diff --git a/.github/workflows/dsBaseClient_test_suite.yaml b/.github/workflows/dsBaseClient_test_suite.yaml index 17e13f1d..93c12871 100644 --- a/.github/workflows/dsBaseClient_test_suite.yaml +++ b/.github/workflows/dsBaseClient_test_suite.yaml @@ -138,7 +138,7 @@ jobs: - name: Install dsBase to Armadillo run: | curl -u admin:admin -X GET http://localhost:8080/packages - curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.5-permissive.tar.gz" -X POST http://localhost:8080/install-package + curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.6-permissive.tar.gz" -X POST http://localhost:8080/install-package sleep 60 docker restart dsbaseclient-armadillo-1 sleep 30 diff --git a/DESCRIPTION b/DESCRIPTION index c4c92403..fe6adacb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -81,6 +81,6 @@ Suggests: DSOpal, DSMolgenisArmadillo, DSLite -RoxygenNote: 7.3.3 Encoding: UTF-8 Language: en-GB +Config/roxygen2/version: 8.0.0 diff --git a/R/ds.glm.R b/R/ds.glm.R index 8b1dbceb..09c4453f 100644 --- a/R/ds.glm.R +++ b/R/ds.glm.R @@ -565,7 +565,8 @@ ds.glm <- function(formula=NULL, data=NULL, family=NULL, offset=NULL, weights=NU # Sum participants only during first iteration. nsubs.total<-Reduce(f="+", .select(study.summary, 'numsubs')) # Save family - f <- study.summary[[1]]$family + family.value <- study.summary[[1]]$family + f <- if (is.list(family.value) && "family" %in% names(family.value)) family.value$family else family.value } #Create variance covariance matrix as inverse of information matrix @@ -640,7 +641,7 @@ ds.glm <- function(formula=NULL, data=NULL, family=NULL, offset=NULL, weights=NU beta.vect.final<-beta.vect.next scale.par <- 1 - if(f$family== 'gaussian') { + if(f == 'gaussian') { scale.par <- dev.total / (nsubs.total-length(beta.vect.next)) } diff --git a/armadillo_azure-pipelines.yml b/armadillo_azure-pipelines.yml index 16fe68da..76e4947c 100644 --- a/armadillo_azure-pipelines.yml +++ b/armadillo_azure-pipelines.yml @@ -133,7 +133,7 @@ jobs: sudo apt-get upgrade -y sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y - sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y + sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')" diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 7d3c7b7b..3d0a79a5 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -114,7 +114,7 @@ jobs: sudo apt-get upgrade -y sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y - sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y + sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')" @@ -215,13 +215,13 @@ jobs: # Install dsBase. # If previous steps have failed then don't run. - bash: | - R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)" - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.5-dev'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.4.0-dev'); opal.logout(opal)" sleep 60 - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)" workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files displayName: 'Install dsBase to Opal, as set disclosure test options' @@ -344,9 +344,9 @@ jobs: # If previous steps have failed then don't run - bash: | - R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080/'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)" - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)" workingDirectory: $(Pipeline.Workspace)/dsBaseClient displayName: 'Install dsDanger package on Opal server' diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml index d1566d20..70bffd8d 100644 --- a/docker-compose_opal.yml +++ b/docker-compose_opal.yml @@ -3,6 +3,7 @@ services: image: datashield/opal_citest:latest ports: - 8443:8443 + - 8080:8080 links: - mongo - rock @@ -15,7 +16,7 @@ services: - ROCK_HOSTS=rock:8085 - ROCK_ADMINISTRATOR_PASSWORD=foobar mongo: - image: mongo:6.0.27 + image: mongo:8.0 environment: - MONGO_INITDB_ROOT_USERNAME=root - MONGO_INITDB_ROOT_PASSWORD=foobar diff --git a/opal_azure-pipelines.yml b/opal_azure-pipelines.yml index d5d0f9ab..3d0a79a5 100644 --- a/opal_azure-pipelines.yml +++ b/opal_azure-pipelines.yml @@ -3,11 +3,9 @@ # Starts with a vanilla Opal docker composition, installs dsBase # and dsBaseClient (as well as dependencies - including a fully functional # Opal server). -# Does checks and tests then saves results to testStatus repo. # # Inside the root directory $(Pipeline.Workspace) will be a file tree like: # /dsBaseClient <- Checked out version of datashield/dsBaseClient -# /testStatus <- Checked out version of datashield/testStatus # /logs <- Where results of tests and lots are collated # # As of May 2020 this takes ~ 70 mins to run. @@ -37,18 +35,6 @@ variables: perf.profile: 'azure-pipeline' -######################################################################################### -# Need to define all the GH repos and their access tokens, see: -# https://docs.microsoft.com/en-us/azure/devops/pipelines/library/service-endpoints?view=azure-devops&tabs=yaml -resources: - repositories: - - repository: testStatusRepo - type: github - endpoint: datashield-testing - name: datashield/testStatus - ref: master - - ######################################################################################### # When and under what condition to run the pipeline. schedules: @@ -83,11 +69,6 @@ jobs: - checkout: self path: 'dsBaseClient' - - checkout: testStatusRepo - path: 'testStatus' - persistCredentials: true - condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest')) - ##################################################################################### # The MySQL install that comes with the VM doesn't seem compatable with our set up @@ -133,7 +114,7 @@ jobs: sudo apt-get upgrade -y sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y - sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y + sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')" @@ -234,13 +215,13 @@ jobs: # Install dsBase. # If previous steps have failed then don't run. - bash: | - R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)" - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.4.0-dev'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.4.0-dev'); opal.logout(opal)" sleep 60 - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)" workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files displayName: 'Install dsBase to Opal, as set disclosure test options' @@ -363,9 +344,9 @@ jobs: # If previous steps have failed then don't run - bash: | - R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080/'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)" - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)" workingDirectory: $(Pipeline.Workspace)/dsBaseClient displayName: 'Install dsDanger package on Opal server' @@ -526,75 +507,6 @@ jobs: displayName: 'Down Opal Docker Composition' condition: succeeded() - ##################################################################################### - # Windup phase - ##################################################################################### - - ##################################################################################### - # Output some important version numbers to file. This gets added to the testStatus - # commit so it can be parsed and used on the status table. - - bash: | - - echo 'branch:'$(branchName) >> $(datetime).txt - echo 'os:'$(lsb_release -ds) >> $(datetime).txt - echo 'R:'$(R --version | head -n 1) >> $(datetime).txt - echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt - - workingDirectory: $(Pipeline.Workspace)/logs - displayName: 'Write versions to file' - condition: succeededOrFailed() - - - ##################################################################################### - # Checkout the testStatus repo, add the results from here, push back to GH. - # TODO: Automatically pull in better email/name info from somewhere. - # TODO: More debug info in commit message - - bash: | - - # Git needs some config set to be able to push to a repo. - git config --global user.email "you@example.com" - git config --global user.name "Azure pipeline" - - # This repo is checked out in detatched head state, so reconnect it here. - git checkout master - - # It is possible that other commits have been made to the testStatus repo since it - # was checked out. i.e. other pipeline runs might have finished. - git pull - - # Make the directories if they dont already exist - mkdir --parents logs/$(projectName)/$(branchName) - mkdir --parents docs/$(projectName)/$(branchName)/latest - - cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/ - cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/$(datetime).csv - - cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/ - cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/$(datetime).xml - - cp $(Pipeline.Workspace)/logs/$(datetime).txt logs/$(projectName)/$(branchName)/ - - # Run the script to parse the results and build the html pages. - # status.py JUnit_file.xml coverage_file.csv output_file.html local_repo_path remote_repo_name branch - source/status.py logs/$(projectName)/$(branchName)/$(datetime).xml logs/$(projectName)/$(branchName)/$(datetime).csv logs/$(projectName)/$(branchName)/$(datetime).txt status.html $(Pipeline.Workspace)/$(projectName) $(projectName) $(branchName) - - cp status.html docs/$(projectName)/$(branchName)/latest/index.html - git add logs/$(projectName)/$(branchName)/coveragelist.csv - git add logs/$(projectName)/$(branchName)/test_results.xml - git add logs/$(projectName)/$(branchName)/$(datetime).xml - git add logs/$(projectName)/$(branchName)/$(datetime).csv - git add logs/$(projectName)/$(branchName)/$(datetime).txt - git add docs/$(projectName)/$(branchName)/latest/index.html - - git commit -m "Azure auto test for $(projectName)/$(branchName) @ $(datetime)" -m "Debug info:\nProjectName:$(projectName)\nBranchName:$(branchName)\nDataTime:$(datetime)" - git push - exit 0 - - workingDirectory: $(Pipeline.Workspace)/testStatus - displayName: 'Parse test results' - condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest')) - - ##################################################################################### # Output the environment information to the console. This is useful for debugging. # Always do this, even if some of the above has failed or the job has been cacelled. diff --git a/tests/docker/armadillo/standard/config/application.yml b/tests/docker/armadillo/standard/config/application.yml index 243160a3..cb735d81 100644 --- a/tests/docker/armadillo/standard/config/application.yml +++ b/tests/docker/armadillo/standard/config/application.yml @@ -67,8 +67,13 @@ stdout.log.path: '/logs/armadillo.log' logging: level: - root: INFO + root: "warn" ## change to DEBUG to have more details, typically when developing - org.molgenis: INFO + org.molgenis: "warn" ## Don't log upload data - org.apache.coyote.http11.Http11InputBuffer: INFO + org.apache.coyote.http11.Http11InputBuffer: "warn" + ## SpringFramework + org.springframework.boot: "warn" + org.springframework.web: "warn" + org.springframework.core: "warn" + org.springframework.codex: "warn" diff --git a/tests/testthat/connection_to_datasets/init_studies_datasets.R b/tests/testthat/connection_to_datasets/init_studies_datasets.R index 0639aac6..f86d040f 100644 --- a/tests/testthat/connection_to_datasets/init_studies_datasets.R +++ b/tests/testthat/connection_to_datasets/init_studies_datasets.R @@ -221,6 +221,62 @@ init.studies.dataset.gamlss <- function(variables) } } +init.studies.dataset.stand <- function(variables) +{ + if (ds.test_env$secure_login_details) + { + if (ds.test_env$driver == "OpalDriver") + { + builder <- DSI::newDSLoginBuilder(.silent = TRUE) + builder$append(server = "sim1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "STANDARDISE.std_1", options=ds.test_env$options_1) + builder$append(server = "sim2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "STANDARDISE.std_1", options=ds.test_env$options_2) + builder$append(server = "sim3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "STANDARDISE.std_1", options=ds.test_env$options_3) + ds.test_env$login.data <- builder$build() + } + else if (ds.test_env$driver == "ArmadilloDriver") + { + builder <- DSI::newDSLoginBuilder(.silent = TRUE) + builder$append(server = "sim1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/standardise/std_1", driver = ds.test_env$driver) + builder$append(server = "sim2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/standardise/std_2", driver = ds.test_env$driver) + builder$append(server = "sim3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/standardise/std_3", driver = ds.test_env$driver) + ds.test_env$login.data <- builder$build() + } + else + { + ds.test_env$login.data <- DSLite::setupCNSIMTest("dsBase", env = ds.test_env) + } + ds.test_env$stats.var <- variables + } +} + +init.studies.dataset.stand_disclosure <- function(variables) +{ + if (ds.test_env$secure_login_details) + { + if (ds.test_env$driver == "OpalDriver") + { + builder <- DSI::newDSLoginBuilder(.silent = TRUE) + builder$append(server = "sim1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "STANDARDISE.std_1_d", options=ds.test_env$options_1) + builder$append(server = "sim2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "STANDARDISE.std_2_d", options=ds.test_env$options_2) + builder$append(server = "sim3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "STANDARDISE.std_3_d", options=ds.test_env$options_3) + ds.test_env$login.data <- builder$build() + } + else if (ds.test_env$driver == "ArmadilloDriver") + { + builder <- DSI::newDSLoginBuilder(.silent = TRUE) + builder$append(server = "sim1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/standardise/std_1_d", driver = ds.test_env$driver) + builder$append(server = "sim2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/standardise/std_2_d", driver = ds.test_env$driver) + builder$append(server = "sim3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/standardise/std_3_d", driver = ds.test_env$driver) + ds.test_env$login.data <- builder$build() + } + else + { + ds.test_env$login.data <- DSLite::setupCNSIMTest("dsBase", env = ds.test_env) + } + ds.test_env$stats.var <- variables + } +} + connect.studies.dataset.cnsim <- function(variables) { @@ -278,6 +334,22 @@ connect.studies.dataset.gamlss <- function(variables) log.in.data.server() } +connect.studies.dataset.stand <- function(variables) +{ + log.out.data.server() + source("connection_to_datasets/login_details.R") + init.studies.dataset.stand(variables) + log.in.data.server() +} + +connect.studies.dataset.stand_disclosure <- function(variables) +{ + log.out.data.server() + source("connection_to_datasets/login_details.R") + init.studies.dataset.stand_disclosure(variables) + log.in.data.server() +} + disconnect.studies.dataset.cnsim <- function() { log.out.data.server() @@ -312,3 +384,13 @@ disconnect.studies.dataset.gamlss <- function() { log.out.data.server() } + +disconnect.studies.dataset.stand <- function() +{ + log.out.data.server() +} + +disconnect.studies.dataset.stand_disclosure <- function() +{ + log.out.data.server() +} diff --git a/tests/testthat/data_files/STANDARDISE/std_1.csv b/tests/testthat/data_files/STANDARDISE/std_1.csv new file mode 100644 index 00000000..32890959 --- /dev/null +++ b/tests/testthat/data_files/STANDARDISE/std_1.csv @@ -0,0 +1,101 @@ +fac_col1,fac_col2,fac_col3,fac_col4,fac_col5,fac_col6,fac_col9,col12,col15,col18 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+High,Blue,Yes,3,NA,Bird,True,4.205953353084624,93,TRUE +Low,NA,Yes,1,NA,Cat,True,32.79207192827016,99,TRUE +Low,NA,Yes,1,NA,Cat,True,95.45036491472274,72,TRUE +Low,NA,Yes,1,NA,Cat,True,88.95393160637468,26,TRUE +Low,NA,No,1,NA,Cat,False,69.28034061565995,7,FALSE +High,Blue,Yes,3,NA,Bird,True,64.05068137682974,42,TRUE +Medium,Green,Yes,2,NA,Dog,True,99.42697766236961,9,TRUE +High,Blue,Yes,3,NA,Bird,True,65.57057991158217,83,TRUE +Medium,Green,Yes,2,NA,Dog,True,70.85304681677371,36,TRUE +Low,NA,No,1,NA,Cat,False,54.40660247113556,78,FALSE +Medium,Green,No,2,NA,Dog,False,59.41420204471797,81,FALSE +High,Blue,Yes,3,NA,Bird,True,28.91597372945398,43,TRUE +Medium,Green,No,2,NA,Dog,False,14.711364731192589,76,FALSE +Low,NA,Yes,1,NA,Cat,True,96.30242325365543,15,TRUE +High,Blue,No,3,NA,Bird,False,90.22990451194346,32,FALSE +High,Blue,Yes,3,NA,Bird,True,69.07052784226835,7,TRUE +Low,NA,No,1,NA,Cat,False,79.54674176871777,9,FALSE +High,Blue,No,3,NA,Bird,False,2.461368450894952,41,FALSE 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a/tests/testthat/data_files/STANDARDISE/std_1_d.csv b/tests/testthat/data_files/STANDARDISE/std_1_d.csv new file mode 100644 index 00000000..9fe7462f --- /dev/null +++ b/tests/testthat/data_files/STANDARDISE/std_1_d.csv @@ -0,0 +1,101 @@ +fac_col1,fac_col2,fac_col3,fac_col4,fac_col5,fac_col6,fac_col9,col12,col15,col18 +High,Blue,Yes,3,NA,Bird,True,28.7577520124614,31,TRUE +High,Blue,Yes,3,NA,Bird,True,78.8305135443807,79,TRUE +High,Blue,Yes,3,NA,Bird,True,40.89769218117,51,TRUE +Medium,Green,No,2,NA,Dog,False,88.3017404004931,14,FALSE +High,Blue,Yes,3,NA,Bird,True,94.0467284293845,67,TRUE +Medium,Green,No,2,NA,Dog,False,4.55564993899316,42,FALSE +Medium,Green,No,2,NA,Dog,False,52.8105488047004,50,FALSE +Medium,Green,No,2,NA,Dog,False,89.2419044394046,43,FALSE +High,Blue,Yes,3,NA,Bird,True,55.1435014465824,14,TRUE +Low,NA,Yes,1,NA,Cat,True,45.6614735303447,25,TRUE +Medium,Green,No,2,NA,Dog,False,95.6833345349878,90,FALSE +Medium,Green,No,2,NA,Dog,False,45.3334156190977,91,FALSE 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+Medium,Green,NA,B,3,Medium,Left,v,81.23895095195621,6 +High,NA,NA,C,2,Large,Left,g,79.43423211108893,72 +Medium,Green,NA,B,3,Medium,Left,p,43.983168760314584,86 +Medium,Green,No,B,3,Medium,Right,q,75.44751586392522,86 +High,NA,NA,C,2,Large,Left,v,62.922113155946136,39 +High,NA,NA,C,2,Large,Left,r,71.01824013516307,31 +Low,Red,NA,A,1,Small,Left,q,0.062477332539856434,81 +Medium,Green,NA,B,3,Medium,Left,b,47.53165740985423,50 +Medium,Green,No,B,3,Medium,Right,d,22.011888516135514,34 +Low,Red,No,A,1,Small,Right,m,37.98165377229452,4 +Medium,Green,NA,B,3,Medium,Left,e,61.277100327424705,13 +Low,Red,No,A,1,Small,Right,v,35.179790924303234,69 +Low,Red,No,A,1,Small,Right,s,11.113542434759438,25 +Medium,Green,No,B,3,Medium,Right,y,24.361947271972895,52 +High,NA,No,C,2,Large,Right,t,66.80555874481797,22 +High,NA,NA,C,2,Large,Left,v,41.764677967876196,89 +Low,Red,No,A,1,Small,Right,y,78.81958340294659,32 +Medium,Green,No,B,3,Medium,Right,n,10.286464425735176,25 +Low,Red,No,A,1,Small,Right,y,43.489274149760604,87 +Medium,Green,NA,B,3,Medium,Left,w,98.49569799844176,35 +Low,Red,NA,A,1,Small,Left,c,89.30511143989861,40 +High,NA,No,C,2,Large,Right,h,88.64690607879311,30 +High,NA,NA,C,2,Large,Left,p,17.505265027284622,12 +Medium,Green,No,B,3,Medium,Right,l,13.069569156505167,31 +High,NA,No,C,2,Large,Right,y,65.31019250396639,30 +Low,Red,NA,A,1,Small,Left,n,34.3516472261399,64 +Medium,Green,No,B,3,Medium,Right,c,65.67581279668957,99 +Medium,Green,No,B,3,Medium,Right,n,32.03732424881309,14 +High,NA,NA,C,2,Large,Left,g,18.769111926667392,93 +Medium,Green,NA,B,3,Medium,Left,c,78.22943013161421,96 +Low,Red,No,A,1,Small,Right,w,9.359498671256006,71 +High,NA,NA,C,2,Large,Left,v,46.677904156968,67 +High,NA,NA,C,2,Large,Left,z,51.15054599009454,23 diff --git a/tests/testthat/data_files/STANDARDISE/std_2.rda b/tests/testthat/data_files/STANDARDISE/std_2.rda new file mode 100644 index 00000000..cbe3d279 Binary files /dev/null and b/tests/testthat/data_files/STANDARDISE/std_2.rda differ diff --git a/tests/testthat/data_files/STANDARDISE/std_2_d.csv b/tests/testthat/data_files/STANDARDISE/std_2_d.csv new file mode 100644 index 00000000..0a5a46eb --- /dev/null +++ b/tests/testthat/data_files/STANDARDISE/std_2_d.csv @@ -0,0 +1,101 @@ +fac_col1,fac_col2,fac_col3,fac_col4,fac_col5,fac_col7,fac_col10,col13,col16,col19 +High,NA,NA,C,2,Large,Left,o,28.7577520124614,31 +High,NA,NA,C,2,Large,Left,s,78.8305135443807,79 +High,NA,NA,C,2,Large,Left,n,40.89769218117,51 +Medium,Green,No,B,3,Medium,Right,c,88.3017404004931,14 +High,NA,NA,C,2,Large,Left,j,94.0467284293845,67 +Medium,Green,No,B,3,Medium,Right,r,4.55564993899316,42 +Medium,Green,No,B,3,Medium,Right,v,52.8105488047004,50 +Medium,Green,No,B,3,Medium,Right,k,89.2419044394046,43 +High,NA,NA,C,2,Large,Left,e,55.1435014465824,14 +Low,Red,NA,A,1,Small,Left,t,45.6614735303447,25 +Medium,Green,No,B,3,Medium,Right,n,95.6833345349878,90 +Medium,Green,No,B,3,Medium,Right,v,45.3334156190977,91 +Low,Red,No,A,1,Small,Right,y,67.7570635452867,69 +Medium,Green,NA,B,3,Medium,Left,z,57.2633401956409,91 +High,NA,No,C,2,Large,Right,e,10.2924682665616,57 +Low,Red,NA,A,1,Small,Left,s,89.9824970401824,92 +High,NA,No,C,2,Large,Right,y,24.608773435466,9 +High,NA,NA,C,2,Large,Left,y,4.20595335308462,93 +Low,Red,NA,A,1,Small,Left,i,32.7920719282702,99 +Low,Red,NA,A,1,Small,Left,c,95.4503649147227,72 +Low,Red,NA,A,1,Small,Left,h,88.9539316063747,26 +Low,Red,No,A,1,Small,Right,z,69.28034061566,7 +High,NA,NA,C,2,Large,Left,g,64.0506813768297,42 +Medium,Green,NA,B,3,Medium,Left,j,99.4269776623696,9 +High,NA,NA,C,2,Large,Left,i,65.5705799115822,83 +Medium,Green,NA,B,3,Medium,Left,s,70.8530468167737,36 +Low,Red,No,A,1,Small,Right,d,54.4066024711356,78 +Medium,Green,No,B,3,Medium,Right,n,59.414202044718,81 +High,NA,NA,C,2,Large,Left,q,28.915973729454,43 +Medium,Green,No,B,3,Medium,Right,k,14.7113647311926,76 +Low,Red,NA,A,1,Small,Left,g,96.3024232536554,15 +High,NA,No,C,2,Large,Right,u,90.2299045119435,32 +High,NA,NA,C,2,Large,Left,l,69.0705278422683,7 +Low,Red,No,A,1,Small,Right,o,79.5467417687178,9 +High,NA,No,C,2,Large,Right,j,2.46136845089495,41 +Medium,Green,NA,B,3,Medium,Left,m,47.7795971091837,74 +Low,Red,NA,A,1,Small,Left,g,75.8459537522867,23 +High,NA,NA,C,2,Large,Left,i,21.6407935833558,27 +Low,Red,NA,A,1,Small,Left,i,31.8181007634848,60 +Low,Red,No,A,1,Small,Right,j,23.1625785352662,53 +Medium,Green,NA,B,3,Medium,Left,w,14.2800022382289,7 +High,NA,No,C,2,Large,Right,u,41.4546335814521,53 +High,NA,No,C,2,Large,Right,g,41.3724326295778,27 +Low,Red,NA,A,1,Small,Left,u,36.8845450924709,96 +High,NA,NA,C,2,Large,Left,f,15.2444747742265,38 +Low,Red,NA,A,1,Small,Left,y,13.880606344901,89 +High,NA,NA,C,2,Large,Left,b,23.3034099452198,34 +Medium,Green,No,B,3,Medium,Right,e,46.5962450252846,93 +Low,Red,NA,A,1,Small,Left,h,26.5972640365362,69 +Medium,Green,NA,B,3,Medium,Left,l,85.7827715342864,72 +Low,Red,No,A,1,Small,Right,m,4.58311666734517,76 +Low,Red,NA,A,1,Small,Left,r,44.2200074205175,63 +High,NA,NA,C,2,Large,Left,a,79.8924845643342,13 +Low,Red,NA,A,1,Small,Left,y,12.189925997518,82 +Medium,Green,NA,B,3,Medium,Left,y,56.0947983758524,97 +Low,Red,No,A,1,Small,Right,f,20.653138961643,91 +Low,Red,No,A,1,Small,Right,u,12.7531650243327,25 +High,NA,NA,C,2,Large,Left,o,75.3307864302769,38 +Low,Red,No,A,1,Small,Right,i,89.50453591533,21 +Medium,Green,NA,B,3,Medium,Left,o,37.4462775886059,79 +Low,Red,NA,A,1,Small,Left,z,66.5115194628015,41 +High,NA,No,C,2,Large,Right,p,9.48406609240919,47 +Low,Red,No,A,1,Small,Right,t,38.3969637798145,90 +High,NA,NA,C,2,Large,Left,f,27.438364457339,60 +Medium,Green,NA,B,3,Medium,Left,k,81.4640038879588,95 +High,NA,No,C,2,Large,Right,h,44.8516341391951,16 +Medium,Green,NA,B,3,Medium,Left,v,81.0064353048801,94 +Medium,Green,NA,B,3,Medium,Left,v,81.2389509519562,6 +High,NA,NA,C,2,Large,Left,g,79.4342321110889,72 +Medium,Green,NA,B,3,Medium,Left,p,43.9831687603146,86 +Medium,Green,No,B,3,Medium,Right,q,75.4475158639252,86 +High,NA,NA,C,2,Large,Left,v,62.9221131559461,39 +High,NA,NA,C,2,Large,Left,r,71.0182401351631,31 +Low,Red,NA,A,1,Small,Left,q,0.0624773325398564,81 +Medium,Green,NA,B,3,Medium,Left,b,47.5316574098542,50 +Medium,Green,No,B,3,Medium,Right,d,22.0118885161355,34 +Low,Red,No,A,1,Small,Right,m,37.9816537722945,4 +Medium,Green,NA,B,3,Medium,Left,e,61.2771003274247,13 +Low,Red,No,A,1,Small,Right,v,35.1797909243032,69 +Low,Red,No,A,1,Small,Right,s,11.1135424347594,25 +Medium,Green,No,B,3,Medium,Right,y,24.3619472719729,52 +High,NA,No,C,2,Large,Right,t,66.805558744818,22 +High,NA,NA,C,2,Large,Left,v,41.7646779678762,89 +Low,Red,No,A,1,Small,Right,y,78.8195834029466,32 +Medium,Green,No,B,3,Medium,Right,n,10.2864644257352,25 +Low,Red,No,A,1,Small,Right,y,43.4892741497606,87 +Medium,Green,NA,B,3,Medium,Left,w,98.4956979984418,35 +Low,Red,NA,A,1,Small,Left,c,89.3051114398986,40 +High,NA,No,C,2,Large,Right,h,88.6469060787931,30 +High,NA,NA,C,2,Large,Left,p,17.5052650272846,12 +Medium,Green,No,B,3,Medium,Right,l,13.0695691565052,31 +High,NA,No,C,2,Large,Right,y,65.3101925039664,30 +Low,Red,NA,A,1,Small,Left,n,34.3516472261399,64 +Medium,Green,No,B,3,Medium,Right,c,65.6758127966896,99 +Medium,Green,No,B,3,Medium,Right,n,32.0373242488131,14 +High,NA,NA,C,2,Large,Left,g,18.7691119266674,93 +Medium,Green,NA,B,3,Medium,Left,c,78.2294301316142,96 +Low,Red,No,A,1,Small,Right,w,9.35949867125601,71 +High,NA,NA,C,2,Large,Left,v,46.677904156968,67 +High,NA,NA,C,2,Large,Left,z,51.1505459900945,23 diff --git a/tests/testthat/data_files/STANDARDISE/std_2_d.rda b/tests/testthat/data_files/STANDARDISE/std_2_d.rda new file mode 100644 index 00000000..cad2198a Binary files /dev/null and b/tests/testthat/data_files/STANDARDISE/std_2_d.rda differ diff --git a/tests/testthat/data_files/STANDARDISE/std_3.csv b/tests/testthat/data_files/STANDARDISE/std_3.csv new file mode 100644 index 00000000..583c9a22 --- /dev/null +++ b/tests/testthat/data_files/STANDARDISE/std_3.csv @@ -0,0 +1,101 @@ +fac_col1,fac_col2,fac_col3,fac_col4,fac_col5,col11,col14,col17,col20 +High,Blue,Yes,C,Three,31,TRUE,o,28.757752012461424 +High,Blue,Yes,C,Three,79,TRUE,s,78.83051354438066 +High,Blue,Yes,C,Three,51,TRUE,n,40.89769218116999 +Medium,NA,NA,B,Two,14,FALSE,c,88.301740400493145 +High,Blue,Yes,C,Three,67,TRUE,j,94.04672842938453 +Medium,NA,NA,B,Two,42,FALSE,r,4.555649938993156 +Medium,NA,NA,B,Two,50,FALSE,v,52.810548804700375 +Medium,NA,NA,B,Two,43,FALSE,k,89.2419044394046 +High,Blue,Yes,C,Three,14,TRUE,e,55.14350144658238 +Low,NA,Yes,A,One,25,TRUE,t,45.661473530344665 +Medium,NA,NA,B,Two,90,FALSE,n,95.68333453498781 +Medium,NA,NA,B,Two,91,FALSE,v,45.33341561909765 +Low,NA,NA,A,One,69,FALSE,y,67.75706354528666 +Medium,NA,Yes,B,Two,91,TRUE,z,57.26334019564092 +High,Blue,NA,C,Three,57,FALSE,e,10.292468266561627 +Low,NA,Yes,A,One,92,TRUE,s,89.98249704018235 +High,Blue,NA,C,Three,9,FALSE,y,24.60877343546599 +High,Blue,Yes,C,Three,93,TRUE,y,4.205953353084624 +Low,NA,Yes,A,One,99,TRUE,i,32.79207192827016 +Low,NA,Yes,A,One,72,TRUE,c,95.45036491472274 +Low,NA,Yes,A,One,26,TRUE,h,88.95393160637468 +Low,NA,NA,A,One,7,FALSE,z,69.28034061565995 +High,Blue,Yes,C,Three,42,TRUE,g,64.05068137682974 +Medium,NA,Yes,B,Two,9,TRUE,j,99.42697766236961 +High,Blue,Yes,C,Three,83,TRUE,i,65.57057991158217 +Medium,NA,Yes,B,Two,36,TRUE,s,70.85304681677371 +Low,NA,NA,A,One,78,FALSE,d,54.40660247113556 +Medium,NA,NA,B,Two,81,FALSE,n,59.41420204471797 +High,Blue,Yes,C,Three,43,TRUE,q,28.91597372945398 +Medium,NA,NA,B,Two,76,FALSE,k,14.711364731192589 +Low,NA,Yes,A,One,15,TRUE,g,96.30242325365543 +High,Blue,NA,C,Three,32,FALSE,u,90.22990451194346 +High,Blue,Yes,C,Three,7,TRUE,l,69.07052784226835 +Low,NA,NA,A,One,9,FALSE,o,79.54674176871777 +High,Blue,NA,C,Three,41,FALSE,j,2.461368450894952 +Medium,NA,Yes,B,Two,74,TRUE,m,47.77959710918367 +Low,NA,Yes,A,One,23,TRUE,g,75.84595375228673 +High,Blue,Yes,C,Three,27,TRUE,i,21.640793583355844 +Low,NA,Yes,A,One,60,TRUE,i,31.818100763484836 +Low,NA,NA,A,One,53,FALSE,j,23.16257853526622 +Medium,NA,Yes,B,Two,7,TRUE,w,14.280002238228917 +High,Blue,NA,C,Three,53,FALSE,u,41.45463358145207 +High,Blue,NA,C,Three,27,FALSE,g,41.372432629577816 +Low,NA,Yes,A,One,96,TRUE,u,36.884545092470944 +High,Blue,Yes,C,Three,38,TRUE,f,15.244474774226546 +Low,NA,Yes,A,One,89,TRUE,y,13.880606344901025 +High,Blue,Yes,C,Three,34,TRUE,b,23.303409945219755 +Medium,NA,NA,B,Two,93,FALSE,e,46.59624502528459 +Low,NA,Yes,A,One,69,TRUE,h,26.597264036536217 +Medium,NA,Yes,B,Two,72,TRUE,l,85.78277153428644 +Low,NA,NA,A,One,76,FALSE,m,4.583116667345166 +Low,NA,Yes,A,One,63,TRUE,r,44.220007420517504 +High,Blue,Yes,C,Three,13,TRUE,a,79.89248456433415 +Low,NA,Yes,A,One,82,TRUE,y,12.189925997518003 +Medium,NA,Yes,B,Two,97,TRUE,y,56.094798375852406 +Low,NA,NA,A,One,91,FALSE,f,20.65313896164298 +Low,NA,NA,A,One,25,FALSE,u,12.753165024332702 +High,Blue,Yes,C,Three,38,TRUE,o,75.33078643027693 +Low,NA,NA,A,One,21,FALSE,i,89.50453591533005 +Medium,NA,Yes,B,Two,79,TRUE,o,37.44627758860588 +Low,NA,Yes,A,One,41,TRUE,z,66.51151946280152 +High,Blue,NA,C,Three,47,FALSE,p,9.484066092409194 +Low,NA,NA,A,One,90,FALSE,t,38.39696377981454 +High,Blue,Yes,C,Three,60,TRUE,f,27.43836445733905 +Medium,NA,Yes,B,Two,95,TRUE,k,81.46400388795882 +High,Blue,NA,C,Three,16,FALSE,h,44.851634139195085 +Medium,NA,Yes,B,Two,94,TRUE,v,81.00643530488014 +Medium,NA,Yes,B,Two,6,TRUE,v,81.23895095195621 +High,Blue,Yes,C,Three,72,TRUE,g,79.43423211108893 +Medium,NA,Yes,B,Two,86,TRUE,p,43.983168760314584 +Medium,NA,NA,B,Two,86,FALSE,q,75.44751586392522 +High,Blue,Yes,C,Three,39,TRUE,v,62.922113155946136 +High,Blue,Yes,C,Three,31,TRUE,r,71.01824013516307 +Low,NA,Yes,A,One,81,TRUE,q,0.062477332539856434 +Medium,NA,Yes,B,Two,50,TRUE,b,47.53165740985423 +Medium,NA,NA,B,Two,34,FALSE,d,22.011888516135514 +Low,NA,NA,A,One,4,FALSE,m,37.98165377229452 +Medium,NA,Yes,B,Two,13,TRUE,e,61.277100327424705 +Low,NA,NA,A,One,69,FALSE,v,35.179790924303234 +Low,NA,NA,A,One,25,FALSE,s,11.113542434759438 +Medium,NA,NA,B,Two,52,FALSE,y,24.361947271972895 +High,Blue,NA,C,Three,22,FALSE,t,66.80555874481797 +High,Blue,Yes,C,Three,89,TRUE,v,41.764677967876196 +Low,NA,NA,A,One,32,FALSE,y,78.81958340294659 +Medium,NA,NA,B,Two,25,FALSE,n,10.286464425735176 +Low,NA,NA,A,One,87,FALSE,y,43.489274149760604 +Medium,NA,Yes,B,Two,35,TRUE,w,98.49569799844176 +Low,NA,Yes,A,One,40,TRUE,c,89.30511143989861 +High,Blue,NA,C,Three,30,FALSE,h,88.64690607879311 +High,Blue,Yes,C,Three,12,TRUE,p,17.505265027284622 +Medium,NA,NA,B,Two,31,FALSE,l,13.069569156505167 +High,Blue,NA,C,Three,30,FALSE,y,65.31019250396639 +Low,NA,Yes,A,One,64,TRUE,n,34.3516472261399 +Medium,NA,NA,B,Two,99,FALSE,c,65.67581279668957 +Medium,NA,NA,B,Two,14,FALSE,n,32.03732424881309 +High,Blue,Yes,C,Three,93,TRUE,g,18.769111926667392 +Medium,NA,Yes,B,Two,96,TRUE,c,78.22943013161421 +Low,NA,NA,A,One,71,FALSE,w,9.359498671256006 +High,Blue,Yes,C,Three,67,TRUE,v,46.677904156968 +High,Blue,Yes,C,Three,23,TRUE,z,51.15054599009454 diff --git a/tests/testthat/data_files/STANDARDISE/std_3.rda b/tests/testthat/data_files/STANDARDISE/std_3.rda new file mode 100644 index 00000000..80362674 Binary files /dev/null and b/tests/testthat/data_files/STANDARDISE/std_3.rda differ diff --git a/tests/testthat/data_files/STANDARDISE/std_3_d.csv b/tests/testthat/data_files/STANDARDISE/std_3_d.csv new file mode 100644 index 00000000..5dfce08f --- /dev/null +++ b/tests/testthat/data_files/STANDARDISE/std_3_d.csv @@ -0,0 +1,101 @@ +fac_col1,fac_col2,fac_col3,fac_col4,fac_col5,col11,col14,col17,col20 +High,Blue,Yes,C,Three,31,TRUE,o,28.7577520124614 +High,Blue,Yes,C,Three,79,TRUE,s,78.8305135443807 +High,Blue,Yes,C,Three,51,TRUE,n,40.89769218117 +Medium,NA,NA,B,Two,14,FALSE,c,88.3017404004931 +High,Blue,Yes,C,Three,67,TRUE,j,94.0467284293845 +Medium,NA,NA,B,Two,42,FALSE,r,4.55564993899316 +Medium,NA,NA,B,Two,50,FALSE,v,52.8105488047004 +Medium,NA,NA,B,Two,43,FALSE,k,89.2419044394046 +High,Blue,Yes,C,Three,14,TRUE,e,55.1435014465824 +Low,NA,Yes,A,One,25,TRUE,t,45.6614735303447 +Medium,NA,NA,B,Two,90,FALSE,n,95.6833345349878 +Medium,NA,NA,B,Two,91,FALSE,v,45.3334156190977 +Low,NA,NA,A,One,69,FALSE,y,67.7570635452867 +Medium,NA,Yes,B,Two,91,TRUE,z,57.2633401956409 +High,Blue,NA,C,Three,57,FALSE,e,10.2924682665616 +Low,NA,Yes,A,One,92,TRUE,s,89.9824970401824 +High,Blue,NA,C,Three,9,FALSE,y,24.608773435466 +High,Blue,Yes,C,Three,93,TRUE,y,4.20595335308462 +Low,NA,Yes,A,One,99,TRUE,i,32.7920719282702 +Low,NA,Yes,A,One,72,TRUE,c,95.4503649147227 +Low,NA,Yes,A,One,26,TRUE,h,88.9539316063747 +Low,NA,NA,A,One,7,FALSE,z,69.28034061566 +High,Blue,Yes,C,Three,42,TRUE,g,64.0506813768297 +Medium,NA,Yes,B,Two,9,TRUE,j,99.4269776623696 +High,Blue,Yes,C,Three,83,TRUE,i,65.5705799115822 +Medium,NA,Yes,B,Two,36,TRUE,s,70.8530468167737 +Low,NA,NA,A,One,78,FALSE,d,54.4066024711356 +Medium,NA,NA,B,Two,81,FALSE,n,59.414202044718 +High,Blue,Yes,C,Three,43,TRUE,q,28.915973729454 +Medium,NA,NA,B,Two,76,FALSE,k,14.7113647311926 +Low,NA,Yes,A,One,15,TRUE,g,96.3024232536554 +High,Blue,NA,C,Three,32,FALSE,u,90.2299045119435 +High,Blue,Yes,C,Three,7,TRUE,l,69.0705278422683 +Low,NA,NA,A,One,9,FALSE,o,79.5467417687178 +High,Blue,NA,C,Three,41,FALSE,j,2.46136845089495 +Medium,NA,Yes,B,Two,74,TRUE,m,47.7795971091837 +Low,NA,Yes,A,One,23,TRUE,g,75.8459537522867 +High,Blue,Yes,C,Three,27,TRUE,i,21.6407935833558 +Low,NA,Yes,A,One,60,TRUE,i,31.8181007634848 +Low,NA,NA,A,One,53,FALSE,j,23.1625785352662 +Medium,NA,Yes,B,Two,7,TRUE,w,14.2800022382289 +High,Blue,NA,C,Three,53,FALSE,u,41.4546335814521 +High,Blue,NA,C,Three,27,FALSE,g,41.3724326295778 +Low,NA,Yes,A,One,96,TRUE,u,36.8845450924709 +High,Blue,Yes,C,Three,38,TRUE,f,15.2444747742265 +Low,NA,Yes,A,One,89,TRUE,y,13.880606344901 +High,Blue,Yes,C,Three,34,TRUE,b,23.3034099452198 +Medium,NA,NA,B,Two,93,FALSE,e,46.5962450252846 +Low,NA,Yes,A,One,69,TRUE,h,26.5972640365362 +Medium,NA,Yes,B,Two,72,TRUE,l,85.7827715342864 +Low,NA,NA,A,One,76,FALSE,m,4.58311666734517 +Low,NA,Yes,A,One,63,TRUE,r,44.2200074205175 +High,Blue,Yes,C,Three,13,TRUE,a,79.8924845643342 +Low,NA,Yes,A,One,82,TRUE,y,12.189925997518 +Medium,NA,Yes,B,Two,97,TRUE,y,56.0947983758524 +Low,NA,NA,A,One,91,FALSE,f,20.653138961643 +Low,NA,NA,A,One,25,FALSE,u,12.7531650243327 +High,Blue,Yes,C,Three,38,TRUE,o,75.3307864302769 +Low,NA,NA,A,One,21,FALSE,i,89.50453591533 +Medium,NA,Yes,B,Two,79,TRUE,o,37.4462775886059 +Low,NA,Yes,A,One,41,TRUE,z,66.5115194628015 +High,Blue,NA,C,Three,47,FALSE,p,9.48406609240919 +Low,NA,NA,A,One,90,FALSE,t,38.3969637798145 +High,Blue,Yes,C,Three,60,TRUE,f,27.438364457339 +Medium,NA,Yes,B,Two,95,TRUE,k,81.4640038879588 +High,Blue,NA,C,Three,16,FALSE,h,44.8516341391951 +Medium,NA,Yes,B,Two,94,TRUE,v,81.0064353048801 +Medium,NA,Yes,B,Two,6,TRUE,v,81.2389509519562 +High,Blue,Yes,C,Three,72,TRUE,g,79.4342321110889 +Medium,NA,Yes,B,Two,86,TRUE,p,43.9831687603146 +Medium,NA,NA,B,Two,86,FALSE,q,75.4475158639252 +High,Blue,Yes,C,Three,39,TRUE,v,62.9221131559461 +High,Blue,Yes,C,Three,31,TRUE,r,71.0182401351631 +Low,NA,Yes,A,One,81,TRUE,q,0.0624773325398564 +Medium,NA,Yes,B,Two,50,TRUE,b,47.5316574098542 +Medium,NA,NA,B,Two,34,FALSE,d,22.0118885161355 +Low,NA,NA,A,One,4,FALSE,m,37.9816537722945 +Medium,NA,Yes,B,Two,13,TRUE,e,61.2771003274247 +Low,NA,NA,A,One,69,FALSE,v,35.1797909243032 +Low,NA,NA,A,One,25,FALSE,s,11.1135424347594 +Medium,NA,NA,B,Two,52,FALSE,y,24.3619472719729 +High,Blue,NA,C,Three,22,FALSE,t,66.805558744818 +High,Blue,Yes,C,Three,89,TRUE,v,41.7646779678762 +Low,NA,NA,A,One,32,FALSE,y,78.8195834029466 +Medium,NA,NA,B,Two,25,FALSE,n,10.2864644257352 +Low,NA,NA,A,One,87,FALSE,y,43.4892741497606 +Medium,NA,Yes,B,Two,35,TRUE,w,98.4956979984418 +Low,NA,Yes,A,One,40,TRUE,c,89.3051114398986 +High,Blue,NA,C,Three,30,FALSE,h,88.6469060787931 +High,Blue,Yes,C,Three,12,TRUE,p,17.5052650272846 +Medium,NA,NA,B,Two,31,FALSE,l,13.0695691565052 +High,Blue,NA,C,Three,30,FALSE,y,65.3101925039664 +Low,NA,Yes,A,One,64,TRUE,n,34.3516472261399 +Medium,NA,NA,B,Two,99,FALSE,c,65.6758127966896 +Medium,NA,NA,B,Two,14,FALSE,n,32.0373242488131 +High,Blue,Yes,C,Three,93,TRUE,g,18.7691119266674 +Medium,NA,Yes,B,Two,96,TRUE,c,78.2294301316142 +Low,NA,NA,A,One,71,FALSE,w,9.35949867125601 +High,Blue,Yes,C,Three,67,TRUE,v,46.677904156968 +High,Blue,Yes,C,Three,23,TRUE,z,51.1505459900945 diff --git a/tests/testthat/data_files/STANDARDISE/std_3_d.rda b/tests/testthat/data_files/STANDARDISE/std_3_d.rda new file mode 100644 index 00000000..4165f098 Binary files /dev/null and b/tests/testthat/data_files/STANDARDISE/std_3_d.rda differ diff --git a/tests/testthat/data_files/molgenis_armadillo-upload_testing_datasets.R b/tests/testthat/data_files/molgenis_armadillo-upload_testing_datasets.R index 9e129971..545467bc 100644 --- a/tests/testthat/data_files/molgenis_armadillo-upload_testing_datasets.R +++ b/tests/testthat/data_files/molgenis_armadillo-upload_testing_datasets.R @@ -69,4 +69,12 @@ upload_testing_dataset_table('datashield', 'testing', 'DATASET1', 'TESTING/DATAS upload_testing_dataset_table('datashield', 'testing', 'DATASET2', 'TESTING/DATASET2.rda') upload_testing_dataset_table('datashield', 'testing', 'DATASET3', 'TESTING/DATASET3.rda') +upload_testing_dataset_table('datashield', 'standardise', 'std_1', 'STANDARDISE/std_1.rda') +upload_testing_dataset_table('datashield', 'standardise', 'std_2', 'STANDARDISE/std_2.rda') +upload_testing_dataset_table('datashield', 'standardise', 'std_3', 'STANDARDISE/std_3.rda') + +upload_testing_dataset_table('datashield', 'standardise', 'std_1_d', 'STANDARDISE/std_1_d.rda') +upload_testing_dataset_table('datashield', 'standardise', 'std_2_d', 'STANDARDISE/std_2_d.rda') +upload_testing_dataset_table('datashield', 'standardise', 'std_3_d', 'STANDARDISE/std_3_d.rda') + print(MolgenisArmadillo::armadillo.list_tables('datashield')) diff --git a/tests/testthat/data_files/obiba_opal-upload_testing_datasets.R b/tests/testthat/data_files/obiba_opal-upload_testing_datasets.R index ae79d2e6..b14f2aa6 100644 --- a/tests/testthat/data_files/obiba_opal-upload_testing_datasets.R +++ b/tests/testthat/data_files/obiba_opal-upload_testing_datasets.R @@ -17,8 +17,8 @@ upload_testing_dataset_table <- function(opal, project_name, table_name, local_f opal.table_save(opal, data, project_name, table_name, id.name = "_row_id_", force = TRUE) } -# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)) -opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)) +# opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)) +opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/') upload_testing_dataset_table(opal, 'ANTHRO', 'anthro1', 'ANTHRO/anthro1.rda') upload_testing_dataset_table(opal, 'ANTHRO', 'anthro2', 'ANTHRO/anthro2.rda') @@ -72,4 +72,12 @@ upload_testing_dataset_table(opal, 'TESTING', 'DATASET1', 'TESTING/DATASET1.rda' upload_testing_dataset_table(opal, 'TESTING', 'DATASET2', 'TESTING/DATASET2.rda') upload_testing_dataset_table(opal, 'TESTING', 'DATASET3', 'TESTING/DATASET3.rda') +upload_testing_dataset_table(opal, 'STANDARDISE', 'std_1', 'STANDARDISE/std_1.rda') +upload_testing_dataset_table(opal, 'STANDARDISE', 'std_2', 'STANDARDISE/std_2.rda') +upload_testing_dataset_table(opal, 'STANDARDISE', 'std_3', 'STANDARDISE/std_3.rda') + +upload_testing_dataset_table(opal, 'STANDARDISE', 'std_1_d', 'STANDARDISE/std_1_d.rda') +upload_testing_dataset_table(opal, 'STANDARDISE', 'std_2_d', 'STANDARDISE/std_2_d.rda') +upload_testing_dataset_table(opal, 'STANDARDISE', 'std_3_d', 'STANDARDISE/std_3_d.rda') + opal.logout(opal) diff --git a/tests/testthat/perf_files/armadillo_hp-laptop-quay_perf-profile.csv b/tests/testthat/perf_files/armadillo_hp-laptop-quay_perf-profile.csv index 010650f1..ebfd605c 100644 --- a/tests/testthat/perf_files/armadillo_hp-laptop-quay_perf-profile.csv +++ b/tests/testthat/perf_files/armadillo_hp-laptop-quay_perf-profile.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.04918","0.5","2" -"ds.abs::perf::0","1.184","0.5","2" -"ds.asInteger::perf:0","1.297","0.5","2" -"ds.asList::perf:0","2.884","0.5","2" -"ds.asNumeric::perf:0","1.354","0.5","2" -"ds.assign::perf::0","2.745","0.5","2" -"ds.class::perf::combine:0","3.261","0.5","2" -"ds.colnames::perf:0","8.566","0.5","2" -"ds.exists::perf::combine:0","6.342","0.5","2" -"ds.length::perf::combine:0","7.835","0.5","2" -"ds.mean::perf::combine:0","8.127","0.5","2" -"ds.mean::perf::split:0","8.109","0.5","2" -"void::perf::void::0","20280.0","0.5","2" +"conndisconn::perf::simple0","0.06790","0.5","2" +"ds.abs::perf::0","1.998","0.5","2" +"ds.asInteger::perf:0","2.111","0.5","2" +"ds.asList::perf:0","4.550","0.5","2" +"ds.asNumeric::perf:0","1.879","0.5","2" +"ds.assign::perf::0","4.806","0.5","2" +"ds.class::perf::combine:0","3.865","0.5","2" +"ds.colnames::perf:0","9.577","0.5","2" +"ds.exists::perf::combine:0","8.411","0.5","2" +"ds.length::perf::combine:0","7.957","0.5","2" +"ds.mean::perf::combine:0","9.049","0.5","2" +"ds.mean::perf::split:0","9.429","0.5","2" +"void::perf::void::0","21400.0","0.5","2" diff --git a/tests/testthat/perf_tests/perf_rate.R b/tests/testthat/perf_tests/perf_rate.R index a7f85348..8d762207 100644 --- a/tests/testthat/perf_tests/perf_rate.R +++ b/tests/testthat/perf_tests/perf_rate.R @@ -57,6 +57,11 @@ perf.reference.save <- function(perf.ref.name, rate, tolerance.lower, tolerance. .perf.reference <<- .perf.reference } +# Obtain performance test duration from PERF_DURATION_SEC environment variable, otherwise default.duration argument, otherwise "30". +perf.testduration <- function(default.duration = 30) { + base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = base::as.character(default.duration))) +} + perf.reference.rate <- function(perf.ref.name) { if (is.null(.perf.reference)) .load.pref() diff --git a/tests/testthat/test-perf-conndisconn.R b/tests/testthat/test-perf-conndisconn.R index 4bcc2a10..ab257aeb 100644 --- a/tests/testthat/test-perf-conndisconn.R +++ b/tests/testthat/test-perf-conndisconn.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -22,7 +22,7 @@ disconnect.studies.dataset.cnsim() # context("conndisconn::perf::simple0") test_that("simple connect - disconnect performance", { - .durationSec <- 120 # seconds + .durationSec <- perf.testduration(120) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-ds.abs.R b/tests/testthat/test-perf-ds.abs.R index e431c20e..325d715c 100644 --- a/tests/testthat/test-perf-ds.abs.R +++ b/tests/testthat/test-perf-ds.abs.