Nothing
tests/testthat/test-acc_loess.R
In dataquieR: Data Quality in Epidemiological Research
test_that("acc_loess works without label_col", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
skip_on_cran() # slow test
skip_if_translated()
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_warning(
expect_error({
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data)
},
regexp = paste(".*Argument group_vars is NULL"),
perl = TRUE
),
regexp =
sprintf(
"(%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("Missing argument .+group_vars.+ without default value.",
"Setting to NULL. As a dataquieR developer")
),
perl = TRUE,
all = TRUE
)
expect_warning(
expect_error({
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data,
min_obs_in_subgroup = 29)
},
regexp = paste(".*Argument group_vars is NULL"),
perl = TRUE
),
regexp =
sprintf(
"(%s)",
paste("Missing argument .+group_vars.+ without default value.",
"Setting to NULL. As a dataquieR developer")
),
perl = TRUE,
all = TRUE
)
expect_warning(
expect_error({
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016")
},
regexp = paste(".*Argument time_vars is NULL"),
perl = TRUE
),
regexp =
sprintf(
"(%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("Missing argument .+time_vars.+ without default value.",
"Setting to NULL. As a dataquieR developer")
),
perl = TRUE,
all = TRUE
)
sd1 <- study_data
sd1[["v00017"]][1:1000] <- NA
expect_message(
res1 <-
acc_loess(resp_vars = "v00014", study_data = sd1,
meta_data = meta_data, group_vars = "v00016",
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
sprintf(
"(%s|%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+v00014.+"),
paste("Due to missing values in v00016",
"93 observations were deleted."),
paste("Due to missing values in v00017",
"931 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
sd1 <- study_data
sd1[["v00017"]] <- as.character(sd1[["v00017"]])
sd1[["v00017"]][1:1000] <- "2001-02-29"
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = sd1,
meta_data = meta_data, group_vars = "v00016",
time_vars = "v00017"), # ===> "LAB_DT_0"
regexp = "Data type transformation of.*NAs"
)
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
min_obs_in_subgroup = 1:2,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste(".+min_obs_in_subgroup.+ should",
"be a scalar integer value, not 2 values."),
perl = TRUE
)
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
resolution = Inf,
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste(".+resolution.+ needs to be a",
"single finite numeric value."),
perl = TRUE
)
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
resolution = "12",
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste(".+resolution.+ needs to be a",
"single finite numeric value."),
perl = TRUE
)
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
resolution = complex(imaginary = 12),
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste(".+resolution.+ needs to be a",
"single finite numeric value."),
perl = TRUE
)
suppressWarnings(
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
plot_data_time = "x",
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste("Argument .+plot_data_time.+ must be",
"a scalar logical value."),
perl = TRUE
)
)
suppressWarnings(
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
plot_data_time = TRUE,
se_line = 42,
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste(".+se_line.+ needs to be a list of arguments",
"for ggplot2..geom_line for the standard error lines."),
perl = TRUE
)
)
sd0 <- study_data
sd0$v00017 <- "XXXX"
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = sd0,
meta_data = meta_data, group_vars = "v00016",
plot_data_time = TRUE,
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste("Data type transformation.*additional NAs"),
perl = TRUE
)
suppressWarnings(
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
plot_data_time = "TRUE",
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste("Argument .+plot_data_time.+ must be",
"a scalar logical value."),
perl = TRUE
)
)
expect_message(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
min_obs_in_subgroup = NA,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup. Default n=30 per level is used."),
paste("301 observations were omitted due to missing values",
"in .+v00014.+"),
paste("Due to missing values in v00016",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_message(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
min_obs_in_subgroup = "x",
