|
| 1 | +#------------------------------------------------------------------------------- |
| 2 | +# Copyright (c) 2019-2020 University of Newcastle upon Tyne. All rights reserved. |
| 3 | +# |
| 4 | +# This program and the accompanying materials |
| 5 | +# are made available under the terms of the GNU Public License v3.0. |
| 6 | +# |
| 7 | +# You should have received a copy of the GNU General Public License |
| 8 | +# along with this program. If not, see <http://www.gnu.org/licenses/>. |
| 9 | +#------------------------------------------------------------------------------- |
| 10 | + |
| 11 | +# |
| 12 | +# Set up |
| 13 | +# |
| 14 | + |
| 15 | +context("SURVIVAL_EXPAND_WITH_MISSING::datachk::setup") |
| 16 | + |
| 17 | +connect.studies.dataset.survival(list('id', 'study.id', 'time.id', 'starttime', 'endtime', 'survtime', 'cens', 'age.60', 'female', 'noise.56', 'pm10.16', 'bmi.26')) |
| 18 | + |
| 19 | +test_that("setup", { |
| 20 | + ds_expect_variables(c("D")) |
| 21 | +}) |
| 22 | + |
| 23 | +# |
| 24 | +# Tests |
| 25 | +# |
| 26 | + |
| 27 | +context("SURVIVAL_EXPAND_WITH_MISSING::datachk") |
| 28 | +test_that("Check SURVIVAL_EXPAND_WITH_MISSING dataset", { |
| 29 | + res.class <- ds.class(x='D') |
| 30 | + expect_length(res.class, 3) |
| 31 | + expect_length(res.class$survival1, 1) |
| 32 | + expect_equal(res.class$survival1, "data.frame") |
| 33 | + expect_length(res.class$survival2, 1) |
| 34 | + expect_equal(res.class$survival2, "data.frame") |
| 35 | + expect_length(res.class$survival3, 1) |
| 36 | + expect_equal(res.class$survival3, "data.frame") |
| 37 | + |
| 38 | + res.length <- ds.length(x='D') |
| 39 | + expect_length(res.length, 4) |
| 40 | + expect_length(res.length$`length of D in survival1`, 1) |
| 41 | + expect_equal(res.length$`length of D in survival1`, 12) |
| 42 | + expect_length(res.length$`length of D in survival2`, 1) |
| 43 | + expect_equal(res.length$`length of D in survival2`, 12) |
| 44 | + expect_length(res.length$`length of D in survival3`, 1) |
| 45 | + expect_equal(res.length$`length of D in survival3`, 12) |
| 46 | + expect_equal(res.length$`total length of D in all studies combined`, 36) |
| 47 | + |
| 48 | + res.colnames <- ds.colnames(x='D') |
| 49 | + expect_length(res.colnames, 3) |
| 50 | + expect_length(res.colnames$survival1, 12) |
| 51 | + expect_equal(res.colnames$survival1, c('id', 'study.id', 'time.id', 'starttime', 'endtime', 'survtime', 'cens', 'age.60', 'female', 'noise.56', 'pm10.16', 'bmi.26')) |
| 52 | + expect_length(res.colnames$survival2, 12) |
| 53 | + expect_equal(res.colnames$survival2, c('id', 'study.id', 'time.id', 'starttime', 'endtime', 'survtime', 'cens', 'age.60', 'female', 'noise.56', 'pm10.16', 'bmi.26')) |
| 54 | + expect_length(res.colnames$survival3, 12) |
| 55 | + expect_equal(res.colnames$survival3, c('id', 'study.id', 'time.id', 'starttime', 'endtime', 'survtime', 'cens', 'age.60', 'female', 'noise.56', 'pm10.16', 'bmi.26')) |
| 56 | + |
| 57 | + res.class.id <- ds.class(x='D$id') |
| 58 | + expect_length(res.class.id, 3) |
| 59 | + expect_length(res.class.id$survival1, 1) |
| 60 | + expect_equal(res.class.id$survival1, "integer") |
| 61 | + expect_length(res.class.id$survival2, 1) |
| 62 | + expect_equal(res.class.id$survival2, "integer") |
| 63 | + expect_length(res.class.id$survival3, 1) |
| 64 | + expect_equal(res.class.id$survival3, "integer") |
| 65 | + |
| 66 | + res.length.id <- ds.length(x='D$id') |
| 67 | + expect_length(res.length.id, 4) |
| 68 | + expect_length(res.length.id$`length of D$id in survival1`, 1) |
| 69 | + expect_equal(res.length.id$`length of D$id in survival1`, 2060) |
| 70 | + expect_length(res.length.id$`length of D$id in survival2`, 1) |
| 71 | + expect_equal(res.length.id$`length of D$id in survival2`, 1640) |
| 72 | + expect_length(res.length.id$`length of D$id in survival3`, 1) |
| 73 | + expect_equal(res.length.id$`length of D$id in survival3`, 2688) |
| 74 | + expect_length(res.length.id$`total length of D$id in all studies combined`, 1) |
| 75 | + expect_equal(res.length.id$`total length of D$id in all studies combined`, 6388) |
| 76 | + |
| 77 | + res.class.study.id <- ds.class(x='D$study.id') |
| 78 | + expect_length(res.class.study.id, 3) |
| 79 | + expect_length(res.class.study.id$survival1, 1) |
| 80 | + expect_equal(res.class.study.id$survival1, "integer") |
| 81 | + expect_length(res.class.study.id$survival2, 1) |
| 82 | + expect_equal(res.class.study.id$survival2, "integer") |
| 83 | + expect_length(res.class.study.id$survival3, 1) |
| 84 | + expect_equal(res.class.study.id$survival3, "integer") |
| 85 | + |
| 86 | + res.length.study.id <- ds.length(x='D$study.id') |
| 87 | + expect_length(res.length.study.id, 4) |
| 88 | + expect_length(res.length.study.id$`length of D$study.id in survival1`, 1) |
| 89 | + expect_equal(res.length.study.id$`length of D$study.id in survival1`, 2060) |
| 90 | + expect_length(res.length.study.id$`length of D$study.id in survival2`, 1) |
| 91 | + expect_equal(res.length.study.id$`length of D$study.id in survival2`, 1640) |
| 92 | + expect_length(res.length.study.id$`length of D$study.id in survival3`, 1) |
| 93 | + expect_equal(res.length.study.id$`length of D$study.id in survival3`, 2688) |
| 94 | + expect_length(res.length.study.id$`total length of D$study.id in all studies combined`, 1) |
| 95 | + expect_equal(res.length.study.id$`total length of D$study.id in all studies combined`, 6388) |
| 96 | + |
| 97 | + res.class.starttime <- ds.class(x='D$starttime') |
| 98 | + expect_length(res.class.starttime, 3) |
| 99 | + expect_length(res.class.starttime$survival1, 1) |
| 100 | + expect_equal(res.class.starttime$survival1, "numeric") |
| 101 | + expect_length(res.class.starttime$survival2, 1) |
| 102 | + expect_equal(res.class.starttime$survival2, "numeric") |
| 103 | + expect_length(res.class.starttime$survival3, 1) |
| 104 | + expect_equal(res.class.starttime$survival3, "numeric") |
| 105 | + |
| 106 | + res.length.starttime <- ds.length(x='D$starttime') |
| 107 | + expect_length(res.length.starttime, 4) |
| 108 | + expect_length(res.length.starttime$`length of D$starttime in survival1`, 1) |
| 109 | + expect_equal(res.length.starttime$`length of D$starttime in survival1`, 2060) |
| 110 | + expect_length(res.length.starttime$`length of D$starttime in survival2`, 1) |
| 111 | + expect_equal(res.length.starttime$`length of D$starttime in survival2`, 1640) |
| 112 | + expect_length(res.length.starttime$`length of D$starttime in survival3`, 1) |
| 113 | + expect_equal(res.length.starttime$`length of D$starttime in survival3`, 2688) |
| 114 | + expect_length(res.length.starttime$`total length of D$starttime in all studies combined`, 1) |
| 115 | + expect_equal(res.length.starttime$`total length of D$starttime in all studies combined`, 6388) |
| 116 | + |
| 117 | + res.class.endtime <- ds.class(x='D$endtime') |
| 118 | + expect_length(res.class.endtime, 3) |
| 119 | + expect_length(res.class.endtime$survival1, 1) |
| 120 | + expect_equal(res.class.endtime$survival1, "numeric") |
| 121 | + expect_length(res.class.endtime$survival2, 1) |
| 122 | + expect_equal(res.class.endtime$survival2, "numeric") |
| 123 | + expect_length(res.class.endtime$survival3, 1) |
| 124 | + expect_equal(res.class.endtime$survival3, "numeric") |
| 125 | + |
| 126 | + res.length.endtime <- ds.length(x='D$endtime') |
| 127 | + expect_length(res.length.endtime, 4) |
| 128 | + expect_length(res.length.endtime$`length of D$endtime in survival1`, 1) |
| 129 | + expect_equal(res.length.endtime$`length of D$endtime in survival1`, 2060) |
| 130 | + expect_length(res.length.endtime$`length of D$endtime in survival2`, 1) |
| 131 | + expect_equal(res.length.endtime$`length of D$endtime in survival2`, 1640) |
| 132 | + expect_length(res.length.endtime$`length of D$endtime in survival3`, 1) |
| 133 | + expect_equal(res.length.endtime$`length of D$endtime in survival3`, 2688) |
| 134 | + expect_length(res.length.endtime$`total length of D$endtime in all studies combined`, 1) |
| 135 | + expect_equal(res.length.endtime$`total length of D$endtime in all studies combined`, 6388) |
| 136 | + |
| 137 | + res.class.survtime <- ds.class(x='D$survtime') |
| 138 | + expect_length(res.class.survtime, 3) |
| 139 | + expect_length(res.class.survtime$survival1, 1) |
| 140 | + expect_equal(res.class.survtime$survival1, "numeric") |
| 141 | + expect_length(res.class.survtime$survival2, 1) |
| 142 | + expect_equal(res.class.survtime$survival2, "numeric") |
| 143 | + expect_length(res.class.survtime$survival3, 1) |
| 144 | + expect_equal(res.class.survtime$survival3, "numeric") |
| 145 | + |
| 146 | + res.length.survtime <- ds.length(x='D$survtime') |
| 147 | + expect_length(res.length.survtime, 4) |
| 148 | + expect_length(res.length.survtime$`length of D$survtime in survival1`, 1) |
| 149 | + expect_equal(res.length.survtime$`length of D$survtime in survival1`, 2060) |
| 150 | + expect_length(res.length.survtime$`length of D$survtime in survival2`, 1) |
| 151 | + expect_equal(res.length.survtime$`length of D$survtime in survival2`, 1640) |
| 152 | + expect_length(res.length.survtime$`length of D$survtime in survival3`, 1) |
| 153 | + expect_equal(res.length.survtime$`length of D$survtime in survival3`, 2688) |
| 154 | + expect_length(res.length.survtime$`total length of D$survtime in all studies combined`, 1) |
| 155 | + expect_equal(res.length.survtime$`total length of D$survtime in all studies combined`, 6388) |
| 156 | + |
| 157 | + res.class.cens <- ds.class(x='D$cens') |
| 158 | + expect_length(res.class.cens, 3) |
| 159 | + expect_length(res.class.cens$survival1, 1) |
| 160 | + expect_equal(res.class.cens$survival1, "factor") |
| 161 | + expect_length(res.class.cens$survival2, 1) |
| 162 | + expect_equal(res.class.cens$survival2, "factor") |
| 163 | + expect_length(res.class.cens$survival3, 1) |
| 164 | + expect_equal(res.class.cens$survival3, "factor") |
| 165 | + |
| 166 | + res.length.cens <- ds.length(x='D$cens') |
| 167 | + expect_length(res.length.cens, 4) |
| 168 | + expect_length(res.length.cens$`length of D$cens in survival1`, 1) |
| 169 | + expect_equal(res.length.cens$`length of D$cens in survival1`, 2060) |
| 170 | + expect_length(res.length.cens$`length of D$cens in survival2`, 1) |
| 171 | + expect_equal(res.length.cens$`length of D$cens in survival2`, 1640) |
| 172 | + expect_length(res.length.cens$`length of D$cens in survival3`, 1) |
| 173 | + expect_equal(res.length.cens$`length of D$cens in survival3`, 2688) |
| 174 | + expect_length(res.length.cens$`total length of D$cens in all studies combined`, 1) |
| 175 | + expect_equal(res.length.cens$`total length of D$cens in all studies combined`, 6388) |
| 176 | + |
| 177 | + res.class.age.60 <- ds.class(x='D$age.60') |
| 178 | + expect_length(res.class.age.60, 3) |
| 179 | + expect_length(res.class.age.60$survival1, 1) |
| 180 | + expect_equal(res.class.age.60$survival1, "numeric") |
| 181 | + expect_length(res.class.age.60$survival2, 1) |
| 182 | + expect_equal(res.class.age.60$survival2, "numeric") |
| 183 | + expect_length(res.class.age.60$survival3, 1) |
| 184 | + expect_equal(res.class.age.60$survival3, "numeric") |
| 185 | + |
| 186 | + res.length.age.60 <- ds.length(x='D$age.60') |
| 187 | + expect_length(res.length.age.60, 4) |
| 188 | + expect_length(res.length.age.60$`length of D$age.60 in survival1`, 1) |
| 189 | + expect_equal(res.length.age.60$`length of D$age.60 in survival1`, 2060) |
| 190 | + expect_length(res.length.age.60$`length of D$age.60 in survival2`, 1) |
| 191 | + expect_equal(res.length.age.60$`length of D$age.60 in survival2`, 1640) |
| 192 | + expect_length(res.length.age.60$`length of D$age.60 in survival3`, 1) |
| 193 | + expect_equal(res.length.age.60$`length of D$age.60 in survival3`, 2688) |
| 194 | + expect_length(res.length.age.60$`total length of D$age.60 in all studies combined`, 1) |
| 195 | + expect_equal(res.length.age.60$`total length of D$age.60 in all studies combined`, 6388) |
| 196 | + |
| 197 | + res.class.female <- ds.class(x='D$female') |
| 198 | + expect_length(res.class.female, 3) |
| 199 | + expect_length(res.class.female$survival1, 1) |
| 200 | + expect_equal(res.class.female$survival1, "factor") |
| 201 | + expect_length(res.class.female$survival2, 1) |
| 202 | + expect_equal(res.class.female$survival2, "factor") |
| 203 | + expect_length(res.class.female$survival3, 1) |
| 204 | + expect_equal(res.class.female$survival3, "factor") |
| 205 | + |
| 206 | + res.length.female <- ds.length(x='D$female') |
| 207 | + expect_length(res.length.female, 4) |
| 208 | + expect_length(res.length.female$`length of D$female in survival1`, 1) |
| 209 | + expect_equal(res.length.female$`length of D$female in survival1`, 2060) |
| 210 | + expect_length(res.length.female$`length of D$female in survival2`, 1) |
| 211 | + expect_equal(res.length.female$`length of D$female in survival2`, 1640) |
| 212 | + expect_length(res.length.female$`length of D$female in survival3`, 1) |
| 213 | + expect_equal(res.length.female$`length of D$female in survival3`, 2688) |
| 214 | + expect_length(res.length.female$`total length of D$female in all studies combined`, 1) |
| 215 | + expect_equal(res.length.female$`total length of D$female in all studies combined`, 6388) |
| 216 | + |
| 217 | + res.class.noise.56 <- ds.class(x='D$noise.56') |
| 218 | + expect_length(res.class.noise.56, 3) |
| 219 | + expect_length(res.class.noise.56$survival1, 1) |
| 220 | + expect_equal(res.class.noise.56$survival1, "numeric") |
| 221 | + expect_length(res.class.noise.56$survival2, 1) |
| 222 | + expect_equal(res.class.noise.56$survival2, "numeric") |
| 223 | + expect_length(res.class.noise.56$survival3, 1) |
| 224 | + expect_equal(res.class.noise.56$survival3, "numeric") |
| 225 | + |
| 226 | + res.length.noise.56 <- ds.length(x='D$noise.56') |
| 227 | + expect_length(res.length.noise.56, 4) |
| 228 | + expect_length(res.length.noise.56$`length of D$noise.56 in survival1`, 1) |
| 229 | + expect_equal(res.length.noise.56$`length of D$noise.56 in survival1`, 2060) |
| 230 | + expect_length(res.length.noise.56$`length of D$noise.56 in survival2`, 1) |
| 231 | + expect_equal(res.length.noise.56$`length of D$noise.56 in survival2`, 1640) |
| 232 | + expect_length(res.length.noise.56$`length of D$noise.56 in survival3`, 1) |
| 233 | + expect_equal(res.length.noise.56$`length of D$noise.56 in survival3`, 2688) |
| 234 | + expect_length(res.length.noise.56$`total length of D$noise.56 in all studies combined`, 1) |
| 235 | + expect_equal(res.length.noise.56$`total length of D$noise.56 in all studies combined`, 6388) |
| 236 | + |
| 237 | + res.class.pm10.16 <- ds.class(x='D$pm10.16') |
| 238 | + expect_length(res.class.pm10.16, 3) |
| 239 | + expect_length(res.class.pm10.16$survival1, 1) |
| 240 | + expect_equal(res.class.pm10.16$survival1, "numeric") |
| 241 | + expect_length(res.class.pm10.16$survival2, 1) |
| 242 | + expect_equal(res.class.pm10.16$survival2, "numeric") |
| 243 | + expect_length(res.class.pm10.16$survival3, 1) |
| 244 | + expect_equal(res.class.pm10.16$survival3, "numeric") |
| 245 | + |
| 246 | + res.length.pm10.16 <- ds.length(x='D$pm10.16') |
| 247 | + expect_length(res.length.pm10.16, 4) |
| 248 | + expect_length(res.length.pm10.16$`length of D$pm10.16 in survival1`, 1) |
| 249 | + expect_equal(res.length.pm10.16$`length of D$pm10.16 in survival1`, 2060) |
| 250 | + expect_length(res.length.pm10.16$`length of D$pm10.16 in survival2`, 1) |
| 251 | + expect_equal(res.length.pm10.16$`length of D$pm10.16 in survival2`, 1640) |
| 252 | + expect_length(res.length.pm10.16$`length of D$pm10.16 in survival3`, 1) |
| 253 | + expect_equal(res.length.pm10.16$`length of D$pm10.16 in survival3`, 2688) |
| 254 | + expect_length(res.length.pm10.16$`total length of D$pm10.16 in all studies combined`, 1) |
| 255 | + expect_equal(res.length.pm10.16$`total length of D$pm10.16 in all studies combined`, 6388) |
| 256 | + |
| 257 | + res.class.bmi.26 <- ds.class(x='D$bmi.26') |
| 258 | + expect_length(res.class.bmi.26, 3) |
| 259 | + expect_length(res.class.bmi.26$survival1, 1) |
| 260 | + expect_equal(res.class.bmi.26$survival1, "numeric") |
| 261 | + expect_length(res.class.bmi.26$survival2, 1) |
| 262 | + expect_equal(res.class.bmi.26$survival2, "numeric") |
| 263 | + expect_length(res.class.bmi.26$survival3, 1) |
| 264 | + expect_equal(res.class.bmi.26$survival3, "numeric") |
| 265 | + |
| 266 | + res.length.bmi.26 <- ds.length(x='D$bmi.26') |
| 267 | + expect_length(res.length.bmi.26, 4) |
| 268 | + expect_length(res.length.bmi.26$`length of D$bmi.26 in survival1`, 1) |
| 269 | + expect_equal(res.length.bmi.26$`length of D$bmi.26 in survival1`, 2060) |
| 270 | + expect_length(res.length.bmi.26$`length of D$bmi.26 in survival2`, 1) |
| 271 | + expect_equal(res.length.bmi.26$`length of D$bmi.26 in survival2`, 1640) |
| 272 | + expect_length(res.length.bmi.26$`length of D$bmi.26 in survival3`, 1) |
| 273 | + expect_equal(res.length.bmi.26$`length of D$bmi.26 in survival3`, 2688) |
| 274 | + expect_length(res.length.bmi.26$`total length of D$bmi.26 in all studies combined`, 1) |
| 275 | + expect_equal(res.length.bmi.26$`total length of D$bmi.26 in all studies combined`, 6388) |
| 276 | +}) |
| 277 | + |
| 278 | +# |
| 279 | +# Tear down |
| 280 | +# |
| 281 | + |
| 282 | +context("SURVIVAL_EXPAND_WITH_MISSING::datachk::shutdown") |
| 283 | + |
| 284 | +test_that("shutdown", { |
| 285 | + ds_expect_variables(c("D")) |
| 286 | +}) |
| 287 | + |
| 288 | +disconnect.studies.dataset.survival() |
| 289 | + |
| 290 | +# |
| 291 | +# Done |
| 292 | +# |
| 293 | + |
| 294 | +context("SURVIVAL_EXPAND_WITH_MISSING::datachk::done") |
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