Rename TaxonLHTCollector to TaxonLHTPredictedGetter

NAMESPACE

@@ -5,8 +5,8 @@ export(FishlifeLHTNameSpace)
 export(MixinUtilities)
 export(PredictedLHTPicker)
 export(TaxaUpdateExtractor)
-export(TaxonLHTCollector)
 export(TaxonLHTPredictor)
+export(TaxonPredictedLHTGetter)
 export(TaxonUpdateExtractor)
 export(UpdatedLHTGenerator)
 export(UpdatedLHTPicker)

R/predicted_lht_picker.R

@@ -32,7 +32,7 @@ PredictedLHTPicker <- R6::R6Class("PredictedLHTPicker", inherit = MixinUtilities
   pick_and_backtransform = function() {
     results <- self$wanted_lht_df
     for (ind_taxon in self$wanted_lht_df$taxon) {
-      taxon_grabber <- TaxonLHTCollector$new(self$master_db, ind_taxon)
+      taxon_grabber <- TaxonPredictedLHTGetter$new(self$master_db, ind_taxon)
       taxon_details <- taxon_grabber$extract()
       subset_estimated_lhts <- private$subset_taxon_detail_matrix(taxon_details$estimated_lhts)
       results <- private$backtransform_and_fill_user_df(subset_estimated_lhts, ind_taxon, results)

R/taxon_lht_collector.R → R/taxon_predicted_lht_getter.R

@@ -1,8 +1,8 @@
 #' Single Taxon LHT GRABBER class
 #'
 #' @description
-#' Class that abstracts away the underlying FishLife dynamics and grab the details of a given taxon
-TaxonLHTCollector <- R6::R6Class("TaxonLHTCollector", public = list(
+#' Abstracts away the underlying FishLife dynamics and grab the predicted LHT details of a given taxon
+TaxonPredictedLHTGetter <- R6::R6Class("TaxonPredictedLHTGetter", public = list(
 
   master_db = NULL,
   taxon = NULL,

R/updated_lht_generator.R

@@ -1,27 +1,27 @@
 #' Multiple Updated LHT Generator class
 #'
 #' @description
-#' Class that allows the streamline-generation of predicted LHTs given new data.
+#' Allows the streamline-generation of updated LHTs given new data.
 UpdatedLHTGenerator <- R6::R6Class("UpdatedLHTGenerator", public = list(
 
   master_db = NULL,
   predicting_lht_df = NULL,
-  func_domains = NULL,
+  transform_function_list = NULL,
   lht_names = NULL,
   # // @formatter:off
   #' @description
   #' Initialise the Updated LHT Generator class
   #'
   #' @param master_db Fishlife database
   #' @param predicting_lht_df dataframe providing the taxon details and their predicting LHT values
-  #' @param func_domains list of transforming function which names must conform to FishLife's expectations
+  #' @param transform_function_list list of transforming function which names must conform to FishLife's expectations
   #' @param lht_names list of user-defined LHT names associated with their FishLife's counterparts
   #' @export
   # // @formatter:on
-  initialize = function(master_db, predicting_lht_df, func_domains, lht_names) {
+  initialize = function(master_db, predicting_lht_df, transform_function_list, lht_names) {
     self$master_db <- master_db
     self$predicting_lht_df <- predicting_lht_df
-    self$func_domains <- func_domains
+    self$transform_function_list <- transform_function_list
     self$lht_names <- lht_names
   },
   # // @formatter:off
@@ -97,7 +97,7 @@ UpdatedLHTGenerator <- R6::R6Class("UpdatedLHTGenerator", public = list(
     updated_lhts <- list()
     for (ind_species in names(all_species_local_lhts)) {
       species_local_lhts <- all_species_local_lhts[[ind_species]]
-      taxon_extractor <- TaxonLHTCollector$new(self$master_db, ind_species)
+      taxon_extractor <- TaxonPredictedLHTGetter$new(self$master_db, ind_species)
       taxon_details <- taxon_extractor$extract()
       if (is.null(taxon_details)) {
         stop(paste("Unable to find life history traits for taxa", ind_species))
@@ -106,7 +106,7 @@ UpdatedLHTGenerator <- R6::R6Class("UpdatedLHTGenerator", public = list(
                                                taxon_details$estimated_lhts,
                                                taxon_details$estimated_covariance,
                                                species_local_lhts,
-                                               self$func_domains)
+                                               self$transform_function_list)
       updated_lhts[[ind_species]] <- taxon_predictor$predict()
     }
     return(updated_lhts)

tests/testthat/test-taxon_lht_predictor.R

@@ -5,7 +5,7 @@ test_that("Testing sample data is loaded properly", {
 
 
 test_that("Predict LHT for a specific taxa", {
-  t_extractor <- TaxonLHTCollector$new(testing_db, "Trisopterus luscus")
+  t_extractor <- TaxonPredictedLHTGetter$new(testing_db, "Trisopterus luscus")
   t.luscus_details <- t_extractor$extract()
   estimated_lhts <- t.luscus_details$estimated_lhts
   estimated_covariance <- t.luscus_details$estimated_covariance

tests/testthat/test-taxon_lht_collector.R → tests/testthat/test-taxon_predicted_lht_getter.R

@@ -1,19 +1,19 @@
 test_that("Unable to find specific species", {
-  t_extractor <- TaxonLHTCollector$new(testing_db, "I do not exist as species")
+  t_extractor <- TaxonPredictedLHTGetter$new(testing_db, "I do not exist as species")
   species_details <- t_extractor$extract()
   expect_equal(is.null(species_details), TRUE)
 })
 
 test_that("Specific species is found", {
-  t_extractor <- TaxonLHTCollector$new(testing_db, "Trisopterus luscus")
+  t_extractor <- TaxonPredictedLHTGetter$new(testing_db, "Trisopterus luscus")
   species_details <- t_extractor$extract()
   expect_equal(is.null(species_details), FALSE)
 })
 
 test_that("Taxon is found and is different to species", {
-  t_extractor <- TaxonLHTCollector$new(testing_db, "Trisopterus")
+  t_extractor <- TaxonPredictedLHTGetter$new(testing_db, "Trisopterus")
   taxon_details <- t_extractor$extract()
-  t_extractor <- TaxonLHTCollector$new(testing_db, "Trisopterus luscus")
+  t_extractor <- TaxonPredictedLHTGetter$new(testing_db, "Trisopterus luscus")
   species_details <- t_extractor$extract()
   expect_equal(is.null(taxon_details), FALSE)
   expect_equal(is.null(species_details), FALSE)

tests/testthat/test-taxon_update_extractor.R

@@ -1,7 +1,7 @@
 test_that("Extraction and backtransformation of predicted LHT values", {
 
   # (1) Fetch ...
-  t_extractor <- TaxonLHTCollector$new(testing_db, "Trisopterus luscus")
+  t_extractor <- TaxonPredictedLHTGetter$new(testing_db, "Trisopterus luscus")
   t.luscus_details <- t_extractor$extract()
 
   estimated_lhts <- t.luscus_details$estimated_lhts