Merge pull request #40 from PetterHopp/dev

NVIdb v0.11.1
NorwegianVeterinaryInstitute · Feb 5, 2024 · 0835838 · 0835838
2 parents efe8b55 + 2bbda02
commit 0835838
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: NVIdb
 Title: Tools to facilitate the use of NVI's databases
-Version: 0.11.0.9000
-Date: 2024-##-##
+Version: 0.11.1
+Date: 2024-02-05
 Authors@R: 
   c(person(given = "Petter",
            family = "Hopp",

diff --git a/NEWS b/NEWS
@@ -1,24 +1,14 @@
-NVIdb 0.11.0.9000 - (2024-##-##)
+NVIdb 0.11.1 - (2024-02-05)
 ----------------------------------------
 
 New features:
 
--
+- set_disease_parameters now accepts the arguments purpose, FUN and select_statement.
 
 
 Bug fixes:
 
--
-
-
-Other changes:
-
--
-
-
-BREAKING CHANGES:
-
--
+- set_disease_parameters now accepts metodekode with 2 digits.
 
 
 NVIdb 0.11.0 - (2024-01-24)

diff --git a/tests/testthat/test_PJS_code_description.R b/tests/testthat/test_PJS_code_description.R
@@ -246,52 +246,52 @@ test_that("Backward translation from description to code", {
 # })
 
 test_that("errors for add_PJS_code_description", {
-  
+
   linewidth <- options("width")
   options(width = 80)
-  
+
   # skip if no connection to 'FAG' have been established
   skip_if_not(dir.exists(set_dir_NVI("FAG")))
-  
+
   # Reads translation table for PJS-codes
   PJS_codes_2_text <- read_PJS_codes_2_text()
-  
-  testdata <- as.data.frame(list("hensiktkode" =  c("01001", "01002"),
+
+  testdata <- as.data.frame(list("hensiktkode" = c("01001", "01002"),
                                   "metodekode" = c("010001", "010002"),
                                   "ansvarlig_seksjon" = c("01", "02")))
-  
+
   expect_error(add_PJS_code_description("testdata",
                                         translation_table = PJS_codes_2_text,
                                         code_colname = c("hensiktkode", "metodekode", "ansvarlig_seksjon"),
                                         PJS_variable_type = c("hensikt", "metode", "seksjon"),
                                         new_column = c("hensikt", "metode", "seksjon")),
                regexp = "Variable 'data': Must be of type 'data.frame', not 'character'.",
                fixed = TRUE)
-  
+
   expect_error(add_PJS_code_description(testdata,
                                         translation_table = PJS_codes_2_text,
                                         code_colname = c("hensiktkoder"),
                                         PJS_variable_type = c("hensikt"),
                                         new_column = c("hensikt")),
                regexp = "but 'hensiktkoder' is not a column in the data.",
                fixed = TRUE)
-  
+
   expect_error(add_PJS_code_description(testdata,
                                         translation_table = PJS_codes_2_text,
                                         code_colname = c("hensiktkode"),
                                         PJS_variable_type = c("hensikter"),
                                         new_column = c("hensikt")),
                regexp = "Variable 'PJS_variable_type': Must be a subset of",
                fixed = TRUE)
-  
+
   expect_error(add_PJS_code_description(testdata,
                                         translation_table = PJS_codes_2_text,
                                         code_colname = c("hensiktkode"),
                                         PJS_variable_type = c("hensikt"),
                                         new_column = c("metodekode")),
                regexp = "The column name(s): 'metodekode' already exist in 'testdata`.",
                fixed = TRUE)
-  
+
   options(width = unlist(linewidth))
 })
 

diff --git a/tests/testthat/test_Prodtilskudd.R b/tests/testthat/test_Prodtilskudd.R
@@ -102,20 +102,20 @@ test_that("errors for copy_Prodtilskudd", {
 })
 
