Maintance update

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

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()
+}

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
+High,Blue,Yes,3,NA,Bird,True,28.757752012461424,31,TRUE
+High,Blue,Yes,3,NA,Bird,True,78.83051354438066,79,TRUE
+High,Blue,Yes,3,NA,Bird,True,40.89769218116999,51,TRUE
+Medium,Green,No,2,NA,Dog,False,88.301740400493145,14,FALSE
+High,Blue,Yes,3,NA,Bird,True,94.04672842938453,67,TRUE
+Medium,Green,No,2,NA,Dog,False,4.555649938993156,42,FALSE
+Medium,Green,No,2,NA,Dog,False,52.810548804700375,50,FALSE
+Medium,Green,No,2,NA,Dog,False,89.2419044394046,43,FALSE
+High,Blue,Yes,3,NA,Bird,True,55.14350144658238,14,TRUE
+Low,NA,Yes,1,NA,Cat,True,45.661473530344665,25,TRUE
+Medium,Green,No,2,NA,Dog,False,95.68333453498781,90,FALSE
+Medium,Green,No,2,NA,Dog,False,45.33341561909765,91,FALSE
+Low,NA,No,1,NA,Cat,False,67.75706354528666,69,FALSE
+Medium,Green,Yes,2,NA,Dog,True,57.26334019564092,91,TRUE
+High,Blue,No,3,NA,Bird,False,10.292468266561627,57,FALSE
+Low,NA,Yes,1,NA,Cat,True,89.98249704018235,92,TRUE
+High,Blue,No,3,NA,Bird,False,24.60877343546599,9,FALSE
+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
+Medium,Green,Yes,2,NA,Dog,True,47.77959710918367,74,TRUE
+Low,NA,Yes,1,NA,Cat,True,75.84595375228673,23,TRUE
+High,Blue,Yes,3,NA,Bird,True,21.640793583355844,27,TRUE
+Low,NA,Yes,1,NA,Cat,True,31.818100763484836,60,TRUE
+Low,NA,No,1,NA,Cat,False,23.16257853526622,53,FALSE
+Medium,Green,Yes,2,NA,Dog,True,14.280002238228917,7,TRUE
+High,Blue,No,3,NA,Bird,False,41.45463358145207,53,FALSE
+High,Blue,No,3,NA,Bird,False,41.372432629577816,27,FALSE
+Low,NA,Yes,1,NA,Cat,True,36.884545092470944,96,TRUE
+High,Blue,Yes,3,NA,Bird,True,15.244474774226546,38,TRUE
+Low,NA,Yes,1,NA,Cat,True,13.880606344901025,89,TRUE
+High,Blue,Yes,3,NA,Bird,True,23.303409945219755,34,TRUE
+Medium,Green,No,2,NA,Dog,False,46.59624502528459,93,FALSE
+Low,NA,Yes,1,NA,Cat,True,26.597264036536217,69,TRUE
+Medium,Green,Yes,2,NA,Dog,True,85.78277153428644,72,TRUE
+Low,NA,No,1,NA,Cat,False,4.583116667345166,76,FALSE
+Low,NA,Yes,1,NA,Cat,True,44.220007420517504,63,TRUE
+High,Blue,Yes,3,NA,Bird,True,79.89248456433415,13,TRUE
+Low,NA,Yes,1,NA,Cat,True,12.189925997518003,82,TRUE
+Medium,Green,Yes,2,NA,Dog,True,56.094798375852406,97,TRUE
+Low,NA,No,1,NA,Cat,False,20.65313896164298,91,FALSE
+Low,NA,No,1,NA,Cat,False,12.753165024332702,25,FALSE
+High,Blue,Yes,3,NA,Bird,True,75.33078643027693,38,TRUE
+Low,NA,No,1,NA,Cat,False,89.50453591533005,21,FALSE
+Medium,Green,Yes,2,NA,Dog,True,37.44627758860588,79,TRUE
+Low,NA,Yes,1,NA,Cat,True,66.51151946280152,41,TRUE
+High,Blue,No,3,NA,Bird,False,9.484066092409194,47,FALSE
+Low,NA,No,1,NA,Cat,False,38.39696377981454,90,FALSE
+High,Blue,Yes,3,NA,Bird,True,27.43836445733905,60,TRUE
+Medium,Green,Yes,2,NA,Dog,True,81.46400388795882,95,TRUE
+High,Blue,No,3,NA,Bird,False,44.851634139195085,16,FALSE
+Medium,Green,Yes,2,NA,Dog,True,81.00643530488014,94,TRUE
+Medium,Green,Yes,2,NA,Dog,True,81.23895095195621,6,TRUE
+High,Blue,Yes,3,NA,Bird,True,79.43423211108893,72,TRUE
+Medium,Green,Yes,2,NA,Dog,True,43.983168760314584,86,TRUE
+Medium,Green,No,2,NA,Dog,False,75.44751586392522,86,FALSE
+High,Blue,Yes,3,NA,Bird,True,62.922113155946136,39,TRUE
+High,Blue,Yes,3,NA,Bird,True,71.01824013516307,31,TRUE
+Low,NA,Yes,1,NA,Cat,True,0.062477332539856434,81,TRUE
+Medium,Green,Yes,2,NA,Dog,True,47.53165740985423,50,TRUE
+Medium,Green,No,2,NA,Dog,False,22.011888516135514,34,FALSE
+Low,NA,No,1,NA,Cat,False,37.98165377229452,4,FALSE
+Medium,Green,Yes,2,NA,Dog,True,61.277100327424705,13,TRUE
+Low,NA,No,1,NA,Cat,False,35.179790924303234,69,FALSE
+Low,NA,No,1,NA,Cat,False,11.113542434759438,25,FALSE
+Medium,Green,No,2,NA,Dog,False,24.361947271972895,52,FALSE
+High,Blue,No,3,NA,Bird,False,66.80555874481797,22,FALSE
+High,Blue,Yes,3,NA,Bird,True,41.764677967876196,89,TRUE
+Low,NA,No,1,NA,Cat,False,78.81958340294659,32,FALSE
+Medium,Green,No,2,NA,Dog,False,10.286464425735176,25,FALSE
+Low,NA,No,1,NA,Cat,False,43.489274149760604,87,FALSE
+Medium,Green,Yes,2,NA,Dog,True,98.49569799844176,35,TRUE
+Low,NA,Yes,1,NA,Cat,True,89.30511143989861,40,TRUE
+High,Blue,No,3,NA,Bird,False,88.64690607879311,30,FALSE
+High,Blue,Yes,3,NA,Bird,True,17.505265027284622,12,TRUE
+Medium,Green,No,2,NA,Dog,False,13.069569156505167,31,FALSE
+High,Blue,No,3,NA,Bird,False,65.31019250396639,30,FALSE
+Low,NA,Yes,1,NA,Cat,True,34.3516472261399,64,TRUE
+Medium,Green,No,2,NA,Dog,False,65.67581279668957,99,FALSE
+Medium,Green,No,2,NA,Dog,False,32.03732424881309,14,FALSE
+High,Blue,Yes,3,NA,Bird,True,18.769111926667392,93,TRUE
+Medium,Green,Yes,2,NA,Dog,True,78.22943013161421,96,TRUE
+Low,NA,No,1,NA,Cat,False,9.359498671256006,71,FALSE
+High,Blue,Yes,3,NA,Bird,True,46.677904156968,67,TRUE
+High,Blue,Yes,3,NA,Bird,True,51.15054599009454,23,TRUE