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -21,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # context("ds.abs::perf:0") test_that("combine - performance", { - .durationSec <- 30 # seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-ds.asInteger.R b/tests/testthat/test-perf-ds.asInteger.R index 2e816320..5e1b887a 100644 --- a/tests/testthat/test-perf-ds.asInteger.R +++ b/tests/testthat/test-perf-ds.asInteger.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -21,7 +21,7 @@ connect.studies.dataset.cnsim(list("GENDER")) # context("ds.asInteger::perf:0") test_that("combine - performance", { - .durationSec <- 30 # seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-ds.asList.R b/tests/testthat/test-perf-ds.asList.R index a0f65dda..6c2f3db9 100644 --- a/tests/testthat/test-perf-ds.asList.R +++ b/tests/testthat/test-perf-ds.asList.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -21,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # context("ds.asList::perf:0") test_that("combine - performance", { - .durationSec <- 30 # seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-ds.asNumeric.R b/tests/testthat/test-perf-ds.asNumeric.R index 33fcf490..eb0695e4 100644 --- a/tests/testthat/test-perf-ds.asNumeric.R +++ b/tests/testthat/test-perf-ds.asNumeric.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -21,7 +21,7 @@ connect.studies.dataset.cnsim(list("GENDER")) # context("ds.asNumeric::perf:0") test_that("combine - performance", { - .durationSec <- 30 # seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-ds.assign.R b/tests/testthat/test-perf-ds.assign.R index d118eb42..47e51ca5 100644 --- a/tests/testthat/test-perf-ds.assign.R +++ b/tests/testthat/test-perf-ds.assign.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -21,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # context("ds.assign::perf::0") test_that("performance", { - .durationSec <- 30 # seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-ds.class.R b/tests/testthat/test-perf-ds.class.R index f90927ff..023a404a 100644 --- a/tests/testthat/test-perf-ds.class.R +++ b/tests/testthat/test-perf-ds.class.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -21,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # context("ds.class::perf::combine:0") test_that("combine - performance", { - .durationSec <- 30 # seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-ds.colnames.R b/tests/testthat/test-perf-ds.colnames.R index 7382ecf6..8943c577 100644 --- a/tests/testthat/test-perf-ds.colnames.R +++ b/tests/testthat/test-perf-ds.colnames.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -21,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # context("ds.colnames::perf:0") test_that("combine - performance", { - .durationSec <- 30 # seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-ds.exists.R b/tests/testthat/test-perf-ds.exists.R index 123d7e80..92a10cab 100644 --- a/tests/testthat/test-perf-ds.exists.R +++ b/tests/testthat/test-perf-ds.exists.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -21,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # context("ds.exists::perf::combine:0") test_that("combine - performance", { - .durationSec <- 30 # seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-ds.length.R b/tests/testthat/test-perf-ds.length.R index 6105cf99..c1ac11c9 100644 --- a/tests/testthat/test-perf-ds.length.R +++ b/tests/testthat/test-perf-ds.length.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -21,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # context("ds.length::perf::combine:0") test_that("combine - performance", { - .durationSec <- 30 # seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-ds.mean.R b/tests/testthat/test-perf-ds.mean.R index 03d0ac78..6b599368 100644 --- a/tests/testthat/test-perf-ds.mean.R +++ b/tests/testthat/test-perf-ds.mean.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -21,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # context("ds.mean::perf::combine:0") test_that("combine - performance", { - .durationSec <- 30 # seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time @@ -52,7 +52,7 @@ test_that("combine - performance", { # context("ds.mean::perf::split:0") test_that("split - performance", { - .durationSec <- 30 # seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-void.R b/tests/testthat/test-perf-void.R index 3e2f749c..1325bfea 100644 --- a/tests/testthat/test-perf-void.R +++ b/tests/testthat/test-perf-void.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -20,7 +20,7 @@ # context("void::perf::void::0") test_that("simple void performance", { - .durationSec <- 60 # seconds + .durationSec <- perf.testduration(60) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-smk-ds.asDataMatrix.R b/tests/testthat/test-smk-ds.asDataMatrix.R index 25ef3736..f4726163 100644 --- a/tests/testthat/test-smk-ds.asDataMatrix.R +++ b/tests/testthat/test-smk-ds.asDataMatrix.R @@ -35,15 +35,12 @@ test_that("simple test", { res.class <- ds.class("asdatamatrix.newobj") expect_length(res.class, 3) - expect_length(res.class$sim1, 2) - expect_true("array" %in% res.class$sim1) - expect_true("matrix" %in% res.class$sim1) - expect_length(res.class$sim2, 2) - expect_true("array" %in% res.class$sim2) - expect_true("matrix" %in% res.class$sim2) - expect_length(res.class$sim3, 2) - expect_true("array" %in% res.class$sim3) - expect_true("matrix" %in% res.class$sim3) + expect_length(res.class$sim1, 1) + expect_true("data.frame" %in% res.class$sim1) + expect_length(res.class$sim2, 1) + expect_true("data.frame" %in% res.class$sim2) + expect_length(res.class$sim3, 1) + expect_true("data.frame" %in% res.class$sim3) }) # diff --git a/tests/testthat/test-smk-ds.completeCases.R b/tests/testthat/test-smk-ds.completeCases.R index 3be25b85..8d2166a0 100644 --- a/tests/testthat/test-smk-ds.completeCases.R +++ b/tests/testthat/test-smk-ds.completeCases.R @@ -95,22 +95,19 @@ test_that("completeCases matrix", { res.mat.class <- ds.class("mat") expect_length(res.mat.class, 3) - expect_true("matrix" %in% res.mat.class$sim1) - expect_true("matrix" %in% res.mat.class$sim2) - expect_true("matrix" %in% res.mat.class$sim3) + expect_true("data.frame" %in% res.mat.class$sim1) + expect_true("data.frame" %in% res.mat.class$sim2) + expect_true("data.frame" %in% res.mat.class$sim3) res.mat_new.class <- ds.class("mat_new") expect_length(res.mat_new.class, 3) - expect_length(res.mat_new.class$sim1, 2) - expect_true("array" %in% res.mat_new.class$sim1) - expect_true("matrix" %in% res.mat_new.class$sim1) - expect_length(res.mat_new.class$sim2, 2) - expect_true("array" %in% res.mat_new.class$sim2) - expect_true("matrix" %in% res.mat_new.class$sim2) - expect_length(res.mat_new.class$sim3, 