v1.0.2.9060

- refactor: Add new fish metrics (nt\_, pi\_, and pt\_) for invertivore - MetricNames.xlsx - metric_values.R
leppott · Nov 5, 2024 · d112e09 · d112e09
1 parent 5a235ac
commit d112e09
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Showing 7 changed files with 27 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: BioMonTools
 Type: Package
 Title: Tools for Biomonitoring and Bioassessment
-Version: 1.0.2.9059
+Version: 1.0.2.9060
 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: 2024-11-01 10:30:11.862667
+    #> Last Update: 2024-11-05 15:45:57.178726
 
 # Version History
 
+## Changes in version 1.0.2.9060 (2024-11-05)
+
+- refactor: Add new fish metrics (nt\_, pi\_, and pt\_) for invertivore
+  - MetricNames.xlsx
+  - metric_values.R
+
 ## Changes in version 1.0.2.9059 (2024-11-01)
 
 - refactor: Update search patterns for some fish trophic metrics

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: 2024-11-01 10:30:11.862667
+    #> Last Update: 2024-11-05 15:45:57.178726
 
 # Version History
 
+## Changes in version 1.0.2.9060 (2024-11-05)
+
+- refactor: Add new fish metrics (nt\_, pi\_, and pt\_) for invertivore
+  - MetricNames.xlsx
+  - metric_values.R
+
 ## Changes in version 1.0.2.9059 (2024-11-01)
 
 - refactor: Update search patterns for some fish trophic metrics

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -18,6 +18,12 @@ cat(paste0("Last Update: ",Sys.time()))
 
 # Version History
 
+## Changes in version 1.0.2.9060 (2024-11-05)
+
+* refactor: Add new fish metrics (nt_, pi_, and pt_) for invertivore
+    * MetricNames.xlsx
+    * metric_values.R
+
 ## Changes in version 1.0.2.9059 (2024-11-01)
 
 * refactor: Update search patterns for some fish trophic metrics

diff --git a/R/metric_values.R b/R/metric_values.R
@@ -4360,6 +4360,9 @@ metric.values.fish <- function(myDF
                        , nt_herbivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
                                                                  & TROPHIC_HB == TRUE]
                                                           , na.rm = TRUE)
+                       , nt_invertivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
+                                                                 & TROPHIC_IV == TRUE]
+                                                          , na.rm = TRUE)
                        , nt_inverttopcarn = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
                                                                       & TROPHIC_IV_TC == TRUE]
                                                                , na.rm = TRUE)
@@ -4390,6 +4393,7 @@ metric.values.fish <- function(myDF
                        , pi_insectivore = 100 * sum(N_TAXA[TROPHIC_IS == TRUE], na.rm = TRUE) / ni_total
                        , pi_insctCypr = 100 * sum(N_TAXA[TROPHIC_IS == TRUE &
                                                          FAMILY == "CYPRINIDAE"], na.rm = TRUE) / ni_total
+                       , pi_invertivore = 100 * sum(N_TAXA[TROPHIC_IV == TRUE], na.rm = TRUE) / ni_total
                        , pi_inverttopcarn = 100 * sum(N_TAXA[TROPHIC_IV_TC == TRUE], na.rm = TRUE) / ni_total
                        , pi_omnivore = 100 * sum(N_TAXA[TROPHIC_OM == TRUE], na.rm = TRUE) / ni_total
                        , pi_planktivore = 100 * sum(N_TAXA[TROPHIC_PL == TRUE], na.rm = TRUE) / ni_total
@@ -4403,6 +4407,7 @@ metric.values.fish <- function(myDF
                        , pt_habitat_beninvert = 100 * nt_habitat_beninvert / nt_total
                        , pt_detritivore = 100 * nt_detritivore / nt_total
                        , pt_herbivore = 100 * nt_herbivore / nt_total
+                       , pt_invertivore = 100 * nt_invertivore / nt_total
                        , pt_inverttopcarn = 100 * nt_inverttopcarn / nt_total
                        , pt_omnivore = 100 * nt_omnivore / nt_total
                        , pt_planktivore = 100 * nt_planktivore / 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 <- "1.0.2.9059"
+pkg_version <- "1.0.2.9060"
 
 # Packages----
 library(BioMonTools)