Nothing
test_that("prep_prepare_dataframes works", {
skip_if_not_installed("withr")
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
acc_test1 <- function(resp_variable, aux_variable,
time_variable, co_variables,
group_vars, study_data, meta_data) {
prep_prepare_dataframes()
invisible(ds1)
}
acc_test2 <- function(resp_variable, aux_variable,
time_variable, co_variables,
group_vars, study_data, meta_data, label_col) {
ds1 <- prep_prepare_dataframes(study_data, meta_data)
invisible(ds1)
}
environment(acc_test1) <- asNamespace("dataquieR")
environment(acc_test2) <- asNamespace("dataquieR")
acc_test3 <- function(resp_variable, aux_variable, time_variable,
co_variables, group_vars, study_data, meta_data,
label_col) {
prep_prepare_dataframes()
invisible(ds1)
}
acc_test4 <- function(resp_variable, aux_variable, time_variable,
co_variables, group_vars, study_data, meta_data,
label_col) {
ds1 <- prep_prepare_dataframes(study_data, meta_data)
invisible(ds1)
}
environment(acc_test3) <- asNamespace("dataquieR")
environment(acc_test4) <- asNamespace("dataquieR")
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_error(
acc_test1(),
regexp = "Need study data as a data frame"
)
expect_error(
acc_test2(),
regexp = "Need study data as a data frame"
)
expect_warning(
acc_test1(study_data = study_data),
regexp =
sprintf(
"(?ms).*(%s|%s|%s|%s).*",
paste("Missing .+meta_data.+, try to guess a preliminary one from the",
"data using .+prep_prepare_dataframes.+. Please consider amending",
"this minimum guess manually."),
paste("Metadata does not provide a filled column called",
".+MISSING_LIST.+ for replacing codes with NAs."),
paste("Metadata does not provide a filled column called .+JUMP_LIST.+",
"for replacing codes with NAs."),
paste("Some code labels or -values",
"are missing from .+meta_data.+.")
),
perl = TRUE
)
expect_error(
acc_test1(meta_data = meta_data),
regexp = "Need study data as a data frame"
)
expect_error(
acc_test2(study_data = 12, meta_data = meta_data),
regexp = "Need study data as a data frame"
)
expect_equal(colnames(acc_test1(study_data = study_data,
meta_data = meta_data)),
c(
"v00000",
"v00001",
"v00002",
"v00003",
"v00103",
"v01003",
"v01002",
"v10000",
"v00004",
"v00005",
"v00006",
"v00007",
"v00008",
"v00009",
"v00109",
"v00010",
"v00011",
"v00012",
"v00013",
"v20000",
"v00014",
"v00015",
"v00016",
"v00017",
"v30000",
"v00018",
"v01018",
"v00019",
"v00020",
"v00021",
"v00022",
"v00023",
"v00024",
"v00025",
"v00026",
"v00027",
"v00028",
"v00029",
"v00030",
"v00031",
"v00032",
"v00033",
"v40000",
"v00034",
"v00035",
"v00036",
"v00037",
"v00038",
"v00039",
"v00040",
"v00041",
"v00042",
"v50000"
)
)
expect_equal(colnames(acc_test2(study_data = study_data,
meta_data = meta_data)),
c(
"v00000",
"v00001",
"v00002",
"v00003",
"v00103",
"v01003",
"v01002",
"v10000",
"v00004",
"v00005",
"v00006",
"v00007",
