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teal.data::datanames() is deprecated in favor of dot-prefix and names() #1239

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merged 16 commits into from
Nov 8, 2024
Merged

teal.data::datanames() is deprecated in favor of dot-prefix and names() #1239

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f5fd36c
feat: deprecates datanames
averissimo Nov 4, 2024
afb209a
feat: use c() instead of teal.code::join()
averissimo Nov 4, 2024
d572661
chore: ls() -> names() and bumps dependencies
averissimo Nov 5, 2024
5556514
chore: bump dependencies
averissimo Nov 5, 2024
08ef56a
fix: bad dependency specification
averissimo Nov 5, 2024
7d12d67
fix: typo
averissimo Nov 5, 2024
0335c66
feat: remove datanames from shinyttests2
averissimo Nov 5, 2024
7f1a06d
fix: missing conversion
averissimo Nov 6, 2024
424ecbd
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
dependabot-preview[bot] Nov 6, 2024
6475d85
chore: trigger CI
averissimo Nov 7, 2024
2b2eac6
fix: missing @env call
averissimo Nov 7, 2024
bb04855
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
dependabot-preview[bot] Nov 7, 2024
e39ac50
fix: e2e tests
averissimo Nov 8, 2024
6f428b2
fix: e2e tests
averissimo Nov 8, 2024
e284b0f
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
dependabot-preview[bot] Nov 8, 2024
7d1e96a
chore: trigger ci
averissimo Nov 8, 2024
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8 changes: 4 additions & 4 deletions DESCRIPTION
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Expand Up @@ -32,8 +32,8 @@ BugReports:
https://github.com/insightsengineering/teal.modules.clinical/issues
Depends:
R (>= 4.0),
teal (>= 0.15.2.9052),
teal.transform (>= 0.5.0),
teal (>= 0.15.2.9079),
teal.transform (>= 0.5.0.9015),
tern (>= 0.9.6)
Imports:
broom (>= 0.7.10),
Expand All @@ -55,8 +55,8 @@ Imports:
shinyvalidate,
shinyWidgets (>= 0.5.1),
stats,
teal.code (>= 0.5.0),
teal.data (>= 0.4.0),
teal.code (>= 0.5.0.9012),
teal.data (>= 0.6.0.9015),
teal.logger (>= 0.2.0.9004),
teal.reporter (>= 0.2.1),
teal.widgets (>= 0.4.0),
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3 changes: 1 addition & 2 deletions R/tm_a_gee.R
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Expand Up @@ -158,8 +158,7 @@ template_a_gee <- function(output_table,
#' ) %>%
#' droplevels()
#' })
#' datanames(data) <- c("ADSL", "ADQS")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' app <- init(
#' data = data,
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5 changes: 2 additions & 3 deletions R/tm_a_mmrm.R
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Expand Up @@ -491,8 +491,7 @@ template_mmrm_plots <- function(fit_name,
#' as.factor() #' making consecutive numeric factor
#' )
#' })
#' datanames(data) <- c("ADSL", "ADQS")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' app <- init(
#' data = data,
Expand Down Expand Up @@ -1402,7 +1401,7 @@ srv_mmrm <- function(id,

all_q <- reactive({
if (!is.null(plot_q()) && !is.null(table_q())) {
teal.code::join(plot_q(), table_q())
c(plot_q(), table_q())
} else if (!is.null(plot_q())) {
plot_q()
} else {
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7 changes: 4 additions & 3 deletions R/tm_g_barchart_simple.R
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Expand Up @@ -32,8 +32,7 @@
#' ADAE <- tmc_ex_adae %>%
#' filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
#' })
#' datanames(data) <- c("ADSL", "ADAE")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADAE <- data[["ADAE"]]
Expand Down Expand Up @@ -421,7 +420,9 @@ srv_g_barchart_simple <- function(id,
count_exprs <- c(count_exprs, count_exprs2, count_str_to_col_exprs)
}

data_list <- sapply(teal.data::datanames(data()), function(x) reactive(data()[[x]]),
data_list <- sapply(
names(data()),
function(x) reactive(data()[[x]]),
simplify = FALSE
)

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3 changes: 1 addition & 2 deletions R/tm_g_ci.R
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Expand Up @@ -202,8 +202,7 @@ template_g_ci <- function(dataname,
#' ADSL <- tmc_ex_adsl
#' ADLB <- tmc_ex_adlb