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("Coulud not convert min_obs_in_subgroup .+x.+ to a number.",
"Set to standard value n=30."),
paste("301 observations were omitted due to missing values",
"in .+v00014.+"),
paste("Due to missing values in v00016",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_message(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
time_vars = "v00017", plot_format = "BOTH") # ===> "LAB_DT_0"
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+v00014.+"),
paste("Due to missing values in v00016",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
2
)
expect_lt(
suppressWarnings(abs(mean(as.numeric(
as.matrix(res1$SummaryPlotList$Loess_fits_combined$data)),
na.rm = TRUE) - 21.82126)), 50
)
})
test_that("acc_loess works with label_col", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_warning(
expect_error({
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data,
label_col = LABEL)
},
regexp = paste(".*Argument group_vars is NULL"),
perl = TRUE
),
regexp =
sprintf(
"(%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("Missing argument .+group_vars.+ without default value.",
"Setting to NULL. As a dataquieR developer")
),
perl = TRUE,
all = TRUE
)
expect_warning(
expect_error({
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
label_col = LABEL)
},
regexp = paste(".*Argument time_vars is NULL"),
perl = TRUE
),
regexp =
sprintf(
"(%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("Missing argument .+time_vars.+ without default value.",
"Setting to NULL. As a dataquieR developer")
),
perl = TRUE,
all = TRUE
)
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "BOTH")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
2
)
skip_on_cran()
expect_lt(
suppressWarnings(abs(mean(as.numeric(
as.matrix(res1$SummaryPlotList$Loess_fits_combined$data)),
na.rm = TRUE) - 21.82126)), 50
)
})
test_that("acc_loess output matches", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "BOTH")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
2
)
skip_on_cran()
skip_if_not(capabilities()["long.double"])
# skip_on_travis() # vdiffr fails
skip_if_not_installed("vdiffr")
vdiffr::expect_doppelganger("loess facets plot for CRP_0 ok",
res1$SummaryPlotList$Loess_fits_facets)
vdiffr::expect_doppelganger("loess combined plot for CRP_0 ok",
res1$SummaryPlotList$Loess_fits_combined)
})
test_that("acc_loess min_obs_in_subgroups with label_col", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
expect_error({
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, min_obs_in_subgroup = 999)
},
regexp = paste("No data left, cannot produce a plot, sorry."),
perl = TRUE
),
regexp =
sprintf(
"(%s|%s|%s)",
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted."),
paste("The following levels: 1 2 3 4 5 have < 30",
"observations and were discarded.")
),
perl = TRUE,
all = TRUE
)
})
test_that("acc_loess with co-vars output matches", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
sd0 <- study_data
sd0$v00003[1:10] <- NA
sd0$v00002[11:20] <- NA
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0", co_vars = c("AGE_0", "SEX_0"),
label_col = LABEL)
,
regexp =
sprintf(
"(%s|%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted."),
paste("Due to missing values in any of AGE_0, SEX_0",
"18 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
sd0 <- study_data
sd0$v00014 <- as.factor(sd0$v00014)
expect_warning(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0", co_vars = c("AGE_0", "SEX_0"),
label_col = LABEL)
,
regexp =
sprintf(
"(%s|%s|%s|%s|%s|%s|%s)",
paste(".+CRP_0.+ is a categorial but not an ordinal variable.",
"I.ll use the levels as ordinals, but this may lead to",
"wrong conclusions."),
paste(".+RP_0.+ is not a metric variable. Ordinal variables may in",
"some cases still be interpretable with the LOESS plots, but",
"be aware that distances are meaningless."),
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted."),
paste("For .*I have .*HARD_LIMITS.* but the column is of type",
".*string.*metadata say .*float.*"),
paste("Argument.*resp_vars.*Variable.*CRP_0.*float.*does not have",
"matching data type in the study data.*string.*")
),
perl = TRUE,
all = TRUE
)
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0", co_vars = c("AGE_0", "SEX_0"),
label_col = LABEL, plot_format = "BOTH")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
2
)
skip_on_cran()
skip_if_not(capabilities()["long.double"])
# skip_on_travis() # vdiffr fails
skip_if_not_installed("vdiffr")