"v00008",
"v00009",
"v00109",
"v00010",
"v00011",
"v00012",
"v00013",
"v20000",
"v00014",
"v00015",
"v00016",
"v00017",
"v30000",
"v00018",
"v01018",
"v00019",
"v00020",
"v00021",
"v00022",
"v00023",
"v00024",
"v00025",
"v00026",
"v00027",
"v00028",
"v00029",
"v00030",
"v00031",
"v00032",
"v00033",
"v40000",
"v00034",
"v00035",
"v00036",
"v00037",
"v00038",
"v00039",
"v00040",
"v00041",
"v00042",
"v50000"
)
)
expect_equal(colnames(acc_test3(study_data = study_data,
meta_data = meta_data)),
c(
"v00000",
"v00001",
"v00002",
"v00003",
"v00103",
"v01003",
"v01002",
"v10000",
"v00004",
"v00005",
"v00006",
"v00007",
"v00008",
"v00009",
"v00109",
"v00010",
"v00011",
"v00012",
"v00013",
"v20000",
"v00014",
"v00015",
"v00016",
"v00017",
"v30000",
"v00018",
"v01018",
"v00019",
"v00020",
"v00021",
"v00022",
"v00023",
"v00024",
"v00025",
"v00026",
"v00027",
"v00028",
"v00029",
"v00030",
"v00031",
"v00032",
"v00033",
"v40000",
"v00034",
"v00035",
"v00036",
"v00037",
"v00038",
"v00039",
"v00040",
"v00041",
"v00042",
"v50000"
)
)
expect_equal(colnames(acc_test4(study_data = study_data,
meta_data = meta_data)),
c(
"v00000",
"v00001",
"v00002",
"v00003",
"v00103",
"v01003",
"v01002",
"v10000",
"v00004",
"v00005",
"v00006",
"v00007",
"v00008",
"v00009",
"v00109",
"v00010",
"v00011",
"v00012",
"v00013",
"v20000",
"v00014",
"v00015",
"v00016",
"v00017",
"v30000",
"v00018",
"v01018",
"v00019",
"v00020",
"v00021",
"v00022",
"v00023",
"v00024",
"v00025",
"v00026",
"v00027",
"v00028",
"v00029",
"v00030",
"v00031",
"v00032",
"v00033",
"v40000",
"v00034",
"v00035",
"v00036",
"v00037",
"v00038",
"v00039",
"v00040",
"v00041",
"v00042",
"v50000"
)
)
expect_equal(
colnames(
acc_test3(
study_data = study_data,
meta_data = meta_data,
label_col = "LABEL"
)
),
c(
"CENTER_0",
"PSEUDO_ID",
"SEX_0",
"AGE_0",
"AGE_GROUP_0",
"AGE_1",
"SEX_1",
"PART_STUDY",
"SBP_0",
"DBP_0",
"GLOBAL_HEALTH_VAS_0",
"ASTHMA_0",
"VO2_CAPCAT_0",
"ARM_CIRC_0",
"ARM_CIRC_DISC_0",
"ARM_CUFF_0",
"USR_VO2_0",
"USR_BP_0",
"EXAM_DT_0",
"PART_PHYS_EXAM",
"CRP_0",
"BSG_0",
"DEV_NO_0",
"LAB_DT_0",
"PART_LAB",
"EDUCATION_0",
"EDUCATION_1",
"FAM_STAT_0",
"MARRIED_0",
"N_CHILD_0",
"EATING_PREFS_0",
"MEAT_CONS_0",
"SMOKING_0",
"SMOKE_SHOP_0",
"N_INJURIES_0",
"N_BIRTH_0",
"INCOME_GROUP_0",
"PREGNANT_0",
"MEDICATION_0",
"N_ATC_CODES_0",
"USR_SOCDEM_0",
"INT_DT_0",
"PART_INTERVIEW",
"ITEM_1_0",
"ITEM_2_0",
"ITEM_3_0",
"ITEM_4_0",
"ITEM_5_0",
"ITEM_6_0",
"ITEM_7_0",
"ITEM_8_0",
"QUEST_DT_0",
"PART_QUESTIONNAIRE"
)
)
expect_equal(
colnames(
acc_test3(
study_data = study_data,
meta_data = meta_data,
label_col = LABEL
)
),
c(
"CENTER_0",
"PSEUDO_ID",
"SEX_0",
"AGE_0",
"AGE_GROUP_0",
"AGE_1",
"SEX_1",
"PART_STUDY",
"SBP_0",
"DBP_0",
"GLOBAL_HEALTH_VAS_0",
"ASTHMA_0",
"VO2_CAPCAT_0",
"ARM_CIRC_0",
"ARM_CIRC_DISC_0",
"ARM_CUFF_0",
"USR_VO2_0",
"USR_BP_0",
"EXAM_DT_0",
"PART_PHYS_EXAM",
