vignettes updating

R/checks.R

@@ -308,14 +308,16 @@ check_regions <- function(regions, stratify_by, stratify_type,
   msg <- "Stratification does not match desired regions:\n"
 
   if(stratify_by %in% c("bcr", "latlong") &
-     any(regions %in% c("country", "prov_state"))) {
+     any(regions %in% c("country", "prov_state"))
+     & stratify_type != "custom" & is.null(regions_index)) {
     stop(msg,
          "BCRs and lat-long degree block stratifications cannot be divided ",
          "into regions with political boundaries ('country', 'prov_state').",
          call. = FALSE)
   }
 
-  if(stratify_by == "prov_state" & "bcr" %in% regions){
+  if(stratify_by == "prov_state" & "bcr" %in% regions
+     & stratify_type != "custom" & is.null(regions_index)){
     stop(msg,
          "The States and Provinces stratification",
          "cannot be divided into BCR regions.",

R/generate-trends.R

@@ -139,13 +139,14 @@ generate_trends <- function(indices,
                             max_year = NULL,
                             quantiles = c(0.025, 0.05, 0.25, 0.75, 0.95, 0.975),
                             slope = FALSE,
+                            gam = FALSE,
                             prob_decrease = NULL,
                             prob_increase = NULL,
                             hpdi = FALSE) {
 
   # Checks
   check_data(indices)
-  check_logical(slope, hpdi)
+  check_logical(slope, hpdi, gam)
   check_numeric(quantiles)
   check_numeric(min_year, max_year, quantiles, prob_decrease, prob_increase,
                 allow_null = TRUE)
@@ -263,6 +264,26 @@ generate_trends <- function(indices,
           .data[[paste0("slope_trend_q_", q1)]])
   }
 
+
+  # Optional gam based trends
+  if(gam) {
+    trends <- trends %>%
+      dplyr::mutate(
+        sl_t = purrr::map(.data$n, calc_gam,
+                          .env$min_year_num, .env$max_year_num),
+        gam_trend = purrr::map_dbl(.data$sl_t, stats::median),
+        gam_trend_q = purrr::map_df(
+          .data$sl_t, ~stats::setNames(
+            calc_quantiles(.x, quantiles, names = FALSE),
+            paste0("gam_trend_q_", quantiles)))) %>%
+      tidyr::unnest("gam_trend_q") %>%
+      dplyr::mutate(
+        "width_of_{q}_percent_credible_interval_gam" :=
+          .data[[paste0("gam_trend_q_", q2)]] -
+          .data[[paste0("gam_trend_q_", q1)]])
+  }
+
+
   # Model conditional probabilities of population change during trends period
   if(!is.null(prob_decrease)) {
     trends <- trends %>%
@@ -292,6 +313,7 @@ generate_trends <- function(indices,
       dplyr::starts_with("trend"),
       dplyr::starts_with("percent_change"),
       dplyr::starts_with("slope"),
+      dplyr::starts_with("gam"),
       dplyr::starts_with("width"),
       dplyr::starts_with("prob"),
       "rel_abundance", "obs_rel_abundance",
@@ -325,6 +347,25 @@ calc_slope <- function(n, min_year_num, max_year_num) {
   as.vector((exp(m) - 1) * 100)
 }
 
+gam_sl <- function(i, wy) {
+  df <- data.frame(i = i,
+                   y = 1:length(i))
+  sm <- mgcv::gam(data = df,
+                  formula = i~s(y))
+  smf <- sm$fitted.values[wy]
+  ny <- wy[2]-wy[1]
+  smt <- (smf[2]-smf[1])*(1/ny)
+}
+
+calc_gam <- function(n, min_year_num, max_year_num) {
+  wy <- c(min_year_num,max_year_num)
+
+  ne <- log(n)
+  m <-  t(apply(ne, 1, FUN = gam_sl, wy))
+
+  as.vector((exp(m) - 1) * 100)
+}
+
 calc_prob_crease <- function(x, p, type = "decrease") {
   if(type == "decrease") f <- function(p) length(x[x < (-1 * p)]) / length(x)
   if(type == "increase") f <- function(p) length(x[x > p]) / length(x)

R/prepare-data.R

@@ -56,7 +56,7 @@ prepare_data <- function(strata_data,
   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){
+  if(strata_data$meta_data$stratify_by == "latlong" & min_n_routes > 1){
     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",
@@ -71,7 +71,7 @@ prepare_data <- function(strata_data,
   # Add in routes
   obs <- strata_data$routes_strata %>%
     dplyr::select("country_num", "state_num", "state", "rpid", "bcr", "year",
-                  "strata_name", "route", "obs_n") %>%
+                  "strata_name", "route", "obs_n","latitude","longitude") %>%
     dplyr::left_join(obs, by = c("route", "rpid", "year")) %>%
     dplyr::mutate(count = tidyr::replace_na(.data$count, 0))
 

R/run-model.R

@@ -104,9 +104,17 @@ run_model <- function(model_data,
   meta_data <- model_data[["meta_data"]]
   raw_data <- model_data[["raw_data"]]
   meta_strata <- model_data[["meta_strata"]]
+
   init_values <- model_data[["init_values"]]
   folds <- model_data[["folds"]]
   model_data <- model_data[["model_data"]]
+
+  if(model_data$n_strata < 2){
+    stop("The data have only 1 stratum. bbsBayes2 models require multiple strata.
+         If there are sufficient routes with data, you can try an alternate stratification
+         (e.g., latlong) where the routes may be redistributed among > 1 strata.")
+  }
+
   species <- stringr::str_remove_all(meta_data[["species"]],
                                       "[^[[:alpha:]]]")
 

data-raw/data_exported.R

@@ -16,7 +16,7 @@ usethis::use_data(species_forms, overwrite = TRUE)
 
 
 species_notes <- readr::read_csv("data-raw/species_notes.csv",
-                                 col_types = "ncc", locale = readr::locale(encoding = "latin1"),
+                                 col_types = "ccnnc", locale = readr::locale(encoding = "latin1"),
                                  progress = FALSE) %>%
   as.data.frame()
 

data-raw/example_model_fits.R

@@ -0,0 +1,75 @@
+
+library(bbsBayes2)
+library(tidyverse)
+
+species <- "Scissor-tailed Flycatcher"
+species <- "Arctic Warbler"
+
+# extract the unique numerical identifier for this species in the BBS database
+species_number <- search_species(species) %>%
+  select(aou) %>%
+  unlist()
+
+s <- stratify("bbs_usgs",
+              species = species) %>%
+  prepare_data()
+
+for(j in 1:nrow(bbs_models)){
+
+  mod <- as.character(bbs_models[j,"model"])
+  var <- as.character(bbs_models[j,"variant"])
+
+  if(var == "spatial"){
+  p <- prepare_spatial(s, strata_map = load_map("bbs_usgs")) %>%
+    prepare_model(model = mod, model_variant = var)
+  }else{
+  p <- prepare_model(s,model = mod,
+                     model_variant = var)
+}
+
+  m <- paste0("output/",
+                      species_number,
+                      "_",
+                      mod,
+                      "_",
+                      var)
+  m2 <- run_model(p,
+                 output_basename = m,
+                 output_dir = "vignettes/articles")
+
+}
+
+
+# latlong fits ------------------------------------------------------------
+
+
+
+s <- stratify("latlong",
+              species = species) %>%
+  prepare_data(min_n_routes = 1)
+
+for(j in 3){
+
+  mod <- as.character(bbs_models[j,"model"])
+  var <- as.character(bbs_models[j,"variant"])
+
+  if(var == "spatial"){
+    p <- prepare_spatial(s, strata_map = load_map("latlong")) %>%
+      prepare_model(model = mod, model_variant = var)
+  }else{
+    p <- prepare_model(s,model = mod,
+                       model_variant = var)
+  }
+
+  m <- paste0("output/",
+              species_number,
+              "_latlong_",
+              mod,
+              "_",
+              var)
+  m2 <- run_model(p,
+                  output_basename = m,
+                  output_dir = "vignettes/articles")
+
+}
+

data-raw/flow_diagram.R

@@ -0,0 +1,79 @@
+library(DiagrammeR)
+gri <- grViz("digraph functions {
+
+  # a 'graph' statement
+  graph [overlap = true, fontsize = 10 compound = true, ranksep = 0.5]
+
+  # several 'node' statements
+  node [shape = rectangle, fontname = 'Courier New',
+        fixedsize = false, style=filled, fillcolor=white]
+
+  fetch [label = 'fetch_bbs_data()', fillcolor=lightblue]
+  remove [label = 'remove_cache()', fillcolor=orange]
+  loadbbs [label = 'load_bbs_data()', fillcolor=lightblue]
+
+  search [label = 'search_species()', fillcolor=orange]
+  strat [label = 'stratify()', fillcolor=lightpink]
+  prepdata [label = 'prepare_data()', fillcolor=lightpink]
+  prepspatial [label = 'prepare_spatial()', fillcolor=lightpink]
+  prepmodel [label = 'prepare_model()', fillcolor=darkolivegreen3]
+  loadmap [label = 'load_map()', fillcolor=orange]
+  assign_ps [label = 'assign_prov_state()', fillcolor=orange]
+
+  runmodel [label = 'run_model()', fillcolor=darkolivegreen3]
+  modelfile [label = 'copy_model_file()', fillcolor=darkolivegreen3]
+
+  conv[label = 'save_model_run()\nget_convergence()\nget_model_vars()\nget_summary()', fillcolor=darkolivegreen3]
+
+  genind [label = 'generate_indices()', fillcolor=thistle]
+  gentre [label = 'generate_trends()', fillcolor=thistle]
+  geo [label = 'plot_geofacet()', fillcolor=thistle]
+  plotind [label = 'plot_indices()', fillcolor=thistle]
+  genmap [label = 'plot_map()', fillcolor=thistle]
+
+
+  # several 'edge' statements
+  edge []
+  fetch->remove [style=dashed]
+  fetch->loadbbs [style=dashed]
+  fetch->strat [style=dashed]
+
+  runmodel->remove [style=dashed]
+
+  modelfile->prepmodel [style=dashed]
+
+  search->strat [style=dashed]
+  strat->prepdata
+  prepdata->prepspatial
+  prepdata->prepmodel [color=grey50]
+  prepspatial->prepmodel [color=grey50]
+  prepmodel->runmodel
+
+
+  runmodel->conv
+  runmodel->genind
+  genind->gentre
+
+  loadmap->assign_ps  [style=dashed]
+  loadmap->genind [style=dashed]
+  loadmap->prepspatial [style=dashed]
+  loadmap->strat [style=dashed]
+
+  genind->plotind
+  genind->geo
+  gentre->geo [color=grey50]
+  gentre->genmap
+
+  # Invisible edges for arranging
+  prepspatial->conv [style=invis]
+}")
+
+
+export_graph(file_name = "flow_diagram.png",
+             graph = gri,
+             file_type = "png",
+    width = 1200,height = 1400)
+print(gri)
+dev.off()
+
+

data-raw/species_notes.csv

@@ -1,7 +1,7 @@
-aou,minimum_year,warning
-4661,1978,Alder and Willow Flycatcher were considered a single species until 1973. It is likely that they are not accurately separated by BBS observers until at least some years after that split.
-4660,1978,Alder and Willow Flycatcher were considered a single species until 1973. It is likely that they are not accurately separated by BBS observers until at least some years after that split.
-10,1990,Clark's and Western Grebe were considered a single species until 1985. It is likely that they are not accurately separated by BBS observers until at least some years after that split.
-10,1990,Clark's and Western Grebe were considered a single species until 1985. It is likely that they are not accurately separated by BBS observers until at least some years after that split.
-22860,1990,Eurasian Collared Dove was introduced into North America in the 1980s. 1990 is the first year that the species was observed on at least 3 BBS routes. 
-6121,1985,Cave Swallows were relatively rare in the areas surveyed by BBS before 1980. There are only two observations during BBS before 1980.
+english,french,aou,minimum_year,warning
+Alder Flycatcher,Moucherolle des aulnes,4661,1978,Alder and Willow Flycatcher were considered a single species until 1973. It is likely that they are not accurately separated by BBS observers until at least some years after that split.
+Willow Flycatcher,Moucherolle des saules,4660,1978,Alder and Willow Flycatcher were considered a single species until 1973. It is likely that they are not accurately separated by BBS observers until at least some years after that split.
+Clark's Grebe,Gr�be � face blanche,11,1990,Clark's and Western Grebe were considered a single species until 1985. It is likely that they are not accurately separated by BBS observers until at least some years after that split.
+Western Grebe,Gr�be �l�gant,10,1990,Clark's and Western Grebe were considered a single species until 1985. It is likely that they are not accurately separated by BBS observers until at least some years after that split.
+Eurasian Collared-Dove,Tourterelle turque,22860,1990,Eurasian Collared Dove was introduced into North America in the 1980s. 1990 is the first year that the species was observed on at least 3 BBS routes. 
+Cave Swallow,Hirondelle � front brun,6121,1985,Cave Swallows were relatively rare in the areas surveyed by BBS before 1980. There are only two observations during BBS before 1980.