vdiffr::expect_doppelganger("loess facets plot for CRP_0 with Covars ok",
res1$SummaryPlotList$Loess_fits_facets)
vdiffr::expect_doppelganger("loess combined plot for CRP_0 with Covars ok",
res1$SummaryPlotList$Loess_fits_combined)
})
test_that("acc_loess works for all time span ranges", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
skip_on_cran() # slow test
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
sd0 <- study_data
v <- subset(meta_data, LABEL == "LAB_DT_0", VAR_NAMES, TRUE)
sd0[[v]] <- min(sd0[[v]], na.rm = TRUE)
expect_error(
suppressWarnings(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL)),
regexp = "span is too small"
)
sd0 <- study_data
expect_error(
suppressWarnings(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 0.1,
label_col = LABEL)),
regexp = "span is too small"
)
expect_error(
suppressWarnings(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 1,
label_col = LABEL)),
regexp = "span is too small"
)
expect_silent(
suppressMessages(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 10,
label_col = LABEL))
)
expect_silent(
suppressMessages(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 100,
label_col = LABEL))
)
expect_silent(
suppressMessages(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 1000,
label_col = LABEL))
)
expect_silent(
suppressMessages(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 10000,
label_col = LABEL))
)
expect_silent(
suppressMessages(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 1000000,
label_col = LABEL))
)
sd0 <- rbind(study_data,
study_data,
study_data,
study_data,
study_data,
study_data,
study_data,
study_data
)
sd0[[v]] <-
as.POSIXct(rnorm(nrow(sd0), sd = as.numeric(as.POSIXct("1972-01-01")),
mean = mean(sd0[[v]], na.rm = TRUE)),
origin = as.POSIXct(as.POSIXct("1970-01-01")))
md0 <- meta_data
md0[md0$LABEL == "LAB_DT_0", HARD_LIMITS] <- NA
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = md0, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 10000,
label_col = LABEL),
regexp = paste(
"Argument .+plot_data_time.+ was not set.",
"Based on the maximum of observations of .... for group .+2.+ > 4000,",
"marks for timepoints featuring data will be turned off."),
perl = TRUE
)
sd0 <- study_data
g <- subset(meta_data, LABEL == "DEV_NO_0", VAR_NAMES, TRUE)
set.seed(42)
sd0[[g]][!is.na(sd0[[g]])] <-
sample(x = 11, size = sum(!is.na(sd0[[g]])),
replace = TRUE) # for >= 11 groups,
# R standard colors are used.
expect_message(
res0 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "BOTH")
)
sd0[[g]][!is.na(sd0[[g]])] <-
sample(x = 10, size = sum(!is.na(sd0[[g]])),
replace = TRUE) # for <= 10 groups,
# dataquieR standard colors are used.
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "BOTH")
)
g <- ggplot2::ggplot_build(res1$SummaryPlotList$Loess_fits_combined)
got1 <- sort(unique(g$data[[1]][["colour"]]))
hex_code <- sort(c( # the dataquieR colors
"#000000", "#B0B0B0", "#E69F00", "#56B4E9", "#009E73",
"#F0E442", "#0072B2", "#D55E00", "#CC79A7", "#8C510A"
))
expect_equal(got1, hex_code)
g <- ggplot2::ggplot_build(res0$SummaryPlotList$Loess_fits_combined)
got0 <- sort(unique(g$data[[1]][["colour"]]))
ggs_default <- sort(ggplot2::scale_color_discrete()$palette(11))
expect_equal(got0, ggs_default)
})
test_that("acc_loess output matches plot_format=auto", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "AUTO")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
1
)
sd1 <- study_data
set.seed(42)
sd1$v00016 <- sample(1:20, size = nrow(sd1), replace = TRUE)
expect_message(
res2 <-
acc_loess(resp_vars = "CRP_0", study_data = sd1,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "AUTO")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res2))
expect_equal(
length(res2$SummaryPlotList),
1
)
skip_on_cran()
# skip_on_travis() # vdiffr fails
skip_if_not_installed("vdiffr")
skip_if_not(capabilities()["long.double"])
vdiffr::expect_doppelganger("loess plot for CRP_0 AUTO1 ok",
res1$SummaryPlotList$CRP_0)
vdiffr::expect_doppelganger("loess plot for CRP_0 AUTO2 ok",
res2$SummaryPlotList$CRP_0)
})
test_that("acc_loess output matches plot_format=combined", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "COMBINED")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
1
)
skip_on_cran()
# skip_on_travis() # vdiffr fails
skip_if_not_installed("vdiffr")
skip_if_not(capabilities()["long.double"])
vdiffr::expect_doppelganger("loess combined plot for CRP_0 COMBINED ok",
res1$SummaryPlotList$CRP_0)
})