"CRP_0",
"BSG_0",
"DEV_NO_0",
"LAB_DT_0",
"PART_LAB",
"EDUCATION_0",
"EDUCATION_1",
"FAM_STAT_0",
"MARRIED_0",
"N_CHILD_0",
"EATING_PREFS_0",
"MEAT_CONS_0",
"SMOKING_0",
"SMOKE_SHOP_0",
"N_INJURIES_0",
"N_BIRTH_0",
"INCOME_GROUP_0",
"PREGNANT_0",
"MEDICATION_0",
"N_ATC_CODES_0",
"USR_SOCDEM_0",
"INT_DT_0",
"PART_INTERVIEW",
"ITEM_1_0",
"ITEM_2_0",
"ITEM_3_0",
"ITEM_4_0",
"ITEM_5_0",
"ITEM_6_0",
"ITEM_7_0",
"ITEM_8_0",
"QUEST_DT_0",
"PART_QUESTIONNAIRE"
)
)
expect_equal(
colnames(
acc_test4(
study_data = study_data,
meta_data = meta_data,
label_col = LABEL
)
),
c(
"CENTER_0",
"PSEUDO_ID",
"SEX_0",
"AGE_0",
"AGE_GROUP_0",
"AGE_1",
"SEX_1",
"PART_STUDY",
"SBP_0",
"DBP_0",
"GLOBAL_HEALTH_VAS_0",
"ASTHMA_0",
"VO2_CAPCAT_0",
"ARM_CIRC_0",
"ARM_CIRC_DISC_0",
"ARM_CUFF_0",
"USR_VO2_0",
"USR_BP_0",
"EXAM_DT_0",
"PART_PHYS_EXAM",
"CRP_0",
"BSG_0",
"DEV_NO_0",
"LAB_DT_0",
"PART_LAB",
"EDUCATION_0",
"EDUCATION_1",
"FAM_STAT_0",
"MARRIED_0",
"N_CHILD_0",
"EATING_PREFS_0",
"MEAT_CONS_0",
"SMOKING_0",
"SMOKE_SHOP_0",
"N_INJURIES_0",
"N_BIRTH_0",
"INCOME_GROUP_0",
"PREGNANT_0",
"MEDICATION_0",
"N_ATC_CODES_0",
"USR_SOCDEM_0",
"INT_DT_0",
"PART_INTERVIEW",
"ITEM_1_0",
"ITEM_2_0",
"ITEM_3_0",
"ITEM_4_0",
"ITEM_5_0",
"ITEM_6_0",
"ITEM_7_0",
"ITEM_8_0",
"QUEST_DT_0",
"PART_QUESTIONNAIRE"
)
)
expect_error(
acc_test2(study_data = NULL, meta_data = meta_data),
regexp = "Need study data as a data frame"
)
expect_error(
prep_prepare_dataframes(.replace_missings = cars),
regexp = paste("Called prepare_dataframes with .replace_missings",
"not being logical(1)"),
fixed = TRUE
)
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
err_test1 <- function(resp_variable, aux_variable,
time_variable, co_variables,
group_vars, study_data, meta_data, label_col) {
prep_prepare_dataframes()
invisible(ds1)
}
environment(err_test1) <- asNamespace("dataquieR")
expect_error(err_test1(label_col = testxx),
rregexp = "Cannot resolve .+label_col = stop.+",
perl = TRUE)
if (exists("testxx")) rm(testxx)
expect_error(err_test1(label_col = stop()),
rregexp = "Cannot resolve .+label_col = testxx.+",
perl = TRUE)
sd99 <- study_data
err_test2 <- function(resp_variable, aux_variable,
time_variable, co_variables,
group_vars, study_data = sd99,
meta_data, label_col) {
prep_prepare_dataframes()
invisible(ds1)
}
environment(err_test2) <- asNamespace("dataquieR")
sd99 <- 42
expect_error(err_test2(meta_data = meta_data),
regexp = "Need study data as a data frame")
err_test3 <- function(resp_variable, aux_variable,
time_variable, co_variables,
group_vars,
meta_data, label_col) {
prep_prepare_dataframes()
invisible(ds1)
}
environment(err_test3) <- asNamespace("dataquieR")
if (exists("study_data")) rm(study_data)
expect_error(err_test3(meta_data = meta_data),
regexp = "Need study data as a data frame")
study_data <- prep_get_data_frame("study_data")
md99 <- meta_data
