Merge pull request #47 from bbsBayes/documentation_update

Documentation update

DESCRIPTION

@@ -43,10 +43,7 @@ Description: The North American Breeding Bird Survey (BBS) is a long-running
   hierarchical Bayesian analysis of BBS data. You can run a full
   model analysis for one or more species that you choose, or you can take
   more control and specify how the data should be stratified, prepared
-  for 'JAGS', or modelled. The functions provided here allow you to replicate
-  analyses performed by the United State Geological Survey (USGS, see Link 
-  and Sauer (2011) <doi:10.1525/auk.2010.09220>) and Canadian Wildlife Service
-  (CWS, see Smith and Edwards (2020) <doi:10.1101/2020.03.26.010215>).
+  for 'Stan', or modelled. 
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

R/checks.R

@@ -78,9 +78,9 @@ check_model <- function(model, model_variant) {
   if(model_variant == "nonhier") {
     if(model != "first_diff") stop("`model_variant` 'nonhier' only allowed ",
                                    "for `first_diff` models", call. = FALSE)
-   warning("Non-hierarchial models are generally not recommended ",
-           "(see ?bbs_models), but provided for compatibility with USGS ",
-           "methods", call. = FALSE, immediate. = TRUE)
+   # warning("Non-hierarchial models are generally not recommended ",
+   #         "(see ?bbs_models), but provided for compatibility with USGS ",
+   #         "methods", call. = FALSE, immediate. = TRUE)
   }
 
   model

R/prepare-data.R

@@ -55,6 +55,13 @@ prepare_data <- function(strata_data,
   check_numeric(min_year, max_year, allow_null = TRUE)
   check_numeric(min_n_routes, min_max_route_years, min_mean_route_years)
   check_logical(quiet)
+  #warning if stratification == latlong and min_n_routes > 1
+  if(strata_data$meta_data$stratify_by == "latlong" & min_n_routes == 3){
+    warning("Many strata with data may have been excluded ",
+            "With latlong stratification, most strata have ",
+            "only 1 route. You may wish to set min_n_routes = 1",
+            call. = FALSE, immediate. = TRUE)
+  }
 
   # Get observations of interest
   obs <- strata_data$birds_strata %>%

inst/CITATION

@@ -1,4 +1,4 @@
-citHeader("To cite bbsBayes2 in publication, please use both:")
+citHeader("To cite bbsBayes2 in publication, please use both: Edwards et al. 2023 and Smith et al. 2023")
 
 citEntry(
   entry = "misc",
@@ -18,7 +18,7 @@ citEntry(
   textVersion = "Smith, A.C., Binley, A., Daly, L., Edwards, B.P.M., Ethier, D., Frei, B., Iles, D., Meehan, T.D., and Michel, N.L., and Smith, P.A. (2023). Spatially explicit Bayesian hierarchical models for avian population status and trends. https://doi.org/10.32942/X2088D"
 )
 
-citHeader("To cite the Breeding Bird Survey data in publication, please use:")
+citHeader("To cite the Breeding Bird Survey data in publication, please use Ziolkowski et al. 2022")
 
 citEntry(
   entry = "misc",
@@ -29,16 +29,3 @@ citEntry(
   textVersion = "Ziolkowski Jr., D.J., Lutmerding, M., Aponte, V.I., and Hudson, M-A.R., 2022, North American Breeding Bird Survey Dataset 1966 - 2021: U.S. Geological Survey data release, https://doi.org/10.5066/P97WAZE5."
 )
 
-citHeader("To cite the original bbsBayes package in publication, please use:")
-
-citEntry(
-  entry = "article",
-  title = "bbsBayes: An R Package for Hierarchical Bayesian Analysis of North American Breeding Bird Survey Data",
-  year = "2021",
-  journal = "Journal of Open Research Software",
-  volume = "9",
-  issue = "1",
-  url = "https://doi.org/10.5334/jors.329",
-  author = "Edwards, Brandon PM and Smith, Adam C",
-  textVersion = "Edwards, B.P.M and A.C. Smith. (2021). bbsBayes: An R Package for Hierarchical Bayesian Analysis of North American Breeding Bird Survey Data. Journal of Open Research Software 9(1), p.19. https://doi.org/10.5334/jors.329"
-)

tests/testthat/test-01_checks.R

@@ -189,7 +189,7 @@ test_that("model/model_file/model_variant checks", {
   for(i in unique(bbs_models$variant)) expect_silent(check_model_variant(i))
   for(i in seq_len(nrow(bbs_models))) {
     if(bbs_models$variant[i] == "nonhier") {
-      expect_warning(check_model(bbs_models$model[i], bbs_models$variant[i]))
+      #expect_warning(check_model(bbs_models$model[i], bbs_models$variant[i]))
     } else {
       expect_silent(check_model(bbs_models$model[i], bbs_models$variant[i]))
     }

tests/testthat/test-07_prepare_model.R

@@ -109,7 +109,8 @@ test_that("prepare_model() first_diff / slope", {
 
   for(i in seq_len(nrow(m))) {
 
-    if(m$variant[i] == "nonhier") ex <- expect_warning else ex <- expect_silent
+    #if(m$variant[i] == "nonhier") ex <- expect_warning else
+    ex <- expect_silent
     ex(md <- prepare_model(p,
                            model = m$model[!!i],
                            model_variant = m$variant[!!i],