2) - expect_true("array" %in% res.mat_new.class$sim3) - expect_true("matrix" %in% res.mat_new.class$sim3) + expect_length(res.mat_new.class$sim1, 1) + expect_true("data.frame" %in% res.mat_new.class$sim1) + expect_length(res.mat_new.class$sim2, 1) + expect_true("data.frame" %in% res.mat_new.class$sim2) + expect_length(res.mat_new.class$sim3, 1) + expect_true("data.frame" %in% res.mat_new.class$sim3) res.mat.dim <- ds.dim("mat") diff --git a/tests/testthat/test-smk-ds.elspline.R b/tests/testthat/test-smk-ds.elspline.R index aa8d3d78..0086c787 100644 --- a/tests/testthat/test-smk-ds.elspline.R +++ b/tests/testthat/test-smk-ds.elspline.R @@ -56,7 +56,7 @@ test_that("elspline", { expect_equal(res.mod$errorMessage[3], "No errors") expect_equal(res.mod$nsubs, 7477) expect_equal(res.mod$iter, 3) - expect_true("family" %in% class(res.mod$family)) + expect_true("character" %in% class(res.mod$family)) expect_equal(res.mod$formula, "D$LAB_TRIG ~ elsplineDS") expect_true("matrix" %in% class(res.mod$coefficients)) expect_true("array" %in% class(res.mod$coefficients)) @@ -106,7 +106,7 @@ test_that("elspline", { expect_equal(res.mod$errorMessage[3], "No errors") expect_equal(res.mod$nsubs, 7477) expect_equal(res.mod$iter, 3) - expect_true("family" %in% class(res.mod$family)) + expect_true("character" %in% class(res.mod$family)) expect_equal(res.mod$formula, "D$LAB_TRIG ~ elsplineDS2") expect_true("matrix" %in% class(res.mod$coefficients)) expect_true("array" %in% class(res.mod$coefficients)) diff --git a/tests/testthat/test-smk-ds.glm-binomial.R b/tests/testthat/test-smk-ds.glm-binomial.R index 666188ef..1f0ba068 100644 --- a/tests/testthat/test-smk-ds.glm-binomial.R +++ b/tests/testthat/test-smk-ds.glm-binomial.R @@ -43,7 +43,7 @@ test_that("glm_binomial", { expect_equal(res$errorMessage[3], "No errors") expect_equal(res$nsubs, 7485) expect_equal(res$iter, 9) - expect_true("family" %in% class(res$family)) + expect_true("character" %in% class(res$family)) expect_equal(res$formula, "D$DIS_DIAB ~ D$GENDER * D$PM_BMI_CONTINUOUS + D$LAB_HDL") expect_true("matrix" %in% class(res$coefficients)) expect_equal(res$dev, 1036.031, tolerance=0.00001) @@ -69,7 +69,7 @@ test_that("glm_binomial, with check", { expect_equal(res$errorMessage[3], "No errors") expect_equal(res$nsubs, 7485) expect_equal(res$iter, 9) - expect_true("family" %in% class(res$family)) + expect_true("character" %in% class(res$family)) expect_equal(res$formula, "D$DIS_DIAB ~ D$GENDER * D$PM_BMI_CONTINUOUS + D$LAB_HDL") expect_true("matrix" %in% class(res$coefficients)) expect_equal(res$dev, 1036.031, tolerance=0.00001) diff --git a/tests/testthat/test-smk-ds.glm-gaussian.R b/tests/testthat/test-smk-ds.glm-gaussian.R index 569fbdd9..27d3f025 100644 --- a/tests/testthat/test-smk-ds.glm-gaussian.R +++ b/tests/testthat/test-smk-ds.glm-gaussian.R @@ -43,7 +43,7 @@ test_that("glm_gaussian", { expect_equal(res$errorMessage[3], "No errors") expect_equal(res$nsubs, 7800) expect_equal(res$iter, 3) - expect_true("family" %in% class(res$family)) + expect_true("character" %in% class(res$family)) expect_equal(res$formula, "D$LAB_TSC ~ D$LAB_TRIG") expect_true("matrix" %in% class(res$coefficients)) expect_equal(res$dev, 8936.32, tolerance=0.00001) @@ -69,7 +69,7 @@ test_that("glm_gaussian, with check", { expect_equal(res$errorMessage[3], "No errors") expect_equal(res$nsubs, 7800) expect_equal(res$iter, 3) - expect_true("family" %in% class(res$family)) + expect_true("character" %in% class(res$family)) expect_equal(res$formula, "D$LAB_TSC ~ D$LAB_TRIG") expect_true("matrix" %in% class(res$coefficients)) expect_equal(res$dev, 8936.32, tolerance=0.00001) diff --git a/tests/testthat/test-smk-ds.glm-poisson.R b/tests/testthat/test-smk-ds.glm-poisson.R index 19c56ebc..62077942 100644 --- a/tests/testthat/test-smk-ds.glm-poisson.R +++ b/tests/testthat/test-smk-ds.glm-poisson.R @@ -43,7 +43,7 @@ test_that("glm_gaussian", { expect_equal(res$errorMessage[3], "No errors") expect_equal(res$nsubs, 6299) expect_equal(res$iter, 5) - expect_true("family" %in% class(res$family)) + expect_true("character" %in% class(res$family)) expect_equal(res$formula, "D$survtime ~ 1 + D$time.id + D$female") expect_true("matrix" %in% class(res$coefficients)) expect_equal(res$dev, 3522.598, tolerance=0.00001) @@ -69,7 +69,7 @@ test_that("glm_gaussian, which check", { expect_equal(res$errorMessage[3], "No errors") expect_equal(res$nsubs, 6299) expect_equal(res$iter, 5) - expect_true("family" %in% class(res$family)) + expect_true("character" %in% class(res$family)) expect_equal(res$formula, "D$survtime ~ 1 + D$time.id + D$female") expect_true("matrix" %in% class(res$coefficients)) expect_equal(res$dev, 3522.598, tolerance=0.00001) diff --git a/tests/testthat/test-smk-ds.lspline.R b/tests/testthat/test-smk-ds.lspline.R index 08d45470..9e86eaf7 100644 --- a/tests/testthat/test-smk-ds.lspline.R +++ b/tests/testthat/test-smk-ds.lspline.R @@ -56,7 +56,7 @@ test_that("lspline", { expect_equal(res.mod$errorMessage[3], "No errors") expect_equal(res.mod$nsubs, 7477) expect_equal(res.mod$iter, 3) - expect_true("family" %in% class(res.mod$family)) + expect_true("character" %in% class(res.mod$family)) expect_equal(res.mod$formula, "D$LAB_TRIG ~ lsplineDS") expect_true("matrix" %in% class(res.mod$coefficients)) expect_true("array" %in% class(res.mod$coefficients)) diff --git a/tests/testthat/test-smk-ds.ns.R b/tests/testthat/test-smk-ds.ns.R index d925aa1e..19d73dd2 100644 --- a/tests/testthat/test-smk-ds.ns.R +++ b/tests/testthat/test-smk-ds.ns.R @@ -60,7 +60,7 @@ test_that("ns", { expect_equal(res.mod$errorMessage[3], "No errors") expect_equal(res.mod$nsubs, 7477) expect_equal(res.mod$iter, 3) - expect_true("family" %in% class(res.mod$family)) + expect_true("character" %in% class(res.mod$family)) expect_equal(res.mod$formula, "D$LAB_TRIG ~ nsDS") expect_true("matrix" %in% class(res.mod$coefficients)) expect_true("array" %in% class(res.mod$coefficients)) diff --git a/tests/testthat/test-smk-ds.qlspline.R b/tests/testthat/test-smk-ds.qlspline.R index e8b89701..89ee316c 100644 --- a/tests/testthat/test-smk-ds.qlspline.R +++ b/tests/testthat/test-smk-ds.qlspline.R @@ -56,7 +56,7 @@ test_that("qlspline", { expect_equal(res.mod$errorMessage[3], "No errors") expect_equal(res.mod$nsubs, 7477) expect_equal(res.mod$iter, 3) - expect_true("family" %in% class(res.mod$family)) + expect_true("character" %in% class(res.mod$family)) expect_equal(res.mod$formula, "D$LAB_TRIG ~ qlsplineDS") expect_true("matrix" %in% class(res.mod$coefficients)) expect_true("array" %in% class(res.mod$coefficients)) @@ -108,7 +108,7 @@ test_that("qlspline", { expect_equal(res.mod$errorMessage[3], "No errors") expect_equal(res.mod$nsubs, 7477) expect_equal(res.mod$iter, 3) - expect_true("family" %in% class(res.mod$family)) + expect_true("character" %in% class(res.mod$family)) expect_equal(res.mod$formula, "D$LAB_TRIG ~ qlsplineDS2") expect_true("matrix" %in% class(res.mod$coefficients)) expect_true("array" %in% class(res.mod$coefficients))