#' })
#' datanames(data) <- c("ADSL", "ADLB")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADLB <- data[["ADLB"]]
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3 changes: 1 addition & 2 deletions R/tm_g_forest_rsp.R
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Expand Up @@ -260,8 +260,7 @@ template_forest_rsp <- function(dataname = "ANL",
#' with_label("Character Result/Finding")) %>%
#' filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
#' })
#' datanames(data) <- c("ADSL", "ADRS")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADRS <- data[["ADRS"]]
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3 changes: 1 addition & 2 deletions R/tm_g_forest_tte.R
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Expand Up @@ -258,8 +258,7 @@ template_forest_tte <- function(dataname = "ANL",
#' ADTTE <- tmc_ex_adtte
#' ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label("Race")
#' })
#' datanames(data) <- c("ADSL", "ADTTE")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADTTE <- data[["ADTTE"]]
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3 changes: 1 addition & 2 deletions R/tm_g_ipp.R
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Expand Up @@ -198,8 +198,7 @@ template_g_ipp <- function(dataname = "ANL",
#' df_explicit_na() %>%
#' filter(AVISIT != "SCREENING")
#' })
#' datanames(data) <- c("ADSL", "ADLB")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADLB <- data[["ADLB"]]
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3 changes: 1 addition & 2 deletions R/tm_g_km.R
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Expand Up @@ -284,8 +284,7 @@ template_g_km <- function(dataname = "ANL",
#' ADSL <- tmc_ex_adsl
#' ADTTE <- tmc_ex_adtte
#' })
#' datanames(data) <- c("ADSL", "ADTTE")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADTTE <- data[["ADTTE"]]
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3 changes: 1 addition & 2 deletions R/tm_g_lineplot.R
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Expand Up @@ -222,8 +222,7 @@ template_g_lineplot <- function(dataname = "ANL",
#' ADLB <- tmc_ex_adlb %>%
#' mutate(AVISIT == fct_reorder(AVISIT, AVISITN, min))
#' })
#' datanames(data) <- c("ADSL", "ADLB")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADLB <- data[["ADLB"]]
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3 changes: 1 addition & 2 deletions R/tm_g_pp_adverse_events.R
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Expand Up @@ -201,8 +201,7 @@ template_adverse_events <- function(dataname = "ANL",
#' ADSL <- tmc_ex_adsl %>%
#' filter(USUBJID %in% ADAE$USUBJID)
#' })
#' datanames(data) <- c("ADSL", "ADAE")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADAE <- data[["ADAE"]]
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1 change: 0 additions & 1 deletion R/tm_g_pp_patient_timeline.R
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Expand Up @@ -378,7 +378,6 @@ template_patient_timeline <- function(dataname = "ANL",
#' )
#' })
#'
#' datanames(data) <- c("ADSL", "ADAE", "ADCM")
#' join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADAE", "ADCM")]
#' adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
#' join_keys(data)["ADCM", "ADCM"] <- adcm_keys
Expand Down
2 changes: 0 additions & 2 deletions R/tm_g_pp_therapy.R
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Expand Up @@ -264,8 +264,6 @@ template_therapy <- function(dataname = "ANL",
#' ADCM$CMAENDTM <- ADCM$AENDTM
#' })
#'
#' datanames(data) <- c("ADSL", "ADCM")
#'
#' join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADCM")]
#' adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
#' join_keys(data)["ADCM", "ADCM"] <- adcm_keys
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3 changes: 1 addition & 2 deletions R/tm_g_pp_vitals.R
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Expand Up @@ -224,8 +224,7 @@ template_vitals <- function(dataname = "ANL",
#' ADSL <- tmc_ex_adsl
#' ADVS <- tmc_ex_advs
#' })
#' datanames(data) <- c("ADSL", "ADVS")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADVS <- data[["ADVS"]]