test_that("acc_loess output matches plot_format=facets", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "FACETS")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
1
)
skip_on_cran()
# skip_on_travis() # vdiffr fails
skip_if_not_installed("vdiffr")
skip_if_not(capabilities()["long.double"])
vdiffr::expect_doppelganger("loess facets plot for CRP_0 FACETS ok",
res1$SummaryPlotList$CRP_0)
})
test_that("acc_loess output matches plot_format=both", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "BOTH")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
2
)
skip_on_cran()
# skip_on_travis() # vdiffr fails
skip_if_not_installed("vdiffr")
skip_if_not(capabilities()["long.double"])
vdiffr::expect_doppelganger("loess facets plot for CRP_0 BOTH ok",
res1$SummaryPlotList$Loess_fits_facets)
vdiffr::expect_doppelganger("loess combined plot for CRP_0 BOTH ok",
res1$SummaryPlotList$Loess_fits_combined)
})
test_that("acc_loess output matches plot_format=invalid1", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "invalid")
,
regexp =
sprintf(
"(%s|%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted."),
paste("Unknown .+plot_format.+: .+invalid.+ --",
"will switch to default value AUTO.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
1
)
})
test_that("acc_loess output matches plot_format=invalid2", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = 1:10)
,
regexp =
sprintf(
"(%s|%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted."),
paste("Unknown .+plot_format.+: .+NOT character.1. STRING AT ALL.+ --",
"will switch to default value AUTO.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
1
)
})
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test_that("acc_loess works without label_col", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
skip_on_cran() # slow test
skip_if_translated()
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_warning(
expect_error({
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data)
},
regexp = paste(".*Argument group_vars is NULL"),
perl = TRUE
),
regexp =
sprintf(
"(%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("Missing argument .+group_vars.+ without default value.",
"Setting to NULL. As a dataquieR developer")
),
perl = TRUE,
all = TRUE
)
expect_warning(
expect_error({
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data,
min_obs_in_subgroup = 29)
},
regexp = paste(".*Argument group_vars is NULL"),
perl = TRUE
),
regexp =
sprintf(
"(%s)",
paste("Missing argument .+group_vars.+ without default value.",
"Setting to NULL. As a dataquieR developer")
),
perl = TRUE,
all = TRUE
)
expect_warning(
expect_error({
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016")
},
regexp = paste(".*Argument time_vars is NULL"),
perl = TRUE
),
regexp =
sprintf(
"(%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("Missing argument .+time_vars.+ without default value.",
"Setting to NULL. As a dataquieR developer")
),
perl = TRUE,
all = TRUE
)
sd1 <- study_data
sd1[["v00017"]][1:1000] <- NA
expect_message(
res1 <-
acc_loess(resp_vars = "v00014", study_data = sd1,
meta_data = meta_data, group_vars = "v00016",
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
sprintf(
"(%s|%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+v00014.+"),
paste("Due to missing values in v00016",
"93 observations were deleted."),
paste("Due to missing values in v00017",
"931 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
sd1 <- study_data
sd1[["v00017"]] <- as.character(sd1[["v00017"]])
sd1[["v00017"]][1:1000] <- "2001-02-29"
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = sd1,
meta_data = meta_data, group_vars = "v00016",
time_vars = "v00017"), # ===> "LAB_DT_0"
regexp = "Data type transformation of.*NAs"
)
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
min_obs_in_subgroup = 1:2,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste(".+min_obs_in_subgroup.+ should",
"be a scalar integer value, not 2 values."),
perl = TRUE
)
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
resolution = Inf,
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste(".+resolution.+ needs to be a",
"single finite numeric value."),
perl = TRUE
)
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
resolution = "12",
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste(".+resolution.+ needs to be a",
"single finite numeric value."),
perl = TRUE
)
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
resolution = complex(imaginary = 12),
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste(".+resolution.+ needs to be a",