 test_that("errors for copy_Prodtilskudd with extracted_date", {
-  
+
   linewidth <- options("width")
   options(width = 80)
-  
+
   expect_error(copy_Prodtilskudd(from_path = tempdir(), to_path = "./", Pkode_year = "last",
                                  Pkode_month = "10", extracted_date = "2023-03-31"),
                regexp = "Contains only missing values. The input 'last' is",
                fixed = TRUE)
-  
-  expect_error(copy_Prodtilskudd(from_path = tempdir(), to_path = "./", Pkode_year = 2020, 
+
+  expect_error(copy_Prodtilskudd(from_path = tempdir(), to_path = "./", Pkode_year = 2020,
                                  Pkode_month = "both", extracted_date = "2023-03-31"),
                regexp = "The inputs 'both' and 'last' are not accepted when",
                fixed = TRUE)
-  
+
   options(width = unlist(linewidth))
 })
 

diff --git a/tests/testthat/test_login.R b/tests/testthat/test_login.R
@@ -41,19 +41,19 @@ test_that("Errors or warnings for login", {
 test_that("Errors or warnings for login_EOS", {
   linewidth <- options("width")
   options(width = 80)
-  
+
   expect_error(login_EOS(dbinterface = "noodbc"),
                regexpr = "Variable 'dbinterface': Must be element of set")
-  
+
   options(width = unlist(linewidth))
 })
 
 test_that("Errors or warnings for login_PJS", {
   linewidth <- options("width")
   options(width = 80)
-  
+
   expect_error(login_PJS(dbinterface = "noodbc"),
                regexpr = "Variable 'dbinterface': Must be element of set")
-  
+
   options(width = unlist(linewidth))
 })
diff --git a/tests/testthat/test_set_disease_parameters.R b/tests/testthat/test_set_disease_parameters.R
@@ -93,7 +93,7 @@ test_that("set disease parameters by direct input", {
                                        missing_art = "non_selected_hensikt"),
                                regexp = "The argument 'missing_art' is deprecated.",
                                fixed = TRUE)
-                               
+
   expect_equal(parameters,
                list("purpose" = NULL,
                     "hensikt2select" = c("0100108018", "0100109003", "0100111003"),
@@ -252,15 +252,15 @@ test_that("errors for set_disease_parameters", {
                                       art2select = c("05%", NA),
                                       include_missing_art = "yes"),
                regexp = "Variable 'include_missing_art': Must be element of set")
-  
+
   expect_error(set_disease_parameters(purpose = NA,
                                       hensikt2delete = "0100108018",
                                       analytt2select = "01220104%",
                                       utbrudd2select = "2",
                                       art2select = c("05%", NA),
                                       include_missing_art = "always"),
                regexp = "Variable 'purpose': May not be NA")
-  
+
   expect_error(set_disease_parameters(purpose = 1,
                                       hensikt2delete = "0100108018",
                                       analytt2select = "01220104%",
@@ -269,7 +269,7 @@ test_that("errors for set_disease_parameters", {
                                       include_missing_art = "always"),
                regexp = "Variable 'purpose': Must be of type 'string' (or 'NULL')",
                fixed = TRUE)
-  
+
   expect_error(set_disease_parameters(purpose = "ok_storfe_virus",
                                       hensikt2delete = "0100108018",
                                       analytt2select = "01220104%",
@@ -280,7 +280,7 @@ test_that("errors for set_disease_parameters", {
                                       select_statement = 1),
                regexp = "Must be of type 'string', * not 'double'",
                fixed = TRUE)
-  
+
   expect_error(set_disease_parameters(purpose = "ok_storfe_virus",
                                       hensikt2delete = "0100108018",
                                       analytt2select = "01220104%",
@@ -291,7 +291,6 @@ test_that("errors for set_disease_parameters", {
                                       select_statement = NULL),
                regexp = "Must be a function (or 'NULL'), not 'character'",
                fixed = TRUE)
-  
+
   options(width = unlist(linewidth))
 })
-
diff --git a/vignettes/NVIdb.pdf b/vignettes/NVIdb.pdf