fix tests for CRAN

ModelOriented · Sep 4, 2019 · 99582f4 · 99582f4
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: modelStudio
 Title: Interactive Studio with Explanations for ML Predictive Models
-Version: 0.1.6
+Version: 0.1.7
 Authors@R:
     c(person("Hubert", "Baniecki", role = c("aut", "cre"), email = "hbaniecki@gmail.com"),
       person("Przemyslaw", "Biecek", role = c("aut"), 

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+# modelStudio 0.1.7
+* fix tests for CRAN
+
 # modelStudio 0.1.6
 Many minor changes stated in #20, most notably:
 * rename `x` parameter to `object` in `modelStudio()`

diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/vignette_modelStudio.html b/docs/articles/vignette_modelStudio.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/modelStudio.html b/docs/reference/modelStudio.html
diff --git a/docs/reference/modelStudioOptions.html b/docs/reference/modelStudioOptions.html
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,4 +1,6 @@
-library(testthat)
-library(modelStudio)
+library("testthat")
+library("modelStudio")
+library("DALEX")
+library("randomForest")
 
 test_check("modelStudio")
diff --git a/tests/testthat/test_modelStudio.R b/tests/testthat/test_modelStudio.R
@@ -1,18 +1,18 @@
 context("Check modelStudio() function")
-library(DALEX)
+
 source("test_objects.R")
 
-ms1 <- modelStudio(explain_glm,
+ms1 <- modelStudio::modelStudio(explain_glm,
                    new_observation = titanic_test[1,-9])
 
-ms2 <- modelStudio(model_glm,
+ms2 <- modelStudio::modelStudio(model_glm,
                    max_features = 5,
                    data = titanic_test[,-9],
                    y = titanic_test$survived == "yes",
                    new_observation = titanic_test[1:2,-9],
                    N = 50, B = 10)
 
-ms3 <- modelStudio(model_glm,
+ms3 <- modelStudio::modelStudio(model_glm,
                    max_features = 5,
                    facet_dim = c(2,3),
                    N = 150,
@@ -23,108 +23,108 @@ ms3 <- modelStudio(model_glm,
                    label = "xxx",
                    new_observation = titanic_test[1:10,-9])
 
-ms4 <- modelStudio(explain_glm_numerical,
+ms4 <- modelStudio::modelStudio(explain_glm_numerical,
                    new_observation = titanic_test[1:2, c(2,6,7,8)],
                    N = 50, B = 10)
 
-ms5 <- modelStudio(explain_glm_not_numerical,
+ms5 <- modelStudio::modelStudio(explain_glm_not_numerical,
                    new_observation = titanic_test[1:2, c(1,3,4,5)],
                    N = 50, B = 10)
 
-ms6 <- modelStudio(explain_model_small,
+ms6 <- modelStudio::modelStudio(explain_model_small,
                    new_observation = titanic_test[1:2, c(1,2)],
                    N = 50, B = 10)
 
-ms_readme <-  modelStudio(explain_titanic_glm,
+ms_readme <-  modelStudio::modelStudio(explain_titanic_glm,
                           new_observations,
                           facet_dim = c(2,2), N = 200, B = 20, time = 0)
 
-ms_rf_apartments <- modelStudio(explain_rf,
+ms_rf_apartments <- modelStudio::modelStudio(explain_rf,
                                 new_observation = apartments[1:2,-1],
                                 N = 50, B = 10, facet_dim = c(3,3),
                                 time = 50, max_features = 4)
 
-both_without_target <- modelStudio(model_titanic_glm,
+both_without_target <- modelStudio::modelStudio(model_titanic_glm,
                                    new_observation = nx,
                                    N = 10,
                                    B = 2,
                                    data = x,
                                    y = y)
 
-both_full <- modelStudio(model_titanic_glm,
+both_full <- modelStudio::modelStudio(model_titanic_glm,
                          new_observation = nz,
                          N = 10,
                          B = 2,
                          data = z,
                          y = y)
 
-obs_without_target_data_full <- modelStudio(model_titanic_glm,
+obs_without_target_data_full <- modelStudio::modelStudio(model_titanic_glm,
                                             new_observation = nx,
                                             N = 10,
                                             B = 2,
                                             data = z,
                                             y = y)
 
-obs_full_data_without_target <- modelStudio(model_titanic_glm,
+obs_full_data_without_target <- modelStudio::modelStudio(model_titanic_glm,
                                             new_observation = nz,
                                             N = 10,
                                             B = 2,
                                             data = x,
                                             y = y)
 
-ms_big <- modelStudio(explain_artifficial,
+ms_big <- modelStudio::modelStudio(explain_artifficial,
                       new_observation = artifficial[1:2,], N = 5, B = 2,
                       facet_dim = c(3,3))
 
-ms_parallel <- modelStudio(explain_glm, new_observation = titanic_test[1:2,-9],
+ms_parallel <- modelStudio::modelStudio(explain_glm, new_observation = titanic_test[1:2,-9],
                            N = 5, B = 2, parallel = TRUE)
 
