v1.0.2.9066

* refactor: Add fish metric permutations of non-native
    + MetricNames.xlsx
    + metric_values.R

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: BioMonTools
 Type: Package
 Title: Tools for Biomonitoring and Bioassessment
-Version: 1.0.2.9065
+Version: 1.0.2.9066
 Author: c(
 	person("Erik W.", "Leppo", email="[email protected]", role=c("aut","cre")), 
 	person("Jen", "Stamp", role="ctb"),

NEWS

@@ -4,10 +4,16 @@ NEWS
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-11-06 16:56:01.846738
+    #> Last Update: 2024-11-07 08:37:32.794045
 
 # Version History
 
+## Changes in version 1.0.2.9066 (2024-11-07)
+
+- refactor: Add fish metric permutations of non-native
+  - MetricNames.xlsx
+  - metric_values.R
+
 ## Changes in version 1.0.2.9065 (2024-11-06)
 
 - fix: Modify fish metrics BCG_ATTR2 to convert to upper case

NEWS.md

@@ -4,10 +4,16 @@ NEWS
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-11-06 16:56:01.846738
+    #> Last Update: 2024-11-07 08:37:32.794045
 
 # Version History
 
+## Changes in version 1.0.2.9066 (2024-11-07)
+
+- refactor: Add fish metric permutations of non-native
+  - MetricNames.xlsx
+  - metric_values.R
+
 ## Changes in version 1.0.2.9065 (2024-11-06)
 
 - fix: Modify fish metrics BCG_ATTR2 to convert to upper case

NEWS.rmd

@@ -18,6 +18,12 @@ cat(paste0("Last Update: ",Sys.time()))
 
 # Version History
 
+## Changes in version 1.0.2.9066 (2024-11-07)
+
+* refactor: Add fish metric permutations of non-native
+    + MetricNames.xlsx
+    + metric_values.R
+
 ## Changes in version 1.0.2.9065 (2024-11-06)
 
 * fix: Modify fish metrics BCG_ATTR2 to convert to upper case

R/metric_values.R

@@ -4257,6 +4257,8 @@ metric.values.fish <- function(myDF
                        , pi_Ictal = 100 * sum(N_TAXA[FAMILY == "ICTALURIDAE"], na.rm = TRUE) / ni_total
                        , pi_native = 100 * sum(N_TAXA[NATIVE == "NATIVE"], na.rm = TRUE) / ni_total
                        , pi_nonnative = 100 * sum(N_TAXA[is.na(NATIVE) | NATIVE != "NATIVE"], na.rm = TRUE) / ni_total
+                       , pi_nonnative_NotNativeNotNA = 100 * sum(N_TAXA[NATIVE != "NATIVE"], na.rm = TRUE) / ni_total
+                       , pi_nonnative_OnlyNonNative = 100 * sum(N_TAXA[NATIVE == "NON-NATIVE"], na.rm = TRUE) / ni_total
                        , pi_Notur = 100 * sum(N_TAXA[GENUS == "NOTURUS"], na.rm = TRUE) / ni_total
                        , pi_sculpin = 100 * sum(N_TAXA[TYPE == "SCULPIN"], na.rm = TRUE) / ni_total
                        , pi_Lepomis = 100 * sum(N_TAXA[GENUS == "LEPOMIS"], na.rm = TRUE) / ni_total
@@ -4297,7 +4299,14 @@ metric.values.fish <- function(myDF
                        , nt_natCyprin = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & FAMILY == "CYPRINIDAE"], na.rm = TRUE)
                        , nt_Lepomis = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & GENUS == "LEPOMIS"], na.rm = TRUE)
                        , nt_native = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & N_TAXA > 0], na.rm = TRUE)
-                       , nt_nonnative = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & (is.na(NATIVE) | NATIVE != "NATIVE")
+                       , nt_nonnative = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
+                                                                 & (is.na(NATIVE) | NATIVE != "NATIVE")
+                                                                 & N_TAXA > 0], na.rm = TRUE)
+                       , nt_nonnative_NotNativeNotNA = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
+                                                                 & (NATIVE != "NATIVE")
+                                                                 & N_TAXA > 0], na.rm = TRUE)
+                       , nt_nonnative_OnlyNonNative = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
+                                                                 & (NATIVE == "NON-NATIVE")
                                                                  & N_TAXA > 0], na.rm = TRUE)
                        , nt_nativenonhybrid = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" &
                                                                          (HYBRID != TRUE | is.na(HYBRID))], na.rm = TRUE)
@@ -4341,6 +4350,8 @@ metric.values.fish <- function(myDF
                        , pt_Lepomis = 100 * nt_Lepomis / nt_total
                        , pt_native = 100 * nt_native / nt_total
                        , pt_nonnative = 100 * nt_nonnative / nt_total
+                       , pt_nonnative_NotNativeNotNA = 100 * nt_nonnative_NotNativeNotNA / nt_total
+                       , pt_nonnative_OnlyNonNative = 100 * nt_nonnative_OnlyNonNative / nt_total
                        , pt_Notur = 100 * nt_Notur / nt_total
                        , pt_Salm = 100 * nt_Salm / nt_total
                        , pt_connect = 100 * nt_connect / nt_total

inst/shiny-examples/BioMonTools/global.R

@@ -1,7 +1,7 @@
 # Shiny Global File
 
 # Version ----
-pkg_version <- "1.0.2.9065"
+pkg_version <- "1.0.2.9066"
 
 # Packages----
 library(BioMonTools)