fix(tests): change storing format of model object files from .json to…

… .RDS and updates test_visualization accordingly
epiverse-trace · Aug 15, 2023 · 034e63e · 034e63e
1 parent ec4335c
commit 034e63e
Show file tree

Hide file tree

Showing 9 changed files with 80 additions and 86 deletions.
diff --git a/tests/testthat/_snaps/visualisation/plot-arrange-simdata-foi.svg b/tests/testthat/_snaps/visualisation/plot-arrange-simdata-foi.svg
diff --git a/tests/testthat/extdata/model_constant.RDS b/tests/testthat/extdata/model_constant.RDS
diff --git a/tests/testthat/extdata/model_constant.json b/tests/testthat/extdata/model_constant.json
diff --git a/tests/testthat/extdata/model_tv_normal.RDS b/tests/testthat/extdata/model_tv_normal.RDS
diff --git a/tests/testthat/extdata/model_tv_normal.json b/tests/testthat/extdata/model_tv_normal.json
diff --git a/tests/testthat/extdata/model_tv_normal_log.RDS b/tests/testthat/extdata/model_tv_normal_log.RDS
diff --git a/tests/testthat/extdata/model_tv_normal_log.json b/tests/testthat/extdata/model_tv_normal_log.json
diff --git a/tests/testthat/models_serialization.R b/tests/testthat/models_serialization.R
@@ -1,13 +1,12 @@
 library(devtools)
-library(dplyr)
 library(serofoi)
 library(testthat)
 
 set.seed(1234) # For reproducibility
 
 #----- Read and prepare data
 data("simdata_large_epi")
-simdata <- simdata_large_epi %>% prepare_serodata()
+simdata <- prepare_serodata(simdata_large_epi)
 no_transm <- 0.0000000001
 big_outbreak   <- 1.5
 foi_sim <- c(rep(no_transm, 32), rep(big_outbreak, 3), rep(no_transm, 15)) # 1 epidemics
@@ -23,11 +22,12 @@ models_list <- lapply(models_to_run,
                       serodata = simdata,
                       n_iters = 1000)
 
-model_constant_json <- jsonlite::serializeJSON(models_list[[1]])
-write_json(model_constant_json, testthat::test_path("extdata", "model_constant.json"))
+saveRDS(models_list[[1]],
+        testthat::test_path("extdata", "model_constant.RDS"))
 
-model_tv_normal_json <- jsonlite::serializeJSON(models_list[[2]])
-write_json(model_tv_normal_json, testthat::test_path("extdata", "model_tv_normal.json"))
+saveRDS(models_list[[2]],
+        testthat::test_path("extdata", "model_tv_normal.RDS"))
+
+saveRDS(models_list[[3]],
+        testthat::test_path("extdata", "model_tv_normal_log.RDS"))
 
-model_tv_normal_log_json <- jsonlite::serializeJSON(models_list[[3]])
-write_json(model_tv_normal_json, testthat::test_path("extdata", "model_tv_normal_log.json"))
diff --git a/tests/testthat/test_visualisation.R b/tests/testthat/test_visualisation.R
@@ -24,28 +24,25 @@ test_that("individual models", {
   size_text <- 6
   max_lambda <- 1.55
 
-  model_constant_json <- jsonlite::fromJSON(testthat::test_path("extdata", "model_constant.json"))
-  model_constant <- jsonlite::unserializeJSON(model_constant_json)
-  constant_plot <- plot_seromodel(model_constant,
-    size_text = size_text,
-    max_lambda = max_lambda,
-    foi_sim = foi_sim
+  model_constant <- readRDS(testthat::test_path("extdata", "model_constant.RDS"))
+  constant_plot <- plot_seromodel(seromodel_object = model_constant,
+                                  size_text = size_text,
+                                  max_lambda = max_lambda,
+                                  foi_sim = foi_sim
   )
 
-  model_tv_normal_json <- fromJSON(testthat::test_path("extdata", "model_tv_normal.json"))
-  model_tv_normal <- jsonlite::unserializeJSON(model_tv_normal_json)
-  tv_normal_plot <- plot_seromodel(model_tv_normal,
-    size_text = size_text,
-    max_lambda = max_lambda,
-    foi_sim = foi_sim
+  model_tv_normal <- readRDS(testthat::test_path("extdata", "model_tv_normal.RDS"))
+  tv_normal_plot <- plot_seromodel(seromodel_object = model_tv_normal,
+                                   size_text = size_text,
+                                   max_lambda = max_lambda,
+                                   foi_sim = foi_sim
   )
 
-  model_tv_normal_log_json <- fromJSON(testthat::test_path("extdata", "model_tv_normal_log.json"))
-  model_tv_normal_log <- jsonlite::unserializeJSON(model_tv_normal_log_json)
-  tv_normal_log_plot <- plot_seromodel(model_tv_normal_log,
-    size_text = size_text,
-    max_lambda = max_lambda,
-    foi_sim = foi_sim
+  model_tv_normal_log <- readRDS(testthat::test_path("extdata", "model_tv_normal_log.RDS"))
+  tv_normal_log_plot <- plot_seromodel(seromodel_object = model_tv_normal_log,
+                                       size_text = size_text,
+                                       max_lambda = max_lambda,
+                                       foi_sim = foi_sim
   )
 
   plot_arrange <- cowplot::plot_grid(constant_plot,