"single finite numeric value."),
perl = TRUE
)
suppressWarnings(
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
plot_data_time = "x",
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste("Argument .+plot_data_time.+ must be",
"a scalar logical value."),
perl = TRUE
)
)
suppressWarnings(
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
plot_data_time = TRUE,
se_line = 42,
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste(".+se_line.+ needs to be a list of arguments",
"for ggplot2..geom_line for the standard error lines."),
perl = TRUE
)
)
sd0 <- study_data
sd0$v00017 <- "XXXX"
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = sd0,
meta_data = meta_data, group_vars = "v00016",
plot_data_time = TRUE,
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste("Data type transformation.*additional NAs"),
perl = TRUE
)
suppressWarnings(
expect_error(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
plot_data_time = "TRUE",
min_obs_in_subgroup = 30,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
paste("Argument .+plot_data_time.+ must be",
"a scalar logical value."),
perl = TRUE
)
)
expect_message(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
min_obs_in_subgroup = NA,
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup. Default n=30 per level is used."),
paste("301 observations were omitted due to missing values",
"in .+v00014.+"),
paste("Due to missing values in v00016",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_message(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
min_obs_in_subgroup = "x",
time_vars = "v00017") # ===> "LAB_DT_0"
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("Coulud not convert min_obs_in_subgroup .+x.+ to a number.",
"Set to standard value n=30."),
paste("301 observations were omitted due to missing values",
"in .+v00014.+"),
paste("Due to missing values in v00016",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_message(
res1 <-
acc_loess(resp_vars = "v00014", study_data = study_data,
meta_data = meta_data, group_vars = "v00016",
time_vars = "v00017", plot_format = "BOTH") # ===> "LAB_DT_0"
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+v00014.+"),
paste("Due to missing values in v00016",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
2
)
expect_lt(
suppressWarnings(abs(mean(as.numeric(
as.matrix(res1$SummaryPlotList$Loess_fits_combined$data)),
na.rm = TRUE) - 21.82126)), 50
)
})
test_that("acc_loess works with label_col", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_warning(
expect_error({
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data,
label_col = LABEL)
},
regexp = paste(".*Argument group_vars is NULL"),
perl = TRUE
),
regexp =
sprintf(
"(%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("Missing argument .+group_vars.+ without default value.",
"Setting to NULL. As a dataquieR developer")
),
perl = TRUE,
all = TRUE
)
expect_warning(
expect_error({
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
label_col = LABEL)
},
regexp = paste(".*Argument time_vars is NULL"),
perl = TRUE
),
regexp =
sprintf(
"(%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("Missing argument .+time_vars.+ without default value.",
"Setting to NULL. As a dataquieR developer")
),
perl = TRUE,
all = TRUE
)
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "BOTH")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
2
)
skip_on_cran()
expect_lt(
suppressWarnings(abs(mean(as.numeric(
as.matrix(res1$SummaryPlotList$Loess_fits_combined$data)),
na.rm = TRUE) - 21.82126)), 50
)
})
test_that("acc_loess output matches", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "BOTH")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
2
)
skip_on_cran()
skip_if_not(capabilities()["long.double"])
# skip_on_travis() # vdiffr fails
skip_if_not_installed("vdiffr")
vdiffr::expect_doppelganger("loess facets plot for CRP_0 ok",
res1$SummaryPlotList$Loess_fits_facets)
vdiffr::expect_doppelganger("loess combined plot for CRP_0 ok",
res1$SummaryPlotList$Loess_fits_combined)
})
test_that("acc_loess min_obs_in_subgroups with label_col", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
expect_error({
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, min_obs_in_subgroup = 999)
},
regexp = paste("No data left, cannot produce a plot, sorry."),
perl = TRUE
),
regexp =
sprintf(
"(%s|%s|%s)",
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted."),
paste("The following levels: 1 2 3 4 5 have < 30",
"observations and were discarded.")
