v1.0.2.9067

* refactor: Add fish metrics; nt/pi/pt BCG_att4 b/m/2 + MetricNames.xlsx + metric_values.R
leppott · Nov 20, 2024 · 738b48d · 738b48d
1 parent 740de91
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: BioMonTools
 Type: Package
 Title: Tools for Biomonitoring and Bioassessment
-Version: 1.0.2.9066
+Version: 1.0.2.9067
 Author: c(
 	person("Erik W.", "Leppo", email="[email protected]", role=c("aut","cre")), 
 	person("Jen", "Stamp", role="ctb"),

diff --git a/NEWS b/NEWS
@@ -4,10 +4,16 @@ NEWS
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-11-07 08:37:32.794045
+    #> Last Update: 2024-11-20 08:24:14.42573
 
 # Version History
 
+## Changes in version 1.0.2.9067 (2024-11-20)
+
+- refactor: Add fish metrics; nt/pi/pt BCG_att4 b/m/2
+  - MetricNames.xlsx
+  - metric_values.R
+
 ## Changes in version 1.0.2.9066 (2024-11-07)
 
 - refactor: Add fish metric permutations of non-native

diff --git a/NEWS.md b/NEWS.md
@@ -4,10 +4,16 @@ NEWS
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-11-07 08:37:32.794045
+    #> Last Update: 2024-11-20 08:24:14.42573
 
 # Version History
 
+## Changes in version 1.0.2.9067 (2024-11-20)
+
+- refactor: Add fish metrics; nt/pi/pt BCG_att4 b/m/2
+  - MetricNames.xlsx
+  - metric_values.R
+
 ## Changes in version 1.0.2.9066 (2024-11-07)
 
 - refactor: Add fish metric permutations of non-native

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -18,6 +18,12 @@ cat(paste0("Last Update: ",Sys.time()))
 
 # Version History
 
+## Changes in version 1.0.2.9067 (2024-11-20)
+
+* refactor: Add fish metrics; nt/pi/pt BCG_att4 b/m/2 
+    + MetricNames.xlsx
+    + metric_values.R
+
 ## Changes in version 1.0.2.9066 (2024-11-07)
 
 * refactor: Add fish metric permutations of non-native

diff --git a/R/metric_values.R b/R/metric_values.R
@@ -4565,6 +4565,15 @@ metric.values.fish <- function(myDF
                                                                  & BCG_ATTR == "4"
                                                                  & NATIVE == "NATIVE"]
                                                           , na.rm = TRUE)
+                 , nt_BCG_att4b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
+                                                           & (BCG_ATTR2 == "4_BETTER")]
+                                                    , na.rm = TRUE)
+                 , nt_BCG_att4m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
+                                                           & (BCG_ATTR2 == "4_MIDDLE")]
+                                                    , na.rm = TRUE)
+                 , nt_BCG_att4w = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
+                                                           & (BCG_ATTR2 == "4_WORSE")]
+                                                    , na.rm = TRUE)
                  , nt_BCG_att4w5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
                                                             & BCG_ATTR2 == "4_WORSE"]
                                                      , na.rm = TRUE) +
@@ -4677,6 +4686,12 @@ metric.values.fish <- function(myDF
                   , pi_BCG_att4native = 100 * sum(N_TAXA[BCG_ATTR == "4"
                                                          & NATIVE == "NATIVE"]
                                                   , na.rm = TRUE) / ni_total
+                 , pi_BCG_att4b = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_BETTER")]
+                                            , na.rm = TRUE) / ni_total
+                 , pi_BCG_att4m = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_MIDDLE")]
+                                            , na.rm = TRUE) / ni_total
+                 , pi_BCG_att4w = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_WORSE")]
+                                            , na.rm = TRUE) / ni_total
                  , pi_BCG_att4w5 = 100 * (sum(N_TAXA[BCG_ATTR2 == "4_WORSE"]
                                               , na.rm = TRUE) +
                                             sum(N_TAXA[BCG_ATTR == "5"]
@@ -4742,6 +4757,9 @@ metric.values.fish <- function(myDF
                   , pt_BCG_att3native = 100 * nt_BCG_att3native / nt_total
                   , pt_BCG_att4 = 100 * nt_BCG_att4 / nt_total
                   , pt_BCG_att4native = 100 * nt_BCG_att4native / nt_total
+                  , pt_BCG_att4b =  100 * nt_BCG_att4b / nt_total
+                  , pt_BCG_att4m =  100 * nt_BCG_att4m / nt_total
+                  , pt_BCG_att4w =  100 * nt_BCG_att4w / nt_total
                   , pt_BCG_att4w5 = 100 * nt_BCG_att4w5 / nt_total
                   , pt_BCG_att5 = 100 * nt_BCG_att5 / nt_total
                   , pt_BCG_att5native = 100 * nt_BCG_att5native / nt_total

diff --git a/inst/extdata/MetricNames.xlsx b/inst/extdata/MetricNames.xlsx
diff --git a/inst/shiny-examples/BioMonTools/global.R b/inst/shiny-examples/BioMonTools/global.R
@@ -1,7 +1,7 @@
 # Shiny Global File
 
 # Version ----
-pkg_version <- "1.0.2.9066"
+pkg_version <- "1.0.2.9067"
 
 # Packages----
 library(BioMonTools)