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3 changes: 1 addition & 2 deletions R/tm_t_abnormality.R
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Expand Up @@ -259,8 +259,7 @@ template_abnormality <- function(parentname,
#' ) %>% with_label("On Treatment Record Flag")
#' )
#' })
#' datanames(data) <- c("ADSL", "ADLB")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADLB <- data[["ADLB"]]
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3 changes: 1 addition & 2 deletions R/tm_t_abnormality_by_worst_grade.R
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Expand Up @@ -265,8 +265,7 @@ template_abnormality_by_worst_grade <- function(parentname, # nolint: object_len
#' ADLB <- tmc_ex_adlb %>%
#' filter(!AVISIT %in% c("SCREENING", "BASELINE"))
#' })
#' datanames(data) <- c("ADSL", "ADLB")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADLB <- data[["ADLB"]]
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3 changes: 1 addition & 2 deletions R/tm_t_ancova.R
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Expand Up @@ -446,8 +446,7 @@ template_ancova <- function(dataname = "ANL",
#' ADSL <- tmc_ex_adsl
#' ADQS <- tmc_ex_adqs
#' })
#' datanames(data) <- c("ADSL", "ADQS")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADQS <- data[["ADQS"]]
Expand Down
3 changes: 1 addition & 2 deletions R/tm_t_binary_outcome.R
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Expand Up @@ -369,8 +369,7 @@ template_binary_outcome <- function(dataname,
#' ) %>%
#' filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
#' })
#' datanames(data) <- c("ADSL", "ADRS")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADRS <- data[["ADRS"]]
Expand Down
6 changes: 2 additions & 4 deletions R/tm_t_coxreg.R
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Expand Up @@ -388,8 +388,7 @@ template_coxreg_m <- function(dataname,
#' ADSL <- tmc_ex_adsl
#' ADTTE <- tmc_ex_adtte
#' })
#' datanames(data) <- c("ADSL", "ADTTE")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADTTE <- data[["ADTTE"]]
Expand Down Expand Up @@ -461,8 +460,7 @@ template_coxreg_m <- function(dataname,
#' )
#' })
#'
#' datanames(data) <- c("ADSL", "ADTTE")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADTTE <- data[["ADTTE"]]
Expand Down
3 changes: 1 addition & 2 deletions R/tm_t_events.R
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Expand Up @@ -472,8 +472,7 @@ template_events <- function(dataname,
#' ADSL <- tmc_ex_adsl
#' ADAE <- tmc_ex_adae
#' })
#' datanames(data) <- c("ADSL", "ADAE")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADAE <- data[["ADAE"]]
Expand Down
7 changes: 3 additions & 4 deletions R/tm_t_events_by_grade.R
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Expand Up @@ -803,13 +803,12 @@ template_events_col_by_grade <- function(dataname,
#' data <- teal_data()
#' data <- within(data, {
#' ADSL <- tmc_ex_adsl
#' lbls_adae <- col_labels(tmc_ex_adae)
#' .lbls_adae <- col_labels(tmc_ex_adae)
#' ADAE <- tmc_ex_adae %>%
#' mutate_if(is.character, as.factor) #' be certain of having factors
#' col_labels(ADAE) <- lbls_adae
#' col_labels(ADAE) <- .lbls_adae
#' })
#' datanames(data) <- c("ADSL", "ADAE")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADAE <- data[["ADAE"]]
Expand Down
3 changes: 1 addition & 2 deletions R/tm_t_events_patyear.R
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Expand Up @@ -204,8 +204,7 @@ template_events_patyear <- function(dataname,
#' mutate(is_event = CNSR == 0) %>%
#' mutate(n_events = as.integer(is_event))
#' })
#' datanames(data) <- c("ADSL", "ADAETTE")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADAETTE <- data[["ADAETTE"]]
Expand Down
19 changes: 9 additions & 10 deletions R/tm_t_events_summary.R
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Expand Up @@ -541,7 +541,7 @@ template_events_summary <- function(anl_name,
#' )
#' ADAE <- tmc_ex_adae
#'
#' add_event_flags <- function(dat) {
#' .add_event_flags <- function(dat) {
#' dat <- dat %>%
#' mutate(
#' TMPFL_SER = AESER == "Y",
Expand All @@ -564,13 +564,12 @@ template_events_summary <- function(anl_name,
#' }
#'
#' #' Generating user-defined event flags.
