Add new functions to calculate expanded composition data and input sample sizes

DESCRIPTION

@@ -15,6 +15,7 @@ Depends:
     R (>= 4.0)
 Imports:
     chron,
+    cli,
     cowplot,
     ggmosaic (>= 0.3.4),
     ggnewscale,
@@ -24,7 +25,9 @@ Imports:
     httr,
     janitor,
     jsonlite,
+    labelled,
     lifecycle,
+    plyr,
     purrr,
     reshape2,
     rlang,

NAMESPACE

@@ -46,9 +46,13 @@ export(est_growth)
 export(estimate_weight_length)
 export(fit_vbgrowth)
 export(get_design_based)
+export(get_expanded_comps)
+export(get_input_n)
 export(get_json)
 export(get_raw_comps)
+export(get_species_info)
 export(get_url)
+export(label_tow_expansion)
 export(plot_age_length_sampling)
 export(plot_bio_patterns)
 export(plot_comps)

R/GetN.fn.R

@@ -55,6 +55,14 @@ GetN.fn <- function(
     printfolder = "forSS3",
     output = NULL,
     verbose = TRUE) {
+  lifecycle::deprecate_soft(
+    when = "2.5",
+    what = "nwfscSurvey::GetN.fn()",
+    details = "The get_expanded_comps() will now do this calculation if specified
+    in the function input via input_sample_size_method. get_expanded_comps() calls
+    internally a new function called get_input_n() to determine the input sample
+    size."
+  )
   species <- match.arg(species)
   type <- match.arg(type)
   n.unq <- NA

R/GetSpp.fn.R

@@ -35,6 +35,13 @@
 #' )
 #'
 GetSpp.fn <- function(species, unident = FALSE) {
+
+  lifecycle::deprecate_soft(
+    when = "2.5",
+    what = "nwfscSurvey::GetSpp.n()",
+    details = "Please switch to get_species_info()."
+  )
+
   # background information
   sppnames <- nwfscSurvey::PullSpp.fn()
   if (!unident) {

R/SurveyAFs.fn.R

@@ -70,6 +70,11 @@ SurveyAFs.fn <- function(
     remove999 = TRUE,
     outputStage1 = FALSE,
     verbose = TRUE) {
+  lifecycle::deprecate_soft(
+    when = "2.5",
+    what = "nwfscSurvey::SurveyAFs.fn()",
+    details = "Please switch to get_expanded_comps()."
+  )
   # Overwrite inputs to use the same code for lengths as ages
   datL <- datA
   lgthBins <- ageBins

R/SurveyLFs.fn.R

@@ -76,6 +76,12 @@ SurveyLFs.fn <- function(
     outputStage1 = FALSE,
     sum100 = TRUE,
     verbose = TRUE) {
+  lifecycle::deprecate_soft(
+    when = "2.5",
+    what = "nwfscSurvey::SurveyLFs.fn()",
+    details = "Please switch to get_expanded_comps()."
+  )
+
   # Check for the number of tows were fish were observed but not measured
   postows <- datTows[which(datTows$total_catch_numbers > 0), ]
   find <- !(postows$Trawl_id %in% datL$Trawl_id)