Merge pull request #125 from NOAA-EDAB/ATLNTS-358_groupNames

Atlnts 358 group names

data-raw/map_functional_group.R → data-raw/create_map_functional_group.R

@@ -2,7 +2,7 @@
 #' 
 #' Write the mapping to a file format (GitHub flavored markdown) that can used on the wiki. 
 #' 
-#'  Requires: andybeet/utilities package for "capitalize_first_letter" function
+#'  Requires: andybeet/abutils package for "capitalize_first_letter" function
 #'            andybeet/dbutils package for create_species_lookup.r and connect_to_database  
 
 # list packages and check to see if needed to be installed
@@ -24,7 +24,7 @@ for (apack in packages$pkgName) {
 }
 
 
-map_functional_group <- function(channel,writeToFile=F) {
+create_map_functional_group <- function(channel,writeToFile=F) {
 
   # read in functional group codes and name from Atlantis input file
   fg <- atlantisom::load_fgs(here::here("currentVersion"),"neus_groups.csv") %>%
@@ -33,7 +33,7 @@ map_functional_group <- function(channel,writeToFile=F) {
   #fg <-  readr::read_csv(here::here("data-raw","initialFunctionalGroupNames.csv"))
 
   # read in species membership to group, then join with functional group names
-  data <- readr::read_csv(here::here("data-raw","Atlantis_1_5_groups_svspp_nespp3.csv")) %>%
+  data <- readr::read_csv(here::here("data-raw/data","Atlantis_1_5_groups_svspp_nespp3.csv")) %>%
     dplyr::mutate(NESPP3 = sprintf("%03d",NESPP3)) %>%
     dplyr::left_join(.,fg,by="Code")
 
@@ -55,15 +55,15 @@ map_functional_group <- function(channel,writeToFile=F) {
     dplyr::full_join(.,NESPP3Data, by="NESPP3") %>%
     dplyr::arrange(Code) %>%
     dplyr::rename(Species = Name,Functional_Group = LongName,Common_Name = COMNAME.y,Scientific_Name=SCIENTIFIC_NAME.y,Species_Itis=SPECIES_ITIS.y)  %>% 
-    dplyr::mutate(Common_Name = utilities::capitalize_first_letter(Common_Name),NESPP3=as.numeric(NESPP3),Species_Itis=as.numeric(Species_Itis)) %>%
+    dplyr::mutate(Common_Name = abutils::capitalize_first_letter(Common_Name),NESPP3=as.numeric(NESPP3),Species_Itis=as.numeric(Species_Itis)) %>%
     dplyr::select(Code,Functional_Group,Species,Scientific_Name,SVSPP,NESPP3,Species_Itis,isFished) %>%
     dplyr::mutate(isFishedSpecies = (Functional_Group==Species) & (isFished==T)) %>% 
     dplyr::select(-isFished)
 
 
   # format to markdown table. Copy output to wiki
   # open file and write
-  outputFile <- here::here("data-raw","functionalGroupNames.txt")
+  outputFile <- here::here("data","functionalGroupNames.txt")
   fileConn<-file(outputFile,open="w")
   header <- paste0("|",paste0(names(masterList),collapse = "|"),"|")
   cat(header,file=fileConn,append=T)
@@ -81,7 +81,7 @@ map_functional_group <- function(channel,writeToFile=F) {
   close(fileConn)
 
   if(writeToFile){
-    readr::write_csv(masterList,here::here("data-raw","functionalGroupNames.csv"))
+    readr::write_csv(masterList,here::here("data","functionalGroupNames.csv"))
   }
 
   return(masterList)

data-raw/create_mapv1groups_to_v2.r

@@ -0,0 +1,30 @@
+#' Read and process changes in groups from V1.0 to V2.0
+#' 
+#' Create a txt file in md format for use in the wiki
+#' 
+
+codes <- readr::read_csv(here::here("data-raw/data","specieslist_v1_2.csv")) %>% 
+  dplyr::select(GroupV1,Atcode,GroupV2,At2code) %>%
+  dplyr::distinct() %>%
+  dplyr::arrange(Atcode,At2code)
+
+# format to markdown table. Copy output to wiki
+# open file and write
+outputFile <- here::here("data","v1v2GroupMap.txt")
+fileConn<-file(outputFile,open="w")
+header <- paste0("|",paste0(names(codes),collapse = "|"),"|")
+cat(header,file=fileConn,append=T)
+cat("\n",file=fileConn,append=T)
+spacer <- paste0("|",paste0(rep("---",ncol(codes)),collapse = "|"),"|")
+cat(spacer,file=fileConn,append=T)
+cat("\n",file=fileConn,append=T)
+
+for (irow in 1:nrow(codes)) {
+  rowData <- paste0("|",paste0(codes[irow,],collapse = "|"),"|")
+  cat(rowData,file=fileConn,append=T)
+  cat("\n",file=fileConn,append=T)
+}
+
+close(fileConn)
+
+

