/
test-datachk-CLUSTER_INT.R
330 lines (291 loc) · 17.9 KB
/
test-datachk-CLUSTER_INT.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
#-------------------------------------------------------------------------------
# Copyright (c) 2019-2022 University of 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.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#-------------------------------------------------------------------------------
#
# Set up
#
context("CLUSTER_INT::datachk::setup")
connect.studies.dataset.cluster.int(list("idSurgery", "trtGrp", "intSurgery", "nDoctors", "idDoctor", "intDoctor", "nPatients", "Male", "age", "BMI", "diabetes", "incid_rate", "private"))
test_that("setup", {
ds_expect_variables(c("D"))
})
#
# Tests
#
context("CLUSTER_INT::datachk")
test_that("Check CLUSTER INT dataset", {
res.class <- ds.class(x='D')
expect_length(res.class, 3)
expect_gte(length(res.class$cluster.int1), 1)
expect_true("data.frame" %in% res.class$cluster.int1)
expect_gte(length(res.class$cluster.int2), 1)
expect_true("data.frame" %in% res.class$cluster.int2)
expect_gte(length(res.class$cluster.int3), 1)
expect_true("data.frame" %in% res.class$cluster.int3)
res.length <- ds.length(x='D')
expect_length(res.length, 4)
expect_length(res.length$`length of D in cluster.int1`, 1)
expect_equal(res.length$`length of D in cluster.int1`, 13)
expect_length(res.length$`length of D in cluster.int2`, 1)
expect_equal(res.length$`length of D in cluster.int2`, 13)
expect_length(res.length$`length of D in cluster.int3`, 1)
expect_equal(res.length$`length of D in cluster.int3`, 13)
expect_equal(res.length$`total length of D in all studies combined`, 39)
res.colnames <- ds.colnames(x='D')
expect_length(res.colnames, 3)
expect_length(res.colnames$cluster.int1, 13)
expect_true(all(res.colnames$cluster.int1 %in% c("idSurgery", "trtGrp", "intSurgery", "nDoctors", "idDoctor", "intDoctor", "nPatients", "Male", "age", "BMI", "diabetes", "incid_rate", "private")))
expect_length(res.colnames$cluster.int2, 13)
expect_true(all(res.colnames$cluster.int2 %in% c("idSurgery", "trtGrp", "intSurgery", "nDoctors", "idDoctor", "intDoctor", "nPatients", "Male", "age", "BMI", "diabetes", "incid_rate", "private")))
expect_length(res.colnames$cluster.int3, 13)
expect_true(all(res.colnames$cluster.int3 %in% c("idSurgery", "trtGrp", "intSurgery", "nDoctors", "idDoctor", "intDoctor", "nPatients", "Male", "age", "BMI", "diabetes", "incid_rate", "private")))
res.class.idsurgery <- ds.class(x='D$idSurgery')
expect_length(res.class.idsurgery, 3)
expect_length(res.class.idsurgery$cluster.int1, 1)
expect_equal(res.class.idsurgery$cluster.int1, "factor")
expect_length(res.class.idsurgery$cluster.int2, 1)
expect_equal(res.class.idsurgery$cluster.int2, "factor")
expect_length(res.class.idsurgery$cluster.int3, 1)
expect_equal(res.class.idsurgery$cluster.int3, "factor")
res.length.idsurgery <- ds.length(x='D$idSurgery')
expect_length(res.length.idsurgery, 4)
expect_length(res.length.idsurgery$`length of D$idSurgery in cluster.int1`, 1)
expect_equal(res.length.idsurgery$`length of D$idSurgery in cluster.int1`, 1056)
expect_length(res.length.idsurgery$`length of D$idSurgery in cluster.int2`, 1)
expect_equal(res.length.idsurgery$`length of D$idSurgery in cluster.int2`, 991)
expect_length(res.length.idsurgery$`length of D$idSurgery in cluster.int3`, 1)
expect_equal(res.length.idsurgery$`length of D$idSurgery in cluster.int3`, 1094)