err_test4 <- function(resp_variable, aux_variable,
time_variable, co_variables,
group_vars, study_data,
meta_data = md99, label_col) {
prep_prepare_dataframes()
invisible(ds1)
}
environment(err_test4) <- asNamespace("dataquieR")
expect_silent(err_test4(study_data = study_data))
md99 <- 42
expect_error(err_test4(study_data = study_data),
regexp = "Need metadata as a data frame")
err_test5 <- function(resp_variable, aux_variable,
time_variable, co_variables,
group_vars, study_data,
meta_data, label_col) {
prep_prepare_dataframes()
invisible(ds1)
}
environment(err_test5) <- asNamespace("dataquieR")
expect_warning(err_test5(study_data = study_data),
regexp = sprintf("(%s|%s|%s)",
paste("Missing .+meta_data.+, try to guess a",
"preliminary one from the data using",
".+prep_prepare_dataframes.+. Please",
"consider amending this minimum guess",
"manually."),
paste("Metadata does not provide a filled",
"column called .+JUMP_LIST.+ for",
"replacing codes with NAs."),
paste("Some code labels or -values",
"are missing from .+meta_data.+.")
),
perl = TRUE,
all = TRUE)
study_data <- tibble::as_tibble(study_data)
meta_data <- tibble::as_tibble(meta_data)
acc_test5 <- function(resp_variable, aux_variable, time_variable,
co_variables, group_vars, study_data, meta_data,
label_col) {
expect_true(tibble::is_tibble(study_data))
expect_true(tibble::is_tibble(meta_data))
prep_prepare_dataframes()
expect_false(tibble::is_tibble(study_data))
expect_false(tibble::is_tibble(meta_data))
expect_false(tibble::is_tibble(ds1))
invisible(ds1)
}
environment(acc_test5) <- asNamespace("dataquieR")
x <- acc_test5(study_data = study_data,
meta_data = meta_data, label_col = LABEL)
md99 <- meta_data
md99$LABEL <- meta_data$VAR_NAMES
y <- acc_test5(study_data = tibble::as_tibble(x),
meta_data = md99, label_col = LABEL)
expect_identical(x, y) # because this has already been mapped.
md99$VAR_NAMES <- NULL
expect_error(
y <- acc_test5(study_data = study_data,
meta_data = md99, label_col = LABEL),
regexp = paste(
"Missing columns.+VAR_NAMES.+from .+meta_data.*"),
perl = TRUE
)
sd99 <- study_data
md99 <- meta_data
colnames(sd99) <- letters[1:ncol(sd99)]
expect_message(
expect_warning(
expect_error(
acc_test3(study_data = sd99, meta_data = md99),
regexp = "No data left. Aborting"
),
regexp = sprintf("(%s|%s)",
paste("Lost 100. of the study data because of",
"missing.not assignable metadata"),
paste("Lost 100. of the metadata because of",
"missing.not assignable study.data")),
perl = TRUE,
all = TRUE),
regexp = sprintf("(%s|%s)",
paste("Did not find any metadata for the following",
"variables from the study data. .+a.+, .+b.+"),
paste("Found metadata for the following variables not",
"found in the study data: .+v00000.+, .+v00001.+,",
".+v00002.+, .+v00003.+, .+v00004.+")),
perl = TRUE,
all = TRUE
)
})
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