Added new zooplankton_index indicator to _ecodata_

Imported new datafiles, wrote new get script and built _ecodata_ with new R datafile

data-raw/get_zooplankton_index.R

@@ -0,0 +1,78 @@
+## Zooplankton Index
+raw.dir <- here::here("data-raw/")
+
+# Define file paths for Calanus finmarchicus index and center of gravity
+falcalfin <- "fallcalfinindex - Sarah Gaichas - NOAA Federal.rds"
+sprcalfin <- "springcalfinindex - Sarah Gaichas - NOAA Federal.rds"
+falcalfincog <- "fallcalfincog - Sarah Gaichas - NOAA Federal.rds"
+sprcalfincog <- "springcalfincog - Sarah Gaichas - NOAA Federal.rds"
+
+# Define file paths for Euphausiids index and center of gravity
+faleuph <- "falleuphindex - Sarah Gaichas - NOAA Federal.rds"
+spreuph <- "springeuphindex - Sarah Gaichas - NOAA Federal.rds"
+faleuphcog <- "falleuphcog - Sarah Gaichas - NOAA Federal.rds"
+spreuphcog <- "springeuphcog - Sarah Gaichas - NOAA Federal.rds"
+
+# Define file paths for small copepods index and center of gravity
+falsmallcope <- "fallsmallcopeSOEindex - Sarah Gaichas - NOAA Federal.rds"
+sprsmallcope <- "springsmallcopeSOEindex - Sarah Gaichas - NOAA Federal.rds"
+falsmallcopecog <- "fallsmallcopeSOEcog - Sarah Gaichas - NOAA Federal.rds"
+sprsmallcopecog <- "springsmallcopeSOEcog - Sarah Gaichas - NOAA Federal.rds"
+
+# Define file paths for large copepods index and center of gravity
+fallgcope <- "falllgcopeALLindex - Sarah Gaichas - NOAA Federal.rds"
+sprlgcope <- "springlgcopeALLindex - Sarah Gaichas - NOAA Federal.rds"
+fallgcopecog <- "falllgcopeALLcog - Sarah Gaichas - NOAA Federal.rds"
+sprlgcopecog <- "springlgcopeALLcog - Sarah Gaichas - NOAA Federal.rds"
+
+# Define file paths for zooplankton volume index and center of gravity
+falzoopvol <- "fallzoopvolindex - Sarah Gaichas - NOAA Federal.rds"
+sprzoopvol <- "springzoopvolindex - Sarah Gaichas - NOAA Federal.rds"
+falzoopvolcog <- "fallzoopvolcog - Sarah Gaichas - NOAA Federal.rds"
+sprzoopvolcog <- "springzoopvolcog - Sarah Gaichas - NOAA Federal.rds"
+
+get_zooplankton_index <- function(save_clean = F){
+
+  # Load input files for Calanus finmarchicus index and center of gravity
+  fallcalfin <- readRDS(file.path(raw.dir, falcalfin))
+  springcalfin <- readRDS(file.path(raw.dir, sprcalfin))
+  fallcalfincog <- readRDS(file.path(raw.dir, falcalfincog))
+  springcalfincog <- readRDS(file.path(raw.dir, sprcalfincog))
+
+  # Load input files for Euphausiids index and center of gravity
+  falleuph <- readRDS(file.path(raw.dir, faleuph))
+  springeuph <- readRDS(file.path(raw.dir, spreuph))
+  falleuphcog <- readRDS(file.path(raw.dir, faleuphcog))
+  springeuphcog <- readRDS(file.path(raw.dir, spreuphcog))
+
+  # Load input files for Calanus finmarchicus index and center of gravity
+  fallsmallcope <- readRDS(file.path(raw.dir, falsmallcope))
+  springsmallcope <- readRDS(file.path(raw.dir, sprsmallcope))
+  fallsmallcopecog <- readRDS(file.path(raw.dir, falsmallcopecog))
+  springsmallcopecog <- readRDS(file.path(raw.dir, sprsmallcopecog))
+
+  # Load input files for Calanus finmarchicus index and center of gravity
+  falllgcope <- readRDS(file.path(raw.dir, fallgcope))
+  springlgcope <- readRDS(file.path(raw.dir, sprlgcope))
+  falllgcopecog <- readRDS(file.path(raw.dir, fallgcopecog))
+  springlgcopecog <- readRDS(file.path(raw.dir, sprlgcopecog))
+
+  # Load input files for Calanus finmarchicus index and center of gravity
+  fallzoopvol <- readRDS(file.path(raw.dir, falzoopvol))
+  springzoopvol <- readRDS(file.path(raw.dir, sprzoopvol))
+  fallzoopvolcog <- readRDS(file.path(raw.dir, falzoopvolcog))
+  springzoopvolcog <- readRDS(file.path(raw.dir, sprzoopvolcog))
+
+  zooplankton_index<- rbind(fallcalfin, springcalfin, fallcalfincog, springcalfincog,
+                            falleuph, springeuph, falleuphcog, springeuphcog, fallsmallcope,
+                            springsmallcope, fallsmallcopecog, springsmallcopecog, falllgcope,
+                            springlgcope, falllgcopecog, springlgcopecog, fallzoopvol,
+                            springzoopvol, fallzoopvolcog, springzoopvolcog)
+
+  if (save_clean){
+    usethis::use_data(zooplankton_index, overwrite = T)
+  } else {
+    return(zooplankton_index)
+  }
+}
+get_zooplankton_index(save_clean = T)