#' ADAE <- ADAE %>% add_event_flags()
#' ADAE <- ADAE %>% .add_event_flags()
#'
#' ae_anl_vars <- names(ADAE)[startsWith(names(ADAE), "TMPFL_")]
#' aesi_vars <- names(ADAE)[startsWith(names(ADAE), "TMP_")]
#' .ae_anl_vars <- names(ADAE)[startsWith(names(ADAE), "TMPFL_")]
#' .aesi_vars <- names(ADAE)[startsWith(names(ADAE), "TMP_")]
#' })
#' datanames(data) <- c("ADSL", "ADAE")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' app <- init(
#' data = data,
Expand All @@ -583,14 +582,14 @@ template_events_summary <- function(anl_name,
#' selected = "ARM"
#' ),
#' flag_var_anl = choices_selected(
#' choices = variable_choices("ADAE", data[["ae_anl_vars"]]),
#' selected = data[["ae_anl_vars"]][1],
#' choices = variable_choices("ADAE", data[[".ae_anl_vars"]]),
#' selected = data[[".ae_anl_vars"]][1],
#' keep_order = TRUE,
#' fixed = FALSE
#' ),
#' flag_var_aesi = choices_selected(
#' choices = variable_choices("ADAE", data[["aesi_vars"]]),
#' selected = data[["aesi_vars"]][1],
#' choices = variable_choices("ADAE", data[[".aesi_vars"]]),
#' selected = data[[".aesi_vars"]][1],
#' keep_order = TRUE,
#' fixed = FALSE
#' ),
Expand Down
7 changes: 3 additions & 4 deletions R/tm_t_exposure.R
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Expand Up @@ -241,7 +241,7 @@ template_exposure <- function(parentname,
#' ADEX <- tmc_ex_adex
#'
#' set.seed(1, kind = "Mersenne-Twister")
#' labels <- col_labels(ADEX, fill = FALSE)
#' .labels <- col_labels(ADEX, fill = FALSE)
#' ADEX <- ADEX %>%
#' distinct(USUBJID, .keep_all = TRUE) %>%
#' mutate(
Expand All @@ -251,10 +251,9 @@ template_exposure <- function(parentname,
#' AVALU = "Days"
#' ) %>%
#' bind_rows(ADEX)
#' col_labels(ADEX) <- labels
#' col_labels(ADEX) <- .labels
#' })
#' datanames(data) <- c("ADSL", "ADEX")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' app <- init(
#' data = data,
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3 changes: 1 addition & 2 deletions R/tm_t_logistic.R
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Expand Up @@ -236,8 +236,7 @@ template_logistic <- function(dataname,
#' ADRS <- tmc_ex_adrs %>%
#' filter(PARAMCD %in% c("BESRSPI", "INVET"))
#' })
#' datanames(data) <- c("ADSL", "ADRS")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADRS <- data[["ADRS"]]
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3 changes: 1 addition & 2 deletions R/tm_t_mult_events.R
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Expand Up @@ -294,8 +294,7 @@ template_mult_events <- function(dataname,
#' ADSL <- tmc_ex_adsl
#' ADCM <- tmc_ex_adcm
#' })
#' datanames(data) <- c("ADSL", "ADCM")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#' adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
#' join_keys(data)["ADCM", "ADCM"] <- adcm_keys
#'
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3 changes: 1 addition & 2 deletions R/tm_t_pp_basic_info.R
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Expand Up @@ -76,8 +76,7 @@ template_basic_info <- function(dataname = "ANL",
#' data <- within(data, {
#' ADSL <- tmc_ex_adsl
#' })
#' datanames(data) <- c("ADSL")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#'
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3 changes: 1 addition & 2 deletions R/tm_t_pp_laboratory.R
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Expand Up @@ -158,8 +158,7 @@ template_laboratory <- function(dataname = "ANL",
#' ADSL <- tmc_ex_adsl
#' ADLB <- tmc_ex_adlb
#' })
#' datanames(data) <- c("ADSL", "ADLB")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADLB <- data[["ADLB"]]
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3 changes: 1 addition & 2 deletions R/tm_t_pp_medical_history.R
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Expand Up @@ -100,8 +100,7 @@ template_medical_history <- function(dataname = "ANL",
#' ADSL <- tmc_ex_adsl
#' ADMH <- tmc_ex_admh
#' })
#' datanames(data) <- c("ADSL", "ADMH")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#'
#' ADSL <- data[["ADSL"]]
#' ADMH <- data[["ADMH"]]
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3 changes: 1 addition & 2 deletions R/tm_t_pp_prior_medication.R
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Expand Up @@ -75,8 +75,7 @@ template_prior_medication <- function(dataname = "ANL",
#' ADCM$CMASTDTM <- ADCM$ASTDTM
#' ADCM$CMAENDTM <- ADCM$AENDTM
#' })
#' datanