-12-20)
+
+- refactor: Modify Shiny single report
+  - Add taxatrans table
+  - Verify sorting of tables by user selections
+  - Add summary color thresholds
+  - Color summary color thresholds
+  - Set column widths
+  - update formulas on NOTES
 
 # BCGcalc 2.0.0.9127 (2023-12-19)
 

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -21,6 +21,16 @@ knitr::opts_chunk$set(
 cat(paste0("Last Update: ",Sys.time()))
 ```
 
+# BCGcalc 2.0.0.9128 (2023-12-20)
+
+* refactor: Modify Shiny single report
+   + Add taxatrans table
+   + Verify sorting of tables by user selections
+   + Add summary color thresholds 
+   + Color summary color thresholds
+   + Set column widths
+   + update formulas on NOTES
+
 # BCGcalc 2.0.0.9127 (2023-12-19)
 
 * refactor: Modify Shiny single report

diff --git a/inst/shiny-examples/BCGcalc/data/report_color_thresholds.csv b/inst/shiny-examples/BCGcalc/data/report_color_thresholds.csv
@@ -0,0 +1,6 @@
+MTTI,ThermClass,nt_ti_stenocold,nt_ti_stenocold_cold,nt_ti_stenocold_cold_cool,pt_ti_stenocold_cold_cool,pi_ti_stenocold_cold_cool,pt_ti_warm_stenowarm,nt_ti_stenowarm,NARRATIVE
+< 16,,>= 3,>= 10,>= 30,>= 65,>= 55,< 5,--,Core cold
+< 19,,>= 1,>= 5,>= 25,>= 50,>= 40,< 10,--,Cold. Salmon and steelhead rearing
+< 21,,--,>= 3,>= 20,>= 35,>= 30,< 15,--,Cool. Inland resident trout and cool water fish species (non-salmonid)
+< 23,,--,>= 1,>= 9,>= 20,>= 10,< 40,--,Transitional Cool-Warm
+>= 23,,--,--,--,--,--,>= 40,>= 2,Very Warm
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 <- "2.0.0.9127"
+pkg_version <- "2.0.0.9128"
 
 # Packages----
 # nolint start

diff --git a/inst/shiny-examples/BCGcalc/scripts/helper_functions.R b/inst/shiny-examples/BCGcalc/scripts/helper_functions.R
@@ -91,7 +91,8 @@ build_report_table <- function(df_template_data
     path_results_user <- file.path(path_results, dn_files_input)
     #
     path_files = file.path("results", "_user_input")
-    tbl_name <- "topindicator"
+    # tbl_name <- "topindicator"
+    tbl_name <- "taxatrans"
     #
     # copy from clipboard
     df_template_data <- read.delim("clipboard")
@@ -101,7 +102,7 @@ build_report_table <- function(df_template_data
                                  , "inclusion"
                                  , "source folder"
                                  , "source file (or suffix)"
-                                 , "color"
+                                 , "color code"
                                  , "sort"
                                  , "notes")
     fld_name_orig    <- names(df_template_data)[1]
@@ -216,7 +217,7 @@ build_report_table <- function(df_template_data
 
     i_exists <- df_import_files[i, fld_exists, TRUE]
     if (i_exists == FALSE) {
-      skip
+      next
     }## IF ~ i_exists
 
     i_file <- df_import_files[i, fld_file, TRUE]

diff --git a/inst/shiny-examples/BCGcalc/server.R b/inst/shiny-examples/BCGcalc/server.R