),
perl = TRUE,
all = TRUE
)
})
test_that("acc_loess with co-vars output matches", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
sd0 <- study_data
sd0$v00003[1:10] <- NA
sd0$v00002[11:20] <- NA
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0", co_vars = c("AGE_0", "SEX_0"),
label_col = LABEL)
,
regexp =
sprintf(
"(%s|%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted."),
paste("Due to missing values in any of AGE_0, SEX_0",
"18 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
sd0 <- study_data
sd0$v00014 <- as.factor(sd0$v00014)
expect_warning(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0", co_vars = c("AGE_0", "SEX_0"),
label_col = LABEL)
,
regexp =
sprintf(
"(%s|%s|%s|%s|%s|%s|%s)",
paste(".+CRP_0.+ is a categorial but not an ordinal variable.",
"I.ll use the levels as ordinals, but this may lead to",
"wrong conclusions."),
paste(".+RP_0.+ is not a metric variable. Ordinal variables may in",
"some cases still be interpretable with the LOESS plots, but",
"be aware that distances are meaningless."),
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted."),
paste("For .*I have .*HARD_LIMITS.* but the column is of type",
".*string.*metadata say .*float.*"),
paste("Argument.*resp_vars.*Variable.*CRP_0.*float.*does not have",
"matching data type in the study data.*string.*")
),
perl = TRUE,
all = TRUE
)
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0", co_vars = c("AGE_0", "SEX_0"),
label_col = LABEL, plot_format = "BOTH")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
2
)
skip_on_cran()
skip_if_not(capabilities()["long.double"])
# skip_on_travis() # vdiffr fails
skip_if_not_installed("vdiffr")
vdiffr::expect_doppelganger("loess facets plot for CRP_0 with Covars ok",
res1$SummaryPlotList$Loess_fits_facets)
vdiffr::expect_doppelganger("loess combined plot for CRP_0 with Covars ok",
res1$SummaryPlotList$Loess_fits_combined)
})
test_that("acc_loess works for all time span ranges", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
skip_on_cran() # slow test
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
sd0 <- study_data
v <- subset(meta_data, LABEL == "LAB_DT_0", VAR_NAMES, TRUE)
sd0[[v]] <- min(sd0[[v]], na.rm = TRUE)
expect_error(
suppressWarnings(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL)),
regexp = "span is too small"
)
sd0 <- study_data
expect_error(
suppressWarnings(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 0.1,
label_col = LABEL)),
regexp = "span is too small"
)
expect_error(
suppressWarnings(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 1,
label_col = LABEL)),
regexp = "span is too small"
)
expect_silent(
suppressMessages(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 10,
label_col = LABEL))
)
expect_silent(
suppressMessages(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 100,
label_col = LABEL))
)
expect_silent(
suppressMessages(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 1000,
label_col = LABEL))
)
expect_silent(
suppressMessages(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 10000,
label_col = LABEL))
)
expect_silent(
suppressMessages(res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 1000000,
label_col = LABEL))
)
sd0 <- rbind(study_data,
study_data,
study_data,
study_data,
study_data,
study_data,
study_data,
study_data
)
sd0[[v]] <-
as.POSIXct(rnorm(nrow(sd0), sd = as.numeric(as.POSIXct("1972-01-01")),
mean = mean(sd0[[v]], na.rm = TRUE)),
origin = as.POSIXct(as.POSIXct("1970-01-01")))
md0 <- meta_data
md0[md0$LABEL == "LAB_DT_0", HARD_LIMITS] <- NA
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = md0, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
resolution = 10000,
label_col = LABEL),
regexp = paste(
"Argument .+plot_data_time.+ was not set.",
"Based on the maximum of observations of .... for group .+2.+ > 4000,",
"marks for timepoints featuring data will be turned off."),
perl = TRUE
)
sd0 <- study_data
g <- subset(meta_data, LABEL == "DEV_NO_0", VAR_NAMES, TRUE)
set.seed(42)
sd0[[g]][!is.na(sd0[[g]])] <-
sample(x = 11, size = sum(!is.na(sd0[[g]])),
replace = TRUE) # for >= 11 groups,
# R standard colors are used.
expect_message(
res0 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "BOTH")
)
