Merge pull request #6 from afsc-gap-products/incorporating_gapindex_3…

…_0_0 updating with gapindex 3.0.0
afsc-gap-products · Nov 26, 2024 · 87eb1d2 · 87eb1d2
2 parents 7c44fe3 + 86441dc
commit 87eb1d2
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: esrindex
 Type: Package
 Title: Abundance index products for Alaska ESRs
-Version: 1.0.0
-Date: 2024-11-08
+Version: 1.0.1
+Date: 2024-11-25
 Authors@R: c(person("Sean", "Rohan", email = "sean.rohan@noaa.gov", role = c("aut", "cre")),
           person("Thaddaeus", "Buser", email = "thaddaeus.buser@noaa.gov", role = "ctb"),
           person("Christina", "Conrath", email = "christina.conrath@noaa.gov", role = "ctb"),

diff --git a/NEWS b/NEWS
@@ -1,3 +1,11 @@
+esrindex 1.0.1 (November 25, 2024)
+----------------------------------------------------------------
+
+BUG FIX
+
+- Update get_group_data() to use gapindex 3.0.0 syntax.
+
+
 esrindex 1.0.0 (November 8, 2024) - First production release
 ----------------------------------------------------------------
 
@@ -74,4 +82,4 @@ esrindex 2024.06.20 (June 20, 2024)
 ----------------------------------------------------------------
 
 Updated sponge and coral groups with the correct SPECIES_CODE 
-range.
+range.
diff --git a/R/get_group_data.R b/R/get_group_data.R
@@ -79,7 +79,7 @@ get_group_data <- function(region,
 
     dat <- try(gapindex::get_data(year_set = min_year:as.numeric(format(Sys.Date(), "%Y")),
                               survey_set = region,
-                              sql_channel = channel,
+                              channel = channel,
                               spp_codes = valid_species_codes), silent = TRUE)
 
     # Warn if there was a gapindex error
@@ -93,14 +93,15 @@ get_group_data <- function(region,
 
     subareas <- dplyr::select(dat$subarea, AREA_ID, AREA_NAME, DESCRIPTION)
 
-    cpue <- gapindex::calc_cpue(racebase_tables = dat)
+    cpue <- gapindex::calc_cpue(gapdata = dat)
 
     if(nrow(cpue) > 0) {
 
-      biomass_strata <- gapindex::calc_biomass_stratum(racebase_tables = dat, cpue = cpue)
+      biomass_strata <- gapindex::calc_biomass_stratum(gapdata = dat, 
+                                                       cpue = cpue)
 
-      subarea_biomass <- gapindex::calc_biomass_subarea(racebase_tables = dat,
-                                                        biomass_strata = biomass_strata)
+      subarea_biomass <- gapindex::calc_biomass_subarea(gapdata = dat,
+                                                        biomass_stratum = biomass_strata)
 
       subarea_biomass_summary <- suppressMessages(
         dplyr::group_by(subarea_biomass, AREA_ID, SPECIES_CODE) |>

diff --git a/chapters/esrindex.bib b/chapters/esrindex.bib
@@ -8,7 +8,7 @@ @misc{esrindex
 @misc{
   gapindex,
   author = {Zack Oyafuso},
-  title = {{gapindex: Standard AFSC GAP Product Calculations. R package version 2.2.0}},
+  title = {{gapindex: Standard AFSC GAP Product Calculations. R package version 3.0.0}},
   year = {2024},
   url = {https://github.com/afsc-gap-products/gapindex}
 }