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
+Low,NA,No,1,NA,Cat,False,67.7570635452867,69,FALSE
+Medium,Green,Yes,2,NA,Dog,True,57.2633401956409,91,TRUE
+High,Blue,No,3,NA,Bird,False,10.2924682665616,57,FALSE
+Low,NA,Yes,1,NA,Cat,True,89.9824970401824,92,TRUE
+High,Blue,No,3,NA,Bird,False,24.608773435466,9,FALSE
+High,Blue,Yes,3,NA,Bird,True,4.20595335308462,93,TRUE
+Low,NA,Yes,1,NA,Cat,True,32.7920719282702,99,TRUE
+Low,NA,Yes,1,NA,Cat,True,95.4503649147227,72,TRUE
+Low,NA,Yes,1,NA,Cat,True,88.9539316063747,26,TRUE
+Low,NA,No,1,NA,Cat,False,69.28034061566,7,FALSE
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+Medium,Green,No,2,NA,Dog,False,32.0373242488131,14,FALSE
+High,Blue,Yes,3,NA,Bird,True,18.7691119266674,93,TRUE
+Medium,Green,Yes,2,NA,Dog,True,78.2294301316142,96,TRUE
+Low,NA,No,1,NA,Cat,False,9.35949867125601,71,FALSE
+High,Blue,Yes,3,NA,Bird,True,46.677904156968,67,TRUE
+High,Blue,Yes,3,NA,Bird,True,51.1505459900945,23,TRUE