expect_length(res.length.idsurgery$`total length of D$idSurgery in all studies combined`, 1)
expect_equal(res.length.idsurgery$`total length of D$idSurgery in all studies combined`, 3141)
res.class.trtgrp <- ds.class(x='D$trtGrp')
expect_length(res.class.trtgrp, 3)
expect_length(res.class.trtgrp$cluster.int1, 1)
expect_equal(res.class.trtgrp$cluster.int1, "factor")
expect_length(res.class.trtgrp$cluster.int2, 1)
expect_equal(res.class.trtgrp$cluster.int2, "factor")
expect_length(res.class.trtgrp$cluster.int3, 1)
expect_equal(res.class.trtgrp$cluster.int3, "factor")
res.length.trtgrp <- ds.length(x='D$trtGrp')
expect_length(res.length.trtgrp, 4)
expect_length(res.length.trtgrp$`length of D$trtGrp in cluster.int1`, 1)
expect_equal(res.length.trtgrp$`length of D$trtGrp in cluster.int1`, 1056)
expect_length(res.length.trtgrp$`length of D$trtGrp in cluster.int2`, 1)
expect_equal(res.length.trtgrp$`length of D$trtGrp in cluster.int2`, 991)
expect_length(res.length.trtgrp$`length of D$trtGrp in cluster.int3`, 1)
expect_equal(res.length.trtgrp$`length of D$trtGrp in cluster.int3`, 1094)
expect_length(res.length.trtgrp$`total length of D$trtGrp in all studies combined`, 1)
expect_equal(res.length.trtgrp$`total length of D$trtGrp in all studies combined`, 3141)
res.class.intsurgery <- ds.class(x='D$intSurgery')
expect_length(res.class.intsurgery, 3)
expect_length(res.class.intsurgery$cluster.int1, 1)
expect_equal(res.class.intsurgery$cluster.int1, "numeric")
expect_length(res.class.intsurgery$cluster.int2, 1)
expect_equal(res.class.intsurgery$cluster.int2, "numeric")
expect_length(res.class.intsurgery$cluster.int3, 1)
expect_equal(res.class.intsurgery$cluster.int3, "numeric")
res.length.intsurgery <- ds.length(x='D$intSurgery')
expect_length(res.length.intsurgery, 4)
expect_length(res.length.intsurgery$`length of D$intSurgery in cluster.int1`, 1)
expect_equal(res.length.intsurgery$`length of D$intSurgery in cluster.int1`, 1056)
expect_length(res.length.intsurgery$`length of D$intSurgery in cluster.int2`, 1)
expect_equal(res.length.intsurgery$`length of D$intSurgery in cluster.int2`, 991)
expect_length(res.length.intsurgery$`length of D$intSurgery in cluster.int3`, 1)
expect_equal(res.length.intsurgery$`length of D$intSurgery in cluster.int3`, 1094)
expect_length(res.length.intsurgery$`total length of D$intSurgery in all studies combined`, 1)
expect_equal(res.length.intsurgery$`total length of D$intSurgery in all studies combined`, 3141)
res.class.nDoctors <- ds.class(x='D$nDoctors')
expect_length(res.class.nDoctors, 3)
expect_length(res.class.nDoctors$cluster.int1, 1)
expect_equal(res.class.nDoctors$cluster.int1, "integer")
expect_length(res.class.nDoctors$cluster.int2, 1)
expect_equal(res.class.nDoctors$cluster.int2, "integer")
expect_length(res.class.nDoctors$cluster.int3, 1)
expect_equal(res.class.nDoctors$cluster.int3, "integer")
res.length.nDoctors <- ds.length(x='D$nDoctors')
expect_length(res.length.nDoctors, 4)
expect_length(res.length.nDoctors$`length of D$nDoctors in cluster.int1`, 1)
expect_equal(res.length.nDoctors$`length of D$nDoctors in cluster.int1`, 1056)
expect_length(res.length.nDoctors$`length of D$nDoctors in cluster.int2`, 1)
expect_equal(res.length.nDoctors$`length of D$nDoctors in cluster.int2`, 991)
expect_length(res.length.nDoctors$`length of D$nDoctors in cluster.int3`, 1)
expect_equal(res.length.nDoctors$`length of D$nDoctors in cluster.int3`, 1094)