data-raw/stockSMART_data.r → data-raw/create_stockSMART_data.r

@@ -1,14 +1,15 @@
-#' Combines the stock SMART data with the Atlantis functional group codes
-#'
-#' Filters out all species that reside on the east coast from stock smart, and assign them with an atlantis functional group code
-#'
+#' Filters stock smart data by Atlantis species
+#' 
+#' Needed for QC for fishing inputs and possibly for reasonability checks
+#' Filters out all species that reside on the east coast from stock smart
+#' 
 #' saves RDS file
 #' 
 #' stockSMARTData.Rds"
 
 library(magrittr)
 
-stockSMART_data <- function() {
+create_stockSMART_data <- function() {
 
   # pulls in all of stockSMART data
   saData <- dplyr::as_tibble(assessmentdata::stockAssessmentData)

data-raw/survdat_biomass.r → data-raw/create_survdat_biomass.r

@@ -1,6 +1,10 @@
-#' Estimate swept area biomass over whole shelf for species in Atlantis present in survey
+#' Creates biomass datafiles needed for reasonability checks
 #' 
-#' Creats RDS files:
+#'  
+#' Estimate swept area biomass (with uncertainty measures) over whole shelf for species in Atlantis
+#' Bottom trawl Survey data is used (survdat) with 3 custom files for scallop, quahogs, surfclams
+#' 
+#' Creates RDS files saved in data folder:
 #' sweptAreaBiomassEPU.RDS
 #' sweptAreaBiomassNEUS_Box.RDS
 #' sweptAreaBiomassNEUS.RDS
@@ -17,12 +21,13 @@ if (pullFromDB) {
   channel <- dbutils::connect_to_database(server,uid)
   survey <- survdat::get_survdat_data(channel)
 } else { # or read in previous pull
+  # eventually this will reside on Github in version controlled package
   survey <- readRDS("C:/Users/andrew.beet/Documents/MyWork/gitHub_repos/survdat/testing/survdat2021.RDS")
 }
 
 ### read in atlantic surfclam data. Poorly sampled in bottom trawl survey
 
-clam <- readr::read_csv(file=here::here("data-raw","surfclam403Biomass.csv"),skip=8) 
+clam <- readr::read_csv(file=here::here("data-raw/data","surfclam403Biomass.csv"),skip=8) 
 # from Dan Hennen swept are biomass
 clam <- clam %>%
   dplyr::select(Yr,Value,StdDev) %>% 
@@ -37,7 +42,7 @@ clam <- clam %>%
 
 ### read in ocean quahog data. Poorly sampled in bottom trawl survey
 
-quahog <- readr::read_csv(file=here::here("data-raw","quahog754Biomass.csv"),skip=8) 
+quahog <- readr::read_csv(file=here::here("data-raw/data","quahog754Biomass.csv"),skip=8) 
 # from Dan Hennen swept are biomass
 quahog <- quahog %>%
   dplyr::select(Yr,Value,StdDev) %>% 
@@ -56,7 +61,7 @@ quahog <- quahog %>%
 #   dplyr::select(Year,Value,Metric, Description, Units)
 # # from 65 Stock assessment table A9.4 p80
 
-scallop <- readr::read_csv(file=here::here("data-raw","scallop401Biomass.csv"),skip=9) 
+scallop <- readr::read_csv(file=here::here("data-raw/data","scallop401Biomass.csv"),skip=9) 
 
 scallops <- scallop %>%
   dplyr::select(Year,Bms,CV_2) %>% 

data-raw/initialFunctionalGroupNames.csv → data-raw/data/initialFunctionalGroupNames.csv

@@ -1,3 +1,10 @@
+# V2.0 Atlantis Functional Group names and Codes. (First Cut)
+#
+# Manually created 
+#
+# Temporary file used to compare with neus groups file to aid in creating main file
+#
+#
 Group Code,Group Name 
 MAK,Atlantic mackerel 
 HER,Atlantic herring