sd0[[g]][!is.na(sd0[[g]])] <-
sample(x = 10, size = sum(!is.na(sd0[[g]])),
replace = TRUE) # for <= 10 groups,
# dataquieR standard colors are used.
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = sd0,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "BOTH")
)
g <- ggplot2::ggplot_build(res1$SummaryPlotList$Loess_fits_combined)
got1 <- sort(unique(g$data[[1]][["colour"]]))
hex_code <- sort(c( # the dataquieR colors
"#000000", "#B0B0B0", "#E69F00", "#56B4E9", "#009E73",
"#F0E442", "#0072B2", "#D55E00", "#CC79A7", "#8C510A"
))
expect_equal(got1, hex_code)
g <- ggplot2::ggplot_build(res0$SummaryPlotList$Loess_fits_combined)
got0 <- sort(unique(g$data[[1]][["colour"]]))
ggs_default <- sort(ggplot2::scale_color_discrete()$palette(11))
expect_equal(got0, ggs_default)
})
test_that("acc_loess output matches plot_format=auto", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "AUTO")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
1
)
sd1 <- study_data
set.seed(42)
sd1$v00016 <- sample(1:20, size = nrow(sd1), replace = TRUE)
expect_message(
res2 <-
acc_loess(resp_vars = "CRP_0", study_data = sd1,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "AUTO")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res2))
expect_equal(
length(res2$SummaryPlotList),
1
)
skip_on_cran()
# skip_on_travis() # vdiffr fails
skip_if_not_installed("vdiffr")
skip_if_not(capabilities()["long.double"])
vdiffr::expect_doppelganger("loess plot for CRP_0 AUTO1 ok",
res1$SummaryPlotList$CRP_0)
vdiffr::expect_doppelganger("loess plot for CRP_0 AUTO2 ok",
res2$SummaryPlotList$CRP_0)
})
test_that("acc_loess output matches plot_format=combined", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "COMBINED")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
1
)
skip_on_cran()
# skip_on_travis() # vdiffr fails
skip_if_not_installed("vdiffr")
skip_if_not(capabilities()["long.double"])
vdiffr::expect_doppelganger("loess combined plot for CRP_0 COMBINED ok",
res1$SummaryPlotList$CRP_0)
})
test_that("acc_loess output matches plot_format=facets", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "FACETS")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
1
)
skip_on_cran()
# skip_on_travis() # vdiffr fails
skip_if_not_installed("vdiffr")
skip_if_not(capabilities()["long.double"])
vdiffr::expect_doppelganger("loess facets plot for CRP_0 FACETS ok",
res1$SummaryPlotList$CRP_0)
})
test_that("acc_loess output matches plot_format=both", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "BOTH")
,
regexp =
sprintf(
"(%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
2
)
skip_on_cran()
# skip_on_travis() # vdiffr fails
skip_if_not_installed("vdiffr")
skip_if_not(capabilities()["long.double"])
vdiffr::expect_doppelganger("loess facets plot for CRP_0 BOTH ok",
res1$SummaryPlotList$Loess_fits_facets)
vdiffr::expect_doppelganger("loess combined plot for CRP_0 BOTH ok",
res1$SummaryPlotList$Loess_fits_combined)
})
test_that("acc_loess output matches plot_format=invalid1", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = "invalid")
,
regexp =
sprintf(
"(%s|%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted."),
paste("Unknown .+plot_format.+: .+invalid.+ --",
"will switch to default value AUTO.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
1
)
})
test_that("acc_loess output matches plot_format=invalid2", {
skip_on_cran() # slow
skip_if_not_installed("withr")
# testthat::local_reproducible_output()
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
for (i in 1:2) {
# This command failed in the first try, but worked in the second try for me.
suppressWarnings(withr::local_locale(c(LC_TIME = "en_US.UTF-8")))
# Linux, macOS
}
if (Sys.getlocale("LC_TIME") != "en_US.UTF-8") {
withr::local_locale(c(LC_TIME = "English.UTF-8")) # Windows
}
meta_data <- prep_get_data_frame("meta_data")
study_data <- prep_get_data_frame("study_data")
expect_message(
res1 <-
acc_loess(resp_vars = "CRP_0", study_data = study_data,
meta_data = meta_data, group_vars = "DEV_NO_0",
time_vars = "LAB_DT_0",
label_col = LABEL, plot_format = 1:10)
,
regexp =
sprintf(
"(%s|%s|%s|%s)",
paste("No min_obs_in_subgroup was set. Default n=30 per",
"level is used."),
paste("301 observations were omitted due to missing values",
"in .+CRP_0.+"),
paste("Due to missing values in DEV_NO_0",
"138 observations were deleted."),
paste("Unknown .+plot_format.+: .+NOT character.1. STRING AT ALL.+ --",
"will switch to default value AUTO.")
),
perl = TRUE,
all = TRUE
)
expect_true("SummaryPlotList" %in% names(res1))
expect_equal(
length(res1$SummaryPlotList),
1
)
})
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