expect_length(res.length.nDoctors$`total length of D$nDoctors in all studies combined`, 1)
expect_equal(res.length.nDoctors$`total length of D$nDoctors in all studies combined`, 3141)
res.class.iddoctor <- ds.class(x='D$idDoctor')
expect_length(res.class.iddoctor, 3)
expect_length(res.class.iddoctor$cluster.int1, 1)
expect_equal(res.class.iddoctor$cluster.int1, "factor")
expect_length(res.class.iddoctor$cluster.int2, 1)
expect_equal(res.class.iddoctor$cluster.int2, "factor")
expect_length(res.class.iddoctor$cluster.int3, 1)
expect_equal(res.class.iddoctor$cluster.int3, "factor")
res.length.iddoctor <- ds.length(x='D$idDoctor')
expect_length(res.length.iddoctor, 4)
expect_length(res.length.iddoctor$`length of D$idDoctor in cluster.int1`, 1)
expect_equal(res.length.iddoctor$`length of D$idDoctor in cluster.int1`, 1056)
expect_length(res.length.iddoctor$`length of D$idDoctor in cluster.int2`, 1)
expect_equal(res.length.iddoctor$`length of D$idDoctor in cluster.int2`, 991)
expect_length(res.length.iddoctor$`length of D$idDoctor in cluster.int3`, 1)
expect_equal(res.length.iddoctor$`length of D$idDoctor in cluster.int3`, 1094)
expect_length(res.length.iddoctor$`total length of D$idDoctor in all studies combined`, 1)
expect_equal(res.length.iddoctor$`total length of D$idDoctor in all studies combined`, 3141)
res.class.intdoctor <- ds.class(x='D$intDoctor')
expect_length(res.class.intdoctor, 3)
expect_length(res.class.intdoctor$cluster.int1, 1)
expect_equal(res.class.intdoctor$cluster.int1, "numeric")
expect_length(res.class.intdoctor$cluster.int2, 1)
expect_equal(res.class.intdoctor$cluster.int2, "numeric")
expect_length(res.class.intdoctor$cluster.int3, 1)
expect_equal(res.class.intdoctor$cluster.int3, "numeric")
res.length.intdoctor <- ds.length(x='D$intDoctor')
expect_length(res.length.intdoctor, 4)
expect_length(res.length.intdoctor$`length of D$intDoctor in cluster.int1`, 1)
expect_equal(res.length.intdoctor$`length of D$intDoctor in cluster.int1`, 1056)
expect_length(res.length.intdoctor$`length of D$intDoctor in cluster.int2`, 1)
expect_equal(res.length.intdoctor$`length of D$intDoctor in cluster.int2`, 991)
expect_length(res.length.intdoctor$`length of D$intDoctor in cluster.int3`, 1)
expect_equal(res.length.intdoctor$`length of D$intDoctor in cluster.int3`, 1094)
expect_length(res.length.intdoctor$`total length of D$intDoctor in all studies combined`, 1)
expect_equal(res.length.intdoctor$`total length of D$intDoctor in all studies combined`, 3141)
res.class.npatients <- ds.class(x='D$nPatients')
expect_length(res.class.npatients, 3)
expect_length(res.class.npatients$cluster.int1, 1)
expect_equal(res.class.npatients$cluster.int1, "integer")
expect_length(res.class.npatients$cluster.int2, 1)
expect_equal(res.class.npatients$cluster.int2, "integer")
expect_length(res.class.npatients$cluster.int3, 1)
expect_equal(res.class.npatients$cluster.int3, "integer")
res.length.npatients <- ds.length(x='D$nPatients')
expect_length(res.length.npatients, 4)
expect_length(res.length.npatients$`length of D$nPatients in cluster.int1`, 1)
expect_equal(res.length.npatients$`length of D$nPatients in cluster.int1`, 1056)
expect_length(res.length.npatients$`length of D$nPatients in cluster.int2`, 1)
expect_equal(res.length.npatients$`length of D$nPatients in cluster.int2`, 991)
expect_length(res.length.npatients$`length of D$nPatients in cluster.int3`, 1)
expect_equal(res.length.npatients$`length of D$nPatients in cluster.int3`, 1094)
expect_length(res.length.npatients$`total length of D$nPatients in all studies combined`, 1)
expect_equal(res.length.npatients$`total length of D$nPatients in all studies combined`, 3141)
res.class.male <- ds.class(x='D$Male')
expect_length(res.class.male, 3)
expect_length(res.class.male$cluster.int1, 1)
expect_equal(res.class.male$cluster.int1, "factor")
expect_length(res.class.male$cluster.int2, 1)
expect_equal(res.class.male$cluster.int2, "factor")
expect_length(res.class.male$cluster.int3, 1)
expect_equal(res.class.male$cluster.int3, "factor")
res.length.male <- ds.length(x='D$Male')
expect_length(res.length.male, 4)
expect_length(res.length.male$`length of D$Male in cluster.int1`, 1)
expect_equal(res.length.male$`length of D$Male in cluster.int1`, 1056)
expect_length(res.length.male$`length of D$Male in cluster.int2`, 1)
expect_equal(res.length.male$`length of D$Male in cluster.int2`, 991)
expect_length(res.length.male$`length of D$Male in cluster.int3`, 1)
expect_equal(res.length.male$`length of D$Male in cluster.int3`, 1094)
expect_length(res.length.male$`total length of D$Male in all studies combined`, 1)
expect_equal(res.length.male$`total length of D$Male in all studies combined`, 3141)
res.class.age <- ds.class(x='D$age')
expect_length(res.class.age, 3)
expect_length(res.class.age$cluster.int1, 1)
expect_equal(res.class.age$cluster.int1, "numeric")
expect_length(res.class.age$cluster.int2, 1)
expect_equal(res.class.age$cluster.int2, "numeric")
expect_length(res.class.age$cluster.int3, 1)
expect_equal(res.class.age$cluster.int3, "numeric")
res.length.age <- ds.length(x='D$age')
expect_length(res.length.age, 4)
expect_length(res.length.age$`length of D$age in cluster.int1`, 1)
expect_equal(res.length.age$`length of D$age in cluster.int1`, 1056)
expect_length(res.length.age$`length of D$age in cluster.int2`, 1)
expect_equal(res.length.age$`length of D$age in cluster.int2`, 991)
expect_length(res.length.age$`length of D$age in cluster.int3`, 1)
expect_equal(res.length.age$`length of D$age in cluster.int3`, 1094)
expect_length(res.length.age$`total length of D$age in all studies combined`, 1)
expect_equal(res.length.age$`total length of D$age in all studies combined`, 3141)
res.class.bmi <- ds.class(x='D$BMI')
expect_length(res.class.bmi, 3)
expect_length(res.class.bmi$cluster.int1, 1)
expect_equal(res.class.bmi$cluster.int1, "numeric")
expect_length(res.class.bmi$cluster.int2, 1)
expect_equal(res.class.bmi$cluster.int2, "numeric")
expect_length(res.class.bmi$cluster.int3, 1)
expect_equal(res.class.bmi$cluster.int3, "numeric")
res.length.bmi <- ds.length(x='D$BMI')
expect_length(res.length.bmi, 4)
expect_length(res.length.bmi$`length of D$BMI in cluster.int1`, 1)
expect_equal(res.length.bmi$`length of D$BMI in cluster.int1`, 1056)
expect_length(res.length.bmi$`length of D$BMI in cluster.int2`, 1)
expect_equal(res.length.bmi$`length of D$BMI in cluster.int2`, 991)
expect_length(res.length.bmi$`length of D$BMI in cluster.int3`, 1)
expect_equal(res.length.bmi$`length of D$BMI in cluster.int3`, 1094)
expect_length(res.length.bmi$`total length of D$BMI in all studies combined`, 1)
expect_equal(res.length.bmi$`total length of D$BMI in all studies combined`, 3141)
res.class.private <- ds.class(x='D$private')
expect_length(res.class.private, 3)
expect_length(res.class.private$cluster.int1, 1)
expect_equal(res.class.private$cluster.int1, "factor")
expect_length(res.class.private$cluster.int2, 1)
expect_equal(res.class.private$cluster.int2, "factor")
expect_length(res.class.private$cluster.int3, 1)
expect_equal(res.class.private$cluster.int3, "factor")
res.length.private <- ds.length(x='D$private')
expect_length(res.length.private, 4)
expect_length(res.length.private$`length of D$private in cluster.int1`, 1)
expect_equal(res.length.private$`length of D$private in cluster.int1`, 1056)
expect_length(res.length.private$`length of D$private in cluster.int2`, 1)
expect_equal(res.length.private$`length of D$private in cluster.int2`, 991)
expect_length(res.length.private$`length of D$private in cluster.int3`, 1)
expect_equal(res.length.private$`length of D$private in cluster.int3`, 1094)
expect_length(res.length.private$`total length of D$private in all studies combined`, 1)
expect_equal(res.length.private$`total length of D$private in all studies combined`, 3141)
res.class.diabetes <- ds.class(x='D$diabetes')
expect_length(res.class.diabetes, 3)
expect_length(res.class.diabetes$cluster.int1, 1)
expect_equal(res.class.diabetes$cluster.int1, "factor")
expect_length(res.class.diabetes$cluster.int2, 1)
expect_equal(res.class.diabetes$cluster.int2, "factor")
expect_length(res.class.diabetes$cluster.int3, 1)
expect_equal(res.class.diabetes$cluster.int3, "factor")
res.length.diabetes <- ds.length(x='D$diabetes')
expect_length(res.length.diabetes, 4)
expect_length(res.length.diabetes$`length of D$diabetes in cluster.int1`, 1)
expect_equal(res.length.diabetes$`length of D$diabetes in cluster.int1`, 1056)
expect_length(res.length.diabetes$`length of D$diabetes in cluster.int2`, 1)
expect_equal(res.length.diabetes$`length of D$diabetes in cluster.int2`, 991)
expect_length(res.length.diabetes$`length of D$diabetes in cluster.int3`, 1)
expect_equal(res.length.diabetes$`length of D$diabetes in cluster.int3`, 1094)
expect_length(res.length.diabetes$`total length of D$diabetes in all studies combined`, 1)
expect_equal(res.length.diabetes$`total length of D$diabetes in all studies combined`, 3141)
res.class.incid_rate <- ds.class(x='D$incid_rate')
expect_length(res.class.incid_rate, 3)
expect_length(res.class.incid_rate$cluster.int1, 1)
expect_equal(res.class.incid_rate$cluster.int1, "integer")
expect_length(res.class.incid_rate$cluster.int2, 1)
expect_equal(res.class.incid_rate$cluster.int2, "integer")
expect_length(res.class.incid_rate$cluster.int3, 1)
expect_equal(res.class.incid_rate$cluster.int3, "integer")
res.length.incid_rate <- ds.length(x='D$incid_rate')
expect_length(res.length.incid_rate, 4)
expect_length(res.length.incid_rate$`length of D$incid_rate in cluster.int1`, 1)
expect_equal(res.length.incid_rate$`length of D$incid_rate in cluster.int1`, 1056)
expect_length(res.length.incid_rate$`length of D$incid_rate in cluster.int2`, 1)
expect_equal(res.length.incid_rate$`length of D$incid_rate in cluster.int2`, 991)
expect_length(res.length.incid_rate$`length of D$incid_rate in cluster.int3`, 1)
expect_equal(res.length.incid_rate$`length of D$incid_rate in cluster.int3`, 1094)
expect_length(res.length.incid_rate$`total length of D$incid_rate in all studies combined`, 1)
expect_equal(res.length.incid_rate$`total length of D$incid_rate in all studies combined`, 3141)
})
#
# Tear down
#
context("CLUSTER_INT::datachk::shutdown")
test_that("shutdown", {
ds_expect_variables(c("D"))
})
disconnect.studies.dataset.cluster.int()
context("CLUSTER_INT::datachk::done")