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StuartWheaterStuartWheater
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Merge pull request #676 from StuartWheater/v6.3.6-dev
Maintance update
2 parents 2cccc17 + 1dff161 commit 50a441b

16 files changed

Lines changed: 705 additions & 1 deletion

‎DESCRIPTION‎

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Original file line numberDiff line numberDiff line change
@@ -81,6 +81,6 @@ Suggests:
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DSOpal,
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DSMolgenisArmadillo,
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DSLite
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RoxygenNote: 7.3.3
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Encoding: UTF-8
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Language: en-GB
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Config/roxygen2/version: 8.0.0

‎tests/testthat/connection_to_datasets/init_studies_datasets.R‎

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Original file line numberDiff line numberDiff line change
@@ -221,6 +221,62 @@ init.studies.dataset.gamlss <- function(variables)
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}
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}
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init.studies.dataset.stand <- function(variables)
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{
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if (ds.test_env$secure_login_details)
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{
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if (ds.test_env$driver == "OpalDriver")
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{
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builder <- DSI::newDSLoginBuilder(.silent = TRUE)
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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$options_1)
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builder$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)
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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$options_3)
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ds.test_env$login.data <- builder$build()
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}
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else if (ds.test_env$driver == "ArmadilloDriver")
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{
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builder <- DSI::newDSLoginBuilder(.silent = TRUE)
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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$driver)
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builder$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)
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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$driver)
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ds.test_env$login.data <- builder$build()
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}
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else
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{
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ds.test_env$login.data <- DSLite::setupCNSIMTest("dsBase", env = ds.test_env)
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}
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ds.test_env$stats.var <- variables
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}
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}
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init.studies.dataset.stand_disclosure <- function(variables)
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{
254+
if (ds.test_env$secure_login_details)
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{
256+
if (ds.test_env$driver == "OpalDriver")
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{
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builder <- DSI::newDSLoginBuilder(.silent = TRUE)
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builder$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)
260+
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$options_2)
261+
builder$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)
262+
ds.test_env$login.data <- builder$build()
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}
264+
else if (ds.test_env$driver == "ArmadilloDriver")
265+
{
266+
builder <- DSI::newDSLoginBuilder(.silent = TRUE)
267+
builder$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)
268+
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$driver)
269+
builder$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)
270+
ds.test_env$login.data <- builder$build()
271+
}
272+
else
273+
{
274+
ds.test_env$login.data <- DSLite::setupCNSIMTest("dsBase", env = ds.test_env)
275+
}
276+
ds.test_env$stats.var <- variables
277+
}
278+
}
279+
224280

225281
connect.studies.dataset.cnsim <- function(variables)
226282
{
@@ -278,6 +334,22 @@ connect.studies.dataset.gamlss <- function(variables)
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log.in.data.server()
279335
}
280336

337+
connect.studies.dataset.stand <- function(variables)
338+
{
339+
log.out.data.server()
340+
source("connection_to_datasets/login_details.R")
341+
init.studies.dataset.stand(variables)
342+
log.in.data.server()
343+
}
344+
345+
connect.studies.dataset.stand_disclosure <- function(variables)
346+
{
347+
log.out.data.server()
348+
source("connection_to_datasets/login_details.R")
349+
init.studies.dataset.stand_disclosure(variables)
350+
log.in.data.server()
351+
}
352+
281353
disconnect.studies.dataset.cnsim <- function()
282354
{
283355
log.out.data.server()
@@ -312,3 +384,13 @@ disconnect.studies.dataset.gamlss <- function()
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{
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log.out.data.server()
314386
}
387+
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disconnect.studies.dataset.stand <- function()
389+
{
390+
log.out.data.server()
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}
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disconnect.studies.dataset.stand_disclosure <- function()
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{
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log.out.data.server()
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}