-ms_parallel_rf <- modelStudio(explain_rf, new_observation = apartments[1:5,-1],
+ms_parallel_rf <- modelStudio::modelStudio(explain_rf, new_observation = apartments[1:5,-1],
                               N = 5, B = 2, parallel = TRUE)
 
 # tests
 
-test_that("explainer/model test", {
-  expect_is(ms1, "r2d3")
-  expect_is(ms2, "r2d3")
-  expect_is(ms3, "r2d3")
+testthat::test_that("explainer/model test", {
+  testthat::expect_is(ms1, "r2d3")
+  testthat::expect_is(ms2, "r2d3")
+  testthat::expect_is(ms3, "r2d3")
 })
 
-test_that("only_numerical", {
-  expect_is(ms4, "r2d3")
+testthat::test_that("only_numerical", {
+  testthat::expect_is(ms4, "r2d3")
 })
 
-test_that("only_not_numerical", {
-  expect_is(ms5, "r2d3")
+testthat::test_that("only_not_numerical", {
+  testthat::expect_is(ms5, "r2d3")
 })
 
-test_that("description test, 2 features", {
-  expect_is(ms6, "r2d3")
+testthat::test_that("description test, 2 features", {
+  testthat::expect_is(ms6, "r2d3")
 })
 
-test_that("README DEMO", {
-  expect_is(ms_readme, "r2d3")
+testthat::test_that("README DEMO", {
+  testthat::expect_is(ms_readme, "r2d3")
 })
 
-test_that("randomForest apartments", {
-  expect_is(ms_rf_apartments, "r2d3")
+testthat::test_that("randomForest apartments", {
+  testthat::expect_is(ms_rf_apartments, "r2d3")
 })
 
-test_that("test various possibilities of data and new obs", {
-  expect_is(both_full, "r2d3")
-  expect_is(both_without_target, "r2d3")
-  expect_is(obs_without_target_data_full, "r2d3")
-  expect_is(obs_full_data_without_target, "r2d3")
+testthat::test_that("test various possibilities of data and new obs", {
+  testthat::expect_is(both_full, "r2d3")
+  testthat::expect_is(both_without_target, "r2d3")
+  testthat::expect_is(obs_without_target_data_full, "r2d3")
+  testthat::expect_is(obs_full_data_without_target, "r2d3")
 })
 
-test_that("more than 10 features", {
-  expect_is(ms_big, "r2d3")
+testthat::test_that("more than 10 features", {
+  testthat::expect_is(ms_big, "r2d3")
 })
 
-test_that("parallel", {
-  expect_is(ms_parallel, "r2d3")
+testthat::test_that("parallel", {
+  testthat::expect_is(ms_parallel, "r2d3")
 })
 
-test_that("parallel rf", {
-  expect_is(ms_parallel_rf, "r2d3")
+testthat::test_that("parallel rf", {
+  testthat::expect_is(ms_parallel_rf, "r2d3")
 })
diff --git a/tests/testthat/test_modelStudioOptions.R b/tests/testthat/test_modelStudioOptions.R
@@ -1,15 +1,15 @@
 context("Check options parameter and modelStudioOptions() function")
-library(DALEX)
+
 source("test_objects.R")
 
-op <- modelStudioOptions()
+op <- modelStudio::modelStudioOptions()
 
-test_that("modelStudioOptions()", {
-  expect_is(op, "list")
-  expect_true(length(op) > 30)
+testthat::test_that("modelStudioOptions()", {
+  testthat::expect_is(op, "list")
+  testthat::expect_true(length(op) > 30)
 })
 
-new_options <- modelStudioOptions(
+new_options <- modelStudio::modelStudioOptions(
   scale_plot = FALSE,
   show_subtitle = TRUE,
   subtitle = "hello",
@@ -73,10 +73,10 @@ new_options <- modelStudioOptions(
   fd_bar_color = NULL
 )
 
-ms <- modelStudio(explain_rf, apartments[1:2,],
+ms <- modelStudio::modelStudio(explain_rf, apartments[1:2,],
                   facet_dim = c(2,3), N = 5, B = 2, show_info = FALSE,
                   options = new_options)
 
-test_that("options parameter", {
-  expect_is(ms, "r2d3")
+testthat::test_that("options parameter", {
+  testthat::expect_is(ms, "r2d3")
 })
diff --git a/tests/testthat/test_objects.R b/tests/testthat/test_objects.R
@@ -1,8 +1,4 @@
-# preparation
-library("modelStudio")
-library("DALEX")
-
-titanic <- na.omit(titanic)
+titanic <- na.omit(DALEX::titanic)
 set.seed(1313)
 
 
@@ -61,9 +57,7 @@ explain_model_small <- DALEX::explain(model_small,
 
 ### randomForest + apartments
 
-library("randomForest")
-
-model_rf <- randomForest(m2.price ~. , data = apartments)
+model_rf <- randomForest::randomForest(m2.price ~. , data = apartments)
 explain_rf <- DALEX::explain(model_rf,
                       data = apartments,
                       y = apartments$m2.price, verbose = TRUE)