diff --git a/NEWS b/NEWS index d4f4c70..f4da678 100644 --- a/NEWS +++ b/NEWS @@ -4,10 +4,16 @@ NEWS - #> Last Update: 2024-08-06 15:24:57.180498 + #> Last Update: 2024-08-07 07:40:11.938594 # Version History +## Changes in version 1.0.2.9049 + +- style: Clean up new additions to metric_values.R + - Move new metrics for GP to alongside previous GP metrics + - Move munging for new metrics to alongside previous munging for TYPE + ## Changes in version 1.0.2.9048 - refactor: Added Great Plains fish metrics (pi_NPL and pi_SALT) diff --git a/NEWS.md b/NEWS.md index d4f4c70..f4da678 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,10 +4,16 @@ NEWS - #> Last Update: 2024-08-06 15:24:57.180498 + #> Last Update: 2024-08-07 07:40:11.938594 # Version History +## Changes in version 1.0.2.9049 + +- style: Clean up new additions to metric_values.R + - Move new metrics for GP to alongside previous GP metrics + - Move munging for new metrics to alongside previous munging for TYPE + ## Changes in version 1.0.2.9048 - refactor: Added Great Plains fish metrics (pi_NPL and pi_SALT) diff --git a/NEWS.rmd b/NEWS.rmd index 7411876..812e430 100644 --- a/NEWS.rmd +++ b/NEWS.rmd @@ -18,6 +18,12 @@ cat(paste0("Last Update: ",Sys.time())) # Version History +## Changes in version 1.0.2.9049 + +* style: Clean up new additions to metric_values.R + + Move new metrics for GP to alongside previous GP metrics + + Move munging for new metrics to alongside previous munging for TYPE + ## Changes in version 1.0.2.9048 * refactor: Added Great Plains fish metrics (pi_NPL and pi_SALT) diff --git a/R/metric_values.R b/R/metric_values.R index 91856bd..16b0526 100644 --- a/R/metric_values.R +++ b/R/metric_values.R @@ -3784,28 +3784,7 @@ metric.values.fish <- function(myDF # each will be TRUE or FALSE # finds any match so "GE, IV" is both "GE" and "IV" - - if (!"ELEVATION_ATTR" %in% names(myDF)) { - myDF[, "ELEVATION_ATTR"] <- NA - }## IF ~ ELEVATION_ATTR - # Remove white space - myDF[, "ELEVATION_ATTR"] <- gsub(" ", "", myDF[, "ELEVATION_ATTR"]) - # code new columns - myDF[, "ELEVATION_LOW"] <- "LOW" == myDF[, "ELEVATION_ATTR"] - myDF[, "ELEVATION_HIGH"] <- "HIGH" == myDF[, "ELEVATION_ATTR"] - - - if (!"GRADIENT_ATTR" %in% names(myDF)) { - myDF[, "GRADIENT_ATTR"] <- NA - }## IF ~ GRADIENT_ATTR - # Remove white space - myDF[, "GRADIENT_ATTR"] <- gsub(" ", "", myDF[, "GRADIENT_ATTR"]) - # code new columns - myDF[, "GRADIENT_LOW"] <- "LOW" == myDF[, "GRADIENT_ATTR"] - myDF[, "GRADIENT_MOD"] <- "MOD" == myDF[, "GRADIENT_ATTR"] - myDF[, "GRADIENT_HIGH"] <- "HIGH" == myDF[, "GRADIENT_ATTR"] - - + ## HABITAT ---- if (!"HABITAT" %in% names(myDF)) { myDF[, "HABITAT"] <- NA }## IF ~ HABITAT @@ -3822,7 +3801,7 @@ metric.values.fish <- function(myDF myDF[, "HABITAT_HW_noT"] <- grepl("HW-T", myDF[,"HABITAT"]) # Headwater Specialist, no Tolerant myDF[, "HABITAT_WE_noT"] <- grepl("WE-T", myDF[,"HABITAT"]) # Wetland, no Tolerant - + ## REPRODUCTION ---- if (!"REPRODUCTION" %in% names(myDF)) { myDF[, "REPRODUCTION"] <- NA }## IF ~ REPRODUCTION @@ -3842,7 +3821,7 @@ metric.values.fish <- function(myDF myDF[, "REPRO_SER"] <- grepl("SER", myDF[,"REPRODUCTION"]) # Serial Spawner myDF[, "REPRO_SILI"] <- grepl("SILI", myDF[,"REPRODUCTION"]) # Simple Lithophil - + ## THERMAL_INDICATOR---- if (!"THERMAL_INDICATOR" %in% names(myDF)) { myDF[, "THERMAL_INDICATOR"] <- NA }## IF ~ THERMAL_INDICATOR @@ -3857,7 +3836,7 @@ metric.values.fish <- function(myDF # exact matches only myDF[, "TI_NA"] <- is.na(myDF[, "THERMAL_INDICATOR"]) - + ## TOLER ---- if (!"TOLER" %in% names(myDF)) { myDF[, "TOLER"] <- NA }## IF ~ TOLER @@ -3876,7 +3855,7 @@ metric.values.fish <- function(myDF myDF[, "TOLER_TCW"] <- grepl("TCW", myDF[,"TOLER"]) myDF[, "TOLER_VT"] <- grepl("VT", myDF[,"TOLER"]) - + ## TROPHIC ---- if (!"TROPHIC" %in% names(myDF)) { myDF[, "TROPHIC"] <- NA }## IF ~ TROPHIC @@ -3898,7 +3877,7 @@ metric.values.fish <- function(myDF myDF[, "TROPHIC_IN_CYP"] <- grepl("INCYP", myDF[, "TROPHIC"]) # Insectivorous Cyprinidae myDF[, "TROPHIC_DEM"] <- grepl("DEM", myDF[, "TROPHIC"]) # Detritivore Minor - + ## TYPE ---- if (!"TYPE" %in% names(myDF)) { myDF[, "TYPE"] <- NA }## IF ~ TYPE @@ -3919,17 +3898,36 @@ metric.values.fish <- function(myDF myDF[, "TYPE_SCHOOL"] <- grepl("SCHOOLING", myDF[,"TYPE"]) # MN, Brook Trout myDF[, "TYPE_BROOKTROUT"] <- grepl("BROOKTROUT", myDF[,"TYPE"]) - - if (!"WSAREA_ATTR" %in% names(myDF)) { - myDF[, "WSAREA_ATTR"] <- NA - }## IF ~ WSAREA_ATTR # GP, Salt myDF[, "TYPE_SALT"] <- grepl("SALT", myDF[, "TYPE"]) - # GP, NPL myDF[, "TYPE_NPL"] <- grepl("NPL", myDF[, "TYPE"]) + ## ELEVATION_ATTR ---- + if (!"ELEVATION_ATTR" %in% names(myDF)) { + myDF[, "ELEVATION_ATTR"] <- NA + }## IF ~ ELEVATION_ATTR + # Remove white space + myDF[, "ELEVATION_ATTR"] <- gsub(" ", "", myDF[, "ELEVATION_ATTR"]) + # code new columns + myDF[, "ELEVATION_LOW"] <- "LOW" == myDF[, "ELEVATION_ATTR"] + myDF[, "ELEVATION_HIGH"] <- "HIGH" == myDF[, "ELEVATION_ATTR"] + + ## GRADIENT_ATTR---- + if (!"GRADIENT_ATTR" %in% names(myDF)) { + myDF[, "GRADIENT_ATTR"] <- NA + }## IF ~ GRADIENT_ATTR + # Remove white space + myDF[, "GRADIENT_ATTR"] <- gsub(" ", "", myDF[, "GRADIENT_ATTR"]) + # code new columns + myDF[, "GRADIENT_LOW"] <- "LOW" == myDF[, "GRADIENT_ATTR"] + myDF[, "GRADIENT_MOD"] <- "MOD" == myDF[, "GRADIENT_ATTR"] + myDF[, "GRADIENT_HIGH"] <- "HIGH" == myDF[, "GRADIENT_ATTR"] + ## WSAREA_ATTR ---- + if (!"WSAREA_ATTR" %in% names(myDF)) { + myDF[, "WSAREA_ATTR"] <- NA + }## IF ~ WSAREA_ATTR # Remove white space myDF[, "WSAREA_ATTR"] <- gsub(" ", "", myDF[, "WSAREA_ATTR"]) # code new columns @@ -3939,8 +3937,7 @@ metric.values.fish <- function(myDF myDF[, "WSAREA_XL"] <- "XLARGE" == myDF[, "WSAREA_ATTR"] - # Create Dominant N #### - + ## Create Dominant N #### if (verbose == TRUE) { # 4 debug_topic <- "Munge, Dom" @@ -4126,8 +4123,7 @@ metric.values.fish <- function(myDF rm(df_dom01_ExclSchool_sum) rm(df_dom02_ExclSchool_sum) - # N_Anomalies ---- - + ## N_Anomalies ---- if (verbose == TRUE) { # 5 debug_topic <- "Munge, anomalies" @@ -4901,6 +4897,13 @@ metric.values.fish <- function(myDF | TAXAID == "FUNDULUS KANSAE" #NORTHERN PLAINS KILLIFISH | TAXAID == "FUNDULUS ZEBRINUS")] #PLAINS KILLIFISH , na.rm = TRUE) + # Great Plains 2024-08-06 + #### GP, SALT + , pi_salt = 100 * sum(N_TAXA[TYPE_SALT == TRUE] + , na.rm = TRUE) / ni_total + #### GP, NPL + , pi_NPL = 100 * sum(N_TAXA[TYPE_NPL == TRUE] + , na.rm = TRUE) / ni_total ### Minnesota (Red Lakes) FIBI, 2024-06-01---- #### MN, ni @@ -5083,15 +5086,6 @@ metric.values.fish <- function(myDF , pi_delt_ExclSchool = 100 * sum(N_ANOMALIES[TYPE_SCHOOL != TRUE] , na.rm = TRUE) / ni_total_ExclSchool - ### Great Plains #### - - #### GP, SALT - , pi_salt = 100 * sum(N_TAXA[TYPE_SALT == TRUE] - , na.rm = TRUE) / ni_total - #### GP, NPL - , pi_NPL = 100 * sum(N_TAXA[TYPE_NPL == TRUE] - , na.rm = TRUE) / ni_total - # diff --git a/inst/shiny-examples/BioMonTools/global.R b/inst/shiny-examples/BioMonTools/global.R index 5dd20cf..7440d65 100644 --- a/inst/shiny-examples/BioMonTools/global.R +++ b/inst/shiny-examples/BioMonTools/global.R @@ -1,7 +1,7 @@ # Shiny Global File # Version ---- -pkg_version <- "1.0.2.9047" +pkg_version <- "1.0.2.9049" # Packages---- library(BioMonTools)