‎tests/testthat/data_files/STANDARDISE/std_1.csv‎

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1+
fac_col1,fac_col2,fac_col3,fac_col4,fac_col5,fac_col6,fac_col9,col12,col15,col18
2+
High,Blue,Yes,3,NA,Bird,True,28.757752012461424,31,TRUE
3+
High,Blue,Yes,3,NA,Bird,True,78.83051354438066,79,TRUE
4+
High,Blue,Yes,3,NA,Bird,True,40.89769218116999,51,TRUE
5+
Medium,Green,No,2,NA,Dog,False,88.301740400493145,14,FALSE
6+
High,Blue,Yes,3,NA,Bird,True,94.04672842938453,67,TRUE
7+
Medium,Green,No,2,NA,Dog,False,4.555649938993156,42,FALSE
8+
Medium,Green,No,2,NA,Dog,False,52.810548804700375,50,FALSE
9+
Medium,Green,No,2,NA,Dog,False,89.2419044394046,43,FALSE
10+
High,Blue,Yes,3,NA,Bird,True,55.14350144658238,14,TRUE
11+
Low,NA,Yes,1,NA,Cat,True,45.661473530344665,25,TRUE
12+
Medium,Green,No,2,NA,Dog,False,95.68333453498781,90,FALSE
13+
Medium,Green,No,2,NA,Dog,False,45.33341561909765,91,FALSE
14+
Low,NA,No,1,NA,Cat,False,67.75706354528666,69,FALSE
15+
Medium,Green,Yes,2,NA,Dog,True,57.26334019564092,91,TRUE
16+
High,Blue,No,3,NA,Bird,False,10.292468266561627,57,FALSE
17+
Low,NA,Yes,1,NA,Cat,True,89.98249704018235,92,TRUE
18+
High,Blue,No,3,NA,Bird,False,24.60877343546599,9,FALSE
19+
High,Blue,Yes,3,NA,Bird,True,4.205953353084624,93,TRUE
20+
Low,NA,Yes,1,NA,Cat,True,32.79207192827016,99,TRUE
21+
Low,NA,Yes,1,NA,Cat,True,95.45036491472274,72,TRUE
22+
Low,NA,Yes,1,NA,Cat,True,88.95393160637468,26,TRUE
23+
Low,NA,No,1,NA,Cat,False,69.28034061565995,7,FALSE
24+
High,Blue,Yes,3,NA,Bird,True,64.05068137682974,42,TRUE
25+
Medium,Green,Yes,2,NA,Dog,True,99.42697766236961,9,TRUE
26+
High,Blue,Yes,3,NA,Bird,True,65.57057991158217,83,TRUE
27+
Medium,Green,Yes,2,NA,Dog,True,70.85304681677371,36,TRUE
28+
Low,NA,No,1,NA,Cat,False,54.40660247113556,78,FALSE
29+
Medium,Green,No,2,NA,Dog,False,59.41420204471797,81,FALSE
30+
High,Blue,Yes,3,NA,Bird,True,28.91597372945398,43,TRUE
31+
Medium,Green,No,2,NA,Dog,False,14.711364731192589,76,FALSE
32+
Low,NA,Yes,1,NA,Cat,True,96.30242325365543,15,TRUE
33+
High,Blue,No,3,NA,Bird,False,90.22990451194346,32,FALSE
34+
High,Blue,Yes,3,NA,Bird,True,69.07052784226835,7,TRUE
35+
Low,NA,No,1,NA,Cat,False,79.54674176871777,9,FALSE
36+
High,Blue,No,3,NA,Bird,False,2.461368450894952,41,FALSE
37+
Medium,Green,Yes,2,NA,Dog,True,47.77959710918367,74,TRUE
38+
Low,NA,Yes,1,NA,Cat,True,75.84595375228673,23,TRUE
39+
High,Blue,Yes,3,NA,Bird,True,21.640793583355844,27,TRUE
40+
Low,NA,Yes,1,NA,Cat,True,31.818100763484836,60,TRUE
41+
Low,NA,No,1,NA,Cat,False,23.16257853526622,53,FALSE
42+
Medium,Green,Yes,2,NA,Dog,True,14.280002238228917,7,TRUE
43+
High,Blue,No,3,NA,Bird,False,41.45463358145207,53,FALSE
44+
High,Blue,No,3,NA,Bird,False,41.372432629577816,27,FALSE
45+
Low,NA,Yes,1,NA,Cat,True,36.884545092470944,96,TRUE
46+
High,Blue,Yes,3,NA,Bird,True,15.244474774226546,38,TRUE
47+
Low,NA,Yes,1,NA,Cat,True,13.880606344901025,89,TRUE
48+
High,Blue,Yes,3,NA,Bird,True,23.303409945219755,34,TRUE
49+
Medium,Green,No,2,NA,Dog,False,46.59624502528459,93,FALSE
50+
Low,NA,Yes,1,NA,Cat,True,26.597264036536217,69,TRUE
51+
Medium,Green,Yes,2,NA,Dog,True,85.78277153428644,72,TRUE
52+
Low,NA,No,1,NA,Cat,False,4.583116667345166,76,FALSE
53+
Low,NA,Yes,1,NA,Cat,True,44.220007420517504,63,TRUE
54+
High,Blue,Yes,3,NA,Bird,True,79.89248456433415,13,TRUE
55+
Low,NA,Yes,1,NA,Cat,True,12.189925997518003,82,TRUE
56+
Medium,Green,Yes,2,NA,Dog,True,56.094798375852406,97,TRUE
57+
Low,NA,No,1,NA,Cat,False,20.65313896164298,91,FALSE
58+
Low,NA,No,1,NA,Cat,False,12.753165024332702,25,FALSE
59+
High,Blue,Yes,3,NA,Bird,True,75.33078643027693,38,TRUE
60+
Low,NA,No,1,NA,Cat,False,89.50453591533005,21,FALSE
61+
Medium,Green,Yes,2,NA,Dog,True,37.44627758860588,79,TRUE
62+
Low,NA,Yes,1,NA,Cat,True,66.51151946280152,41,TRUE
63+
High,Blue,No,3,NA,Bird,False,9.484066092409194,47,FALSE
64+
Low,NA,No,1,NA,Cat,False,38.39696377981454,90,FALSE
65+
High,Blue,Yes,3,NA,Bird,True,27.43836445733905,60,TRUE
66+
Medium,Green,Yes,2,NA,Dog,True,81.46400388795882,95,TRUE
67+
High,Blue,No,3,NA,Bird,False,44.851634139195085,16,FALSE
68+
Medium,Green,Yes,2,NA,Dog,True,81.00643530488014,94,TRUE
69+
Medium,Green,Yes,2,NA,Dog,True,81.23895095195621,6,TRUE
70+
High,Blue,Yes,3,NA,Bird,True,79.43423211108893,72,TRUE
71+
Medium,Green,Yes,2,NA,Dog,True,43.983168760314584,86,TRUE
72+
Medium,Green,No,2,NA,Dog,False,75.44751586392522,86,FALSE
73+
High,Blue,Yes,3,NA,Bird,True,62.922113155946136,39,TRUE
74+
High,Blue,Yes,3,NA,Bird,True,71.01824013516307,31,TRUE
75+
Low,NA,Yes,1,NA,Cat,True,0.062477332539856434,81,TRUE
76+
Medium,Green,Yes,2,NA,Dog,True,47.53165740985423,50,TRUE
77+
Medium,Green,No,2,NA,Dog,False,22.011888516135514,34,FALSE
78+
Low,NA,No,1,NA,Cat,False,37.98165377229452,4,FALSE
79+
Medium,Green,Yes,2,NA,Dog,True,61.277100327424705,13,TRUE
80+
Low,NA,No,1,NA,Cat,False,35.179790924303234,69,FALSE
81+
Low,NA,No,1,NA,Cat,False,11.113542434759438,25,FALSE
82+
Medium,Green,No,2,NA,Dog,False,24.361947271972895,52,FALSE
83+
High,Blue,No,3,NA,Bird,False,66.80555874481797,22,FALSE
84+
High,Blue,Yes,3,NA,Bird,True,41.764677967876196,89,TRUE
85+
Low,NA,No,1,NA,Cat,False,78.81958340294659,32,FALSE
86+
Medium,Green,No,2,NA,Dog,False,10.286464425735176,25,FALSE
87+
Low,NA,No,1,NA,Cat,False,43.489274149760604,87,FALSE
88+
Medium,Green,Yes,2,NA,Dog,True,98.49569799844176,35,TRUE
89+
Low,NA,Yes,1,NA,Cat,True,89.30511143989861,40,TRUE
90+
High,Blue,No,3,NA,Bird,False,88.64690607879311,30,FALSE
91+
High,Blue,Yes,3,NA,Bird,True,17.505265027284622,12,TRUE
92+
Medium,Green,No,2,NA,Dog,False,13.069569156505167,31,FALSE
93+
High,Blue,No,3,NA,Bird,False,65.31019250396639,30,FALSE
94+
Low,NA,Yes,1,NA,Cat,True,34.3516472261399,64,TRUE
95+
Medium,Green,No,2,NA,Dog,False,65.67581279668957,99,FALSE
96+
Medium,Green,No,2,NA,Dog,False,32.03732424881309,14,FALSE
97+
High,Blue,Yes,3,NA,Bird,True,18.769111926667392,93,TRUE
98+
Medium,Green,Yes,2,NA,Dog,True,78.22943013161421,96,TRUE
99+
Low,NA,No,1,NA,Cat,False,9.359498671256006,71,FALSE
100+
High,Blue,Yes,3,NA,Bird,True,46.677904156968,67,TRUE
101+
High,Blue,Yes,3,NA,Bird,True,51.15054599009454,23,TRUE

‎tests/testthat/data_files/STANDARDISE/std_1.rda‎

1.44 KB
Binary file not shown.

‎tests/testthat/data_files/STANDARDISE/std_1_d.csv‎

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fac_col1,fac_col2,fac_col3,fac_col4,fac_col5,fac_col6,fac_col9,col12,col15,col18
2+
High,Blue,Yes,3,NA,Bird,True,28.7577520124614,31,TRUE
3+
High,Blue,Yes,3,NA,Bird,True,78.8305135443807,79,TRUE
4+
High,Blue,Yes,3,NA,Bird,True,40.89769218117,51,TRUE
5+
Medium,Green,No,2,NA,Dog,False,88.3017404004931,14,FALSE
6+
High,Blue,Yes,3,NA,Bird,True,94.0467284293845,67,TRUE
7+
Medium,Green,No,2,NA,Dog,False,4.55564993899316,42,FALSE
8+
Medium,Green,No,2,NA,Dog,False,52.8105488047004,50,FALSE
9+
Medium,Green,No,2,NA,Dog,False,89.2419044394046,43,FALSE
10+
High,Blue,Yes,3,NA,Bird,True,55.1435014465824,14,TRUE
11+
Low,NA,Yes,1,NA,Cat,True,45.6614735303447,25,TRUE
12+
Medium,Green,No,2,NA,Dog,False,95.6833345349878,90,FALSE
13+
Medium,Green,No,2,NA,Dog,False,45.3334156190977,91,FALSE
14+
Low,NA,No,1,NA,Cat,False,67.7570635452867,69,FALSE
15+
Medium,Green,Yes,2,NA,Dog,True,57.2633401956409,91,TRUE
16+
High,Blue,No,3,NA,Bird,False,10.2924682665616,57,FALSE
17+
Low,NA,Yes,1,NA,Cat,True,89.9824970401824,92,TRUE
18+
High,Blue,No,3,NA,Bird,False,24.608773435466,9,FALSE
19+
High,Blue,Yes,3,NA,Bird,True,4.20595335308462,93,TRUE
20+
Low,NA,Yes,1,NA,Cat,True,32.7920719282702,99,TRUE
21+
Low,NA,Yes,1,NA,Cat,True,95.4503649147227,72,TRUE
22+
Low,NA,Yes,1,NA,Cat,True,88.9539316063747,26,TRUE
23+
Low,NA,No,1,NA,Cat,False,69.28034061566,7,FALSE
24+
High,Blue,Yes,3,NA,Bird,True,64.0506813768297,42,TRUE
25+
Medium,Green,Yes,2,NA,Dog,True,99.4269776623696,9,TRUE
26+
High,Blue,Yes,3,NA,Bird,True,65.5705799115822,83,TRUE
27+
Medium,Green,Yes,2,NA,Dog,True,70.8530468167737,36,TRUE
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Low,NA,No,1,NA,Cat,False,54.4066024711356,78,FALSE
29+
Medium,Green,No,2,NA,Dog,False,59.414202044718,81,FALSE
30+
High,Blue,Yes,3,NA,Bird,True,28.915973729454,43,TRUE
31+
Medium,Green,No,2,NA,Dog,False,14.7113647311926,76,FALSE
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Low,NA,Yes,1,NA,Cat,True,96.3024232536554,15,TRUE
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High,Blue,No,3,NA,Bird,False,90.2299045119435,32,FALSE
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High,Blue,Yes,3,NA,Bird,True,69.0705278422683,7,TRUE
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Low,NA,No,1,NA,Cat,False,79.5467417687178,9,FALSE
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High,Blue,No,3,NA,Bird,False,2.46136845089495,41,FALSE
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Medium,Green,Yes,2,NA,Dog,True,47.7795971091837,74,TRUE
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Low,NA,Yes,1,NA,Cat,True,75.8459537522867,23,TRUE
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High,Blue,Yes,3,NA,Bird,True,21.6407935833558,27,TRUE
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Low,NA,Yes,1,NA,Cat,True,31.8181007634848,60,TRUE
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Low,NA,No,1,NA,Cat,False,23.1625785352662,53,FALSE
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Medium,Green,Yes,2,NA,Dog,True,14.2800022382289,7,TRUE
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High,Blue,No,3,NA,Bird,False,41.4546335814521,53,FALSE
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High,Blue,No,3,NA,Bird,False,41.3724326295778,27,FALSE
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Low,NA,Yes,1,NA,Cat,True,44.2200074205175,63,TRUE
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High,Blue,Yes,3,NA,Bird,True,79.8924845643342,13,TRUE
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Low,NA,Yes,1,NA,Cat,True,12.189925997518,82,TRUE
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Medium,Green,Yes,2,NA,Dog,True,56.0947983758524,97,TRUE
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Low,NA,No,1,NA,Cat,False,20.653138961643,91,FALSE
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Low,NA,No,1,NA,Cat,False,12.7531650243327,25,FALSE
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High,Blue,Yes,3,NA,Bird,True,75.3307864302769,38,TRUE
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Low,NA,No,1,NA,Cat,False,89.50453591533,21,FALSE
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Medium,Green,Yes,2,NA,Dog,True,37.4462775886059,79,TRUE
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Low,NA,Yes,1,NA,Cat,True,66.5115194628015,41,TRUE
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High,Blue,No,3,NA,Bird,False,9.48406609240919,47,FALSE
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Low,NA,No,1,NA,Cat,False,38.3969637798145,90,FALSE
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High,Blue,Yes,3,NA,Bird,True,27.438364457339,60,TRUE
66+
Medium,Green,Yes,2,NA,Dog,True,81.4640038879588,95,TRUE
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High,Blue,No,3,NA,Bird,False,44.8516341391951,16,FALSE
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Medium,Green,Yes,2,NA,Dog,True,81.0064353048801,94,TRUE
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Medium,Green,Yes,2,NA,Dog,True,81.2389509519562,6,TRUE
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High,Blue,Yes,3,NA,Bird,True,79.4342321110889,72,TRUE
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Medium,Green,Yes,2,NA,Dog,True,43.9831687603146,86,TRUE
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Medium,Green,No,2,NA,Dog,False,75.4475158639252,86,FALSE
73+
High,Blue,Yes,3,NA,Bird,True,62.9221131559461,39,TRUE
74+
High,Blue,Yes,3,NA,Bird,True,71.0182401351631,31,TRUE
75+
Low,NA,Yes,1,NA,Cat,True,0.0624773325398564,81,TRUE
76+
Medium,Green,Yes,2,NA,Dog,True,47.5316574098542,50,TRUE
77+
Medium,Green,No,2,NA,Dog,False,22.0118885161355,34,FALSE
78+
Low,NA,No,1,NA,Cat,False,37.9816537722945,4,FALSE
79+
Medium,Green,Yes,2,NA,Dog,True,61.2771003274247,13,TRUE
80+
Low,NA,No,1,NA,Cat,False,35.1797909243032,69,FALSE
81+
Low,NA,No,1,NA,Cat,False,11.1135424347594,25,FALSE
82+
Medium,Green,No,2,NA,Dog,False,24.3619472719729,52,FALSE
83+
High,Blue,No,3,NA,Bird,False,66.805558744818,22,FALSE
84+
High,Blue,Yes,3,NA,Bird,True,41.7646779678762,89,TRUE
85+
Low,NA,No,1,NA,Cat,False,78.8195834029466,32,FALSE
86+
Medium,Green,No,2,NA,Dog,False,10.2864644257352,25,FALSE
87+
Low,NA,No,1,NA,Cat,False,43.4892741497606,87,FALSE
88+
Medium,Green,Yes,2,NA,Dog,True,98.4956979984418,35,TRUE
89+
Low,NA,Yes,1,NA,Cat,True,89.3051114398986,40,TRUE
90+
High,Blue,No,3,NA,Bird,False,88.6469060787931,30,FALSE
91+
High,Blue,Yes,3,NA,Bird,True,17.5052650272846,12,TRUE
92+
Medium,Green,No,2,NA,Dog,False,13.0695691565052,31,FALSE
93+
High,Blue,No,3,NA,Bird,False,65.3101925039664,30,FALSE
94+
Low,NA,Yes,1,NA,Cat,True,34.3516472261399,64,TRUE
95+
Medium,Green,No,2,NA,Dog,False,65.6758127966896,99,FALSE
96+
Medium,Green,No,2,NA,Dog,False,32.0373242488131,14,FALSE
97+
High,Blue,Yes,3,NA,Bird,True,18.7691119266674,93,TRUE
98+
Medium,Green,Yes,2,NA,Dog,True,78.2294301316142,96,TRUE
99+
Low,NA,No,1,NA,Cat,False,9.35949867125601,71,FALSE
100+
High,Blue,Yes,3,NA,Bird,True,46.677904156968,67,TRUE
101+
High,Blue,Yes,3,NA,Bird,True,51.1505459900945,23,TRUE

‎tests/testthat/data_files/STANDARDISE/std_1_d.rda‎

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