define replicate_df as coming from sdmTMB; include devtools and here in vignettes that use them

Author: e-perl-NOAA

R/clean_and_resample.R

@@ -41,7 +41,7 @@
 #' dir_out <- here::here("vignettes", "output")
 #' catch <- surveyresamplr::noaa_nwfsc_catch
 #' bio <- surveyresamplr::noaa_nwfsc_bio
-#' grid_yrs <- replicate_df(
+#' grid_yrs <- sdmTMB::replicate_df(
 #'   dat = surveyresamplr::noaa_nwfsc_catch, time_name = "year",
 #'   time_values = unique(catch$year)
 #' )

inst/r/run.R

@@ -326,7 +326,7 @@ pred_grid <- california_current_grid |> # rename x and y cols
     area_km2 = area_km2_WCGBTS
   ) |>
   dplyr::mutate(srvy = "CA")
-grid_yrs <- replicate_df(pred_grid, "year", unique(catch$year))
+grid_yrs <- sdmTMB::replicate_df(pred_grid, "year", unique(catch$year))
 
 ### Variables ------------------------------------------------------------------
 
@@ -555,7 +555,7 @@ catch <- noaa_afsc_catch |> dplyr::filter(srvy == "NBS")
 ### Load grid data -------------------------------------------------------------
 
 load(paste0(wd, "grids/noaa_afsc_nbs_pred_grid_depth.rdata"), verbose = TRUE)
-grid_yrs <- replicate_df(pred_grid_depth, "year", unique(catch$year))
+grid_yrs <- sdmTMB::replicate_df(pred_grid_depth, "year", unique(catch$year))
 
 ### Variables ------------------------------------------------------------------
 
@@ -781,7 +781,7 @@ catch <- noaa_afsc_catch |> dplyr::filter(srvy == "GOA")
 ### Load grid data -------------------------------------------------------------
 
 load(paste0(wd, "grids/noaa_afsc_goa_pred_grid_depth.rdata"), verbose = TRUE)
-grid_yrs <- replicate_df(pred_grid_depth, "year", unique(catch$year))
+grid_yrs <- sdmTMB::replicate_df(pred_grid_depth, "year", unique(catch$year))
 
 ### Variables ------------------------------------------------------------------
 
@@ -861,7 +861,7 @@ catch <- noaa_afsc_catch |> dplyr::filter(srvy == "AI")
 ### Load grid data -------------------------------------------------------------
 
 load(paste0(wd, "grids/noaa_afsc_ai_pred_grid_depth.rdata"), verbose = TRUE)
-grid_yrs <- replicate_df(pred_grid_depth, "year", unique(catch$year))
+grid_yrs <- sdmTMB::replicate_df(pred_grid_depth, "year", unique(catch$year))
 
 ### Variables ------------------------------------------------------------------
 
@@ -963,7 +963,7 @@ catch <- noaa_nefsc_catch |> dplyr::filter(srvy == "SPRING")
 ### Load grid data -------------------------------------------------------------
 
 load(paste0(wd, "grids/noaa_nefsc_nwa_pred_grid_depth.rdata"), verbose = TRUE)
-grid_yrs <- replicate_df(pred_grid_depth, "year", unique(catch$year))
+grid_yrs <- sdmTMB::replicate_df(pred_grid_depth, "year", unique(catch$year))
 
 ### Variables ------------------------------------------------------------------
 
@@ -1066,7 +1066,7 @@ catch <- noaa_nefsc_catch |> dplyr::filter(srvy == "FALL")
 ### Load grid data -------------------------------------------------------------
 
 load(paste0(wd, "grids/noaa_nefsc_nwa_pred_grid_depth.rdata"), verbose = TRUE)
-grid_yrs <- replicate_df(pred_grid_depth, "year", unique(catch$year))
+grid_yrs <- sdmTMB::replicate_df(pred_grid_depth, "year", unique(catch$year))
 
 ### Variables ------------------------------------------------------------------
 

vignettes/afsc-ebs.Rmd

@@ -23,6 +23,8 @@ options(future.globals.maxSize = 1 * 1024^4) # Allow up to 1 TB for globals
 # Here we list all the packages we will need for this whole process
 # We'll also use this in our works cited page.
 PKG <- c(
+  "devtools",
+  "here",
   "surveyresamplr",
   "dplyr",
   "tidyr",

vignettes/afsc-goa.Rmd

@@ -28,7 +28,8 @@ PKG <- c(
   "tidyr",
   "purrr",
   "ggplot2",
-  "flextable"
+  "flextable",
+  "sdmTMB"
 )
 
 pkg_install <- function(p) {
@@ -84,7 +85,7 @@ catch <- surveyresamplr::noaa_afsc_catch |>
 
 ### Load grid data -------------------------------------------------------------
 
-grid_yrs <- replicate_df(surveyresamplr::noaa_afsc_goa_pred_grid_depth, "year", 
+grid_yrs <- sdmTMB::replicate_df(surveyresamplr::noaa_afsc_goa_pred_grid_depth, "year", 
                          unique(catch$year))
 
 ### Variables ------------------------------------------------------------------

vignettes/afsc-nbs.Rmd

@@ -28,7 +28,8 @@ PKG <- c(
   "tidyr",
   "purrr",
   "ggplot2",
-  "flextable"
+  "flextable",
+  "sdmTMB"
 )
 
 pkg_install <- function(p) {
@@ -87,7 +88,7 @@ catch <- surveyresamplr::noaa_afsc_catch |>
 
 ### Load grid data -------------------------------------------------------------
 
-grid_yrs <- replicate_df(surveyresamplr::noaa_afsc_nbs_pred_grid_depth, "year", 
+grid_yrs <- sdmTMB::replicate_df(surveyresamplr::noaa_afsc_nbs_pred_grid_depth, "year", 
                          unique(catch$year))
 
 ### Variables ------------------------------------------------------------------

vignettes/nefsc.Rmd

@@ -29,7 +29,8 @@ PKG <- c(
   "tidyr",
   "purrr",
   "ggplot2",
-  "flextable"
+  "flextable",
+  "sdmTMB"
 )
 
 pkg_install <- function(p) {
@@ -105,7 +106,7 @@ catch <- surveyresamplr::noaa_nefsc_catch |> dplyr::filter(srvy == "SPRING")
 
 ### Load grid data -------------------------------------------------------------
 
-grid_yrs <- replicate_df(surveyresamplr::noaa_nefsc_pred_grid_depth, "year", 
+grid_yrs <- sdmTMB::replicate_df(surveyresamplr::noaa_nefsc_pred_grid_depth, "year", 
                          unique(catch$year))
 
 ### Variables ------------------------------------------------------------------
@@ -188,7 +189,7 @@ catch <- surveyresamplr::noaa_nefsc_catch |> dplyr::filter(srvy == "FALL")
 
 ### Load grid data -------------------------------------------------------------
 
-grid_yrs <- replicate_df(surveyresamplr::noaa_nefsc_pred_grid_depth, "year", 
+grid_yrs <- sdmTMB::replicate_df(surveyresamplr::noaa_nefsc_pred_grid_depth, "year", 
                          unique(catch$year))
 
 ### Variables ------------------------------------------------------------------