Merge pull request #185 from allometric/lfs

Implementing model.RDS download

.Rbuildignore

@@ -7,7 +7,7 @@
 ^pkgdown$
 ^_pkgdown\.yml$
 ^inst/extdata/allometric_models\.RDS$
-^inst/extdata/pub_list\.RDS$
+^inst/extdata/params_path\.RDS$
 ^LICENSE\.md$
 ^README\.Rmd$
 ^Meta$

NAMESPACE

@@ -22,6 +22,7 @@ export(check_models_installed)
 export(get_component_defs)
 export(get_measure_defs)
 export(get_variable_def)
+export(ingest_models)
 export(install_models)
 export(load_models)
 export(load_parameter_frame)

R/install.R

@@ -108,41 +108,45 @@ download_models <- function(verbose) {
 #' \href{https://github.com/allometric/models}{here}. The user must install
 #' these models themselves using this function. This function clones the models
 #' repository within the allometric package directory and constructs a local
-#' dataframe containing the models. This dataframe is stored in the global
-#' environment variable `allometric_models` upon completion of the function.
-#' Refer to `allometric::allometric_models` for further information.
+#' dataframe containing the models. Refer to `load_models()` for information
+#' about loading the models dataframe.
 #'
+#' @param ingest If `TRUE`, model publication files are run locally, otherwise
+#' a previously prepared `.RDS` file is used as the models data.
 #' @param redownload If `TRUE`, models are re-downloaded from the remote
 #' repository.
-#' @param ignore_cache If `TRUE`, models are re-installed regardless of their
-#' installation timestamp. Otherwise, only newly modified model files are reran.
-#' This is primarily for development purposes.
 #' @param verbose If `TRUE`, print verbose messages as models are installed.
 #' @return No return value, installs models into the package directory.
 #' @export
-install_models <- function(redownload = FALSE,
-    ignore_cache = FALSE, verbose = TRUE
-  ) {
+install_models <- function(ingest = FALSE, redownload = TRUE, verbose = TRUE) {
   downloaded <- check_models_downloaded(verbose)
 
-  if(!downloaded || redownload) {
+  if (!downloaded || redownload) {
     download_models(verbose)
   }
 
-  allometric_models <- ingest_models(verbose)
+  if (ingest) {
+    models <- ingest_models(verbose)
 
-  out_path <- file.path(
-    system.file("extdata", package = "allometric"), "allometric_models.RDS"
-  )
+    out_path <- file.path(
+      system.file("models-main", package = "allometric"), "models.RDS"
+    )
 
-  if(verbose) {
-    n_models <- nrow(allometric_models)
+    saveRDS(models, out_path)
+  } else {
+    models <- readRDS(
+      file.path(
+        system.file("models-main", package = "allometric"), "models.RDS"
+      )
+    )
+  }
+
+  if (verbose) {
+    n_models <- nrow(models)
     msg <- paste(
       n_models,
-      "models succesfully installed, use load_models() to view them.\n"
+      "models are currently installed, use load_models() to view them.\n"
     )
     cat(msg)
   }
-
-  saveRDS(allometric_models, out_path)
 }

R/load.R

@@ -9,20 +9,33 @@
 #' @export
 load_parameter_frame <- function(name) {
   csv_name <- paste(name, ".csv", sep = "")
-
-  if(allometric_options$param_search_path == "package") {
+  param_search_path <- read_params_path()
+
+  if(param_search_path == "package") {
     file_path <- system.file(
       "models-main/parameters", csv_name,
       package = "allometric"
     )
   } else {
-    file_path <- file.path(allometric_options$param_search_path, csv_name)
+    file_path <- file.path(param_search_path, csv_name)
   }
 
   table <- utils::read.csv(file_path, na.strings = "")
   tibble::as_tibble(table)
 }
 
+write_params_path_rds <- function(params_path) {
+  params_path <- list(params_path = params_path)
+  rds_path <- file.path(system.file("extdata", package = "allometric"), "params_path.RDS")
+  saveRDS(params_path, rds_path)
+}
+
+read_params_path <- function() {
+  rds_path <- file.path(system.file("extdata", package = "allometric"), "params_path.RDS")
+  rds <- readRDS(rds_path)
+  rds$params_path
+}
+
 my_function <- function(family, genus, species) {
   Taxa(
     Taxon(
@@ -220,7 +233,7 @@ aggregate_taxa <- function(table, remove_taxa_cols = TRUE) {
 #' @export
 load_models <- function() {
   rds_path <- system.file(
-    "extdata/allometric_models.RDS",
+    "models-main/models.RDS",
     package = "allometric"
   )
 

R/publication_processing.R

@@ -131,7 +131,7 @@ map_publications <- function(verbose, func, pub_path = NULL, params_path = NULL)
   }
 
   if(!is.null(params_path)) {
-    allometric_options[["param_search_path"]] <- params_path
+    write_params_path_rds(params_path)
   }
 
   pub_specs <- get_pub_file_specs(pub_path)
@@ -158,7 +158,14 @@ map_publications <- function(verbose, func, pub_path = NULL, params_path = NULL)
       pub <- get(pub_name, envir = pub_env)
       output[[pub_name]] <- func(pub)
     }, error = function(e) {
-      warning(paste("Publication file", pub_name, "encountered an error during execution."))
+      warning(
+        paste(
+          "Publication file",
+          pub_name,
+          "encountered an error during execution:",
+          e
+        )
+      )
     })
 
     if (verbose) {
@@ -171,12 +178,17 @@ map_publications <- function(verbose, func, pub_path = NULL, params_path = NULL)
 
   # reset the param search path
   if(!is.null(params_path)) {
-    allometric_options[["param_search_path"]] <- "package"
+    write_params_path_rds("pacakge")
   }
 
   output
 }
 
+#' Ingest a set of models by running the publication files
+#'
+#' @param pub_path A path to a directory containing publication files
+#' @param params_path A path to a directory containing parameter files
+#' @export
 ingest_models <- function(verbose, pub_path = NULL, params_path = NULL) {
   out_order <- c(
     "id", "model_type", "country", "region", "taxa"

R/zzz.R

@@ -43,6 +43,4 @@ suffixes <- utils::read.csv(
 
 var_defs <- prepare_var_defs(var_defs_pre, measure_defs, component_defs)
 
-allometric_options <- list(
-  param_search_path = "package"
-)
+write_params_path_rds("package")

_pkgdown.yml

@@ -2,6 +2,10 @@ url: http://allometric.github.io/allometric
 template:
   params:
     bootswatch: cosmo
+navbar:
+  structure:
+    left: [intro, reference, articles]
+    right: [search, github]
 reference:
 - title: Analysis Functions
   desc: These functions are used to conduct inventory analysis with allometric models and inspect their contents.
@@ -37,6 +41,7 @@ reference:
   - get_variable_def
   - get_component_defs
   - get_measure_defs
+  - ingest_models
   - load_parameter_frame
   - map_publications
   - FixedEffectsModel