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leppottleppott
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v1.2.4.9004
* refactor: Add new fish ageclass metrics, Issue #129 * tests: Update fish tests with new column, ageclass
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‎DESCRIPTION‎

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Package: BioMonTools
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Type: Package
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Title: Biomonitoring and Bioassessment Calculations
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Version: 1.2.4.903
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Version: 1.2.4.9004
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Authors@R: c(
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person("Erik W.", "Leppo",
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email="Erik.Leppo@tetratech.com",

‎NEWS‎

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<!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
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#> Last Update: 2025-12-15 12:16:15.035087
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#> Last Update: 2025-12-26 15:31:28.075211
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# Version History
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## Changes in version 1.2.4.9004 (2025-12-26)
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- refactor: Add new fish ageclass metrics, Issue \#129
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- tests: Update fish tests with new column, ageclass
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## Changes in version 1.2.4.9003 (2025-12-15)
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- refactor: Update MetricScoring.xlsx for EGLE_2025 (MI)

‎NEWS.md‎

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<!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
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#> Last Update: 2025-12-15 12:16:15.035087
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#> Last Update: 2025-12-26 15:31:28.075211
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# Version History
1010

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## Changes in version 1.2.4.9004 (2025-12-26)
12+
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- refactor: Add new fish ageclass metrics, Issue \#129
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- tests: Update fish tests with new column, ageclass
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## Changes in version 1.2.4.9003 (2025-12-15)
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- refactor: Update MetricScoring.xlsx for EGLE_2025 (MI)

‎NEWS.rmd‎

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# Version History
2020

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## Changes in version 1.2.4.9004 (2025-12-26)
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* refactor: Add new fish ageclass metrics, Issue #129
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* tests: Update fish tests with new column, ageclass
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## Changes in version 1.2.4.9003 (2025-12-15)
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* refactor: Update MetricScoring.xlsx for EGLE_2025 (MI)

‎R/metric_values.R‎

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@@ -3758,7 +3758,7 @@ metric.values.fish <- function(myDF
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, "BCG_ATTR2")
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col.req_logical <- c("EXCLUDE", "HYBRID")
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col.req_numeric <- c("N_TAXA", "N_ANOMALIES", "SAMP_BIOMASS", "DA_MI2"
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, "SAMP_WIDTH_M", "SAMP_LENGTH_M", "TOLVAL2"
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, "SAMP_WIDTH_M", "SAMP_LENGTH_M", "TOLVAL2", "AGECLASS"
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)
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col.req <- c(col.req_character, col.req_logical, col.req_numeric)
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# col.req <- c("SAMPLEID", "TAXAID", "N_TAXA", "EXCLUDE"
@@ -4481,6 +4481,7 @@ metric.values.fish <- function(myDF
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, nt_natCent = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & FAMILY == "CENTRARCHIDAE"], na.rm = TRUE)
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, nt_natinsctCypr = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" &
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TROPHIC_IS == TRUE & FAMILY == "CYPRINIDAE"], na.rm = TRUE)
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, nt_natLeuc = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & FAMILY == "LEUCISCIDAE"], na.rm = TRUE)
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, nt_natrbs = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & TYPE == "RBS"], na.rm = TRUE)
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, nt_Petro = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "PETROMYZONTIDAE"], na.rm = TRUE)
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, nt_Salm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "SALMONIDAE"], na.rm = TRUE)
@@ -4539,6 +4540,10 @@ metric.values.fish <- function(myDF
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, nt_invertivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
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& TROPHIC_IV == TRUE]
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, na.rm = TRUE)
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, nt_invert_native = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
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& TROPHIC_IV == TRUE
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& NATIVE == "NATIVE"]
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, na.rm = TRUE)
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, nt_inverttopcarn = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
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& TROPHIC_IV_TC == TRUE]
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, na.rm = TRUE)
@@ -4570,6 +4575,7 @@ metric.values.fish <- function(myDF
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, pi_insctCypr = 100 * sum(N_TAXA[TROPHIC_IS == TRUE &
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FAMILY == "CYPRINIDAE"], na.rm = TRUE) / ni_total
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, pi_invertivore = 100 * sum(N_TAXA[TROPHIC_IV == TRUE], na.rm = TRUE) / ni_total
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, pi_invert_native = 100 * sum(N_TAXA[TROPHIC_IV == TRUE & NATIVE == "NATIVE"], na.rm = TRUE) / ni_total
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, pi_inverttopcarn = 100 * sum(N_TAXA[TROPHIC_IV_TC == TRUE], na.rm = TRUE) / ni_total
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, pi_omnivore = 100 * sum(N_TAXA[TROPHIC_OM == TRUE], na.rm = TRUE) / ni_total
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, pi_planktivore = 100 * sum(N_TAXA[TROPHIC_PL == TRUE], na.rm = TRUE) / ni_total
@@ -4584,17 +4590,24 @@ metric.values.fish <- function(myDF
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, pt_detritivore = 100 * nt_detritivore / nt_total
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, pt_herbivore = 100 * nt_herbivore / nt_total
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, pt_invertivore = 100 * nt_invertivore / nt_total
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, pt_invert_native = 100 * nt_invert_native / nt_total
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, pt_inverttopcarn = 100 * nt_inverttopcarn / nt_total
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, pt_omnivore = 100 * nt_omnivore / nt_total
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, pt_planktivore = 100 * nt_planktivore / nt_total
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, pt_topcarn = 100 * nt_topcarn / nt_total
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#
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## Tolerance ####
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, nt_tv_intol = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & TOLER == "INTOLERANT"], na.rm = TRUE)
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, nt_tv_intolhwi = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & (TOLER == "INTOLERANT" |
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TOLER == "HWI")], na.rm = TRUE)
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, pi_tv_toler = 100 * sum(N_TAXA[TOLER == "TOLERANT"], na.rm = TRUE) / ni_total
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, nt_tv_intol = dplyr::n_distinct(
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TAXAID[EXCLUDE != TRUE & TOLER == "INTOLERANT"],
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na.rm = TRUE)
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, nt_tv_intolhwi = dplyr::n_distinct(
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TAXAID[EXCLUDE != TRUE &
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(TOLER == "INTOLERANT" | TOLER == "HWI")],
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na.rm = TRUE)
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, pi_tv_toler = 100 *
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sum(N_TAXA[TOLER == "TOLERANT"], na.rm = TRUE) /
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ni_total
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#
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@@ -5069,7 +5082,7 @@ metric.values.fish <- function(myDF
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, na.rm = TRUE) / ni_total
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, pi_repro_migratory = 100 * sum(N_TAXA[REPRO_MIG == TRUE]
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, na.rm = TRUE) / ni_total
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, pi_repro_lithophil = 100 * sum(N_TAXA[REPRO_LITH == TRUE]
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, pi_repro_lithophil = 100 * sum(N_TAXA[REPRO_LITH == TRUE]
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, na.rm = TRUE) / ni_total
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### Repro, pt ----
@@ -5107,6 +5120,35 @@ metric.values.fish <- function(myDF
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, pt_habitat_w = 100 * nt_habitat_w / nt_total
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, pt_habitat_f = 100 * nt_habitat_f / nt_total
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## Age Class ----
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# Young of Year, YOY is ageclass 1 or 2
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, d_ac_yoy_Cott = max(0,
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min(1,
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dplyr::n_distinct(
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TAXAID[(EXCLUDE != TRUE &
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FAMILY == "COTTIDAE") &
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(AGECLASS == 1 |
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AGECLASS == 2)],
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na.rm = TRUE),
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na.rm = TRUE),
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na.rm = TRUE)
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, d_ac_yoy_rbt = max(0,
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min(1,
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dplyr::n_distinct(
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TAXAID[(EXCLUDE != TRUE &
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TAXAID == "ONCORHYNCHUS MYKISS") &
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(AGECLASS == 1 |
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AGECLASS == 2)],
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na.rm = TRUE),
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na.rm = TRUE),
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na.rm = TRUE)
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, n_ac_Cott = dplyr::n_distinct(AGECLASS[EXCLUDE != TRUE &
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FAMILY == "COTTIDAE"],
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na.rm = TRUE)
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, n_ac_rbt = dplyr::n_distinct(AGECLASS[EXCLUDE != TRUE &
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TAXAID == "ONCORHYNCHUS MYKISS"],
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na.rm = TRUE)
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## SPECIAL ----
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# odd ball metrics that don't fit the above groupings
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# OR are really different and probably only applicable

‎inst/extdata/MetricNames.xlsx‎

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‎tests/testthat/test_metric_names.R‎

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@@ -224,6 +224,8 @@ testthat::test_that("metric.values, names, fish, Function, xlNames", {
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# Munge (v1.0.2.9015, 2024-04-29)
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df_fish$TOLVAL2 <- NA_integer_
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df_fish$BCG_ATTR2 <- NA_character_
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# 2025-12-26
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df_fish$AGECLASS <- c(NA, 1:10)
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# Function
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df_metval <- BioMonTools::metric.values(df_fish
@@ -312,6 +314,8 @@ testthat::test_that("metric.values, names, fish, Function, xlScoring", {
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# Munge (v1.0.2.9015, 2024-04-29)
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df_fish$TOLVAL2 <- NA_integer_
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df_fish$BCG_ATTR2 <- NA_character_
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# 2025-12-26
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df_fish$AGECLASS <- c(NA, 1:10)
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# Function
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df_metval <- BioMonTools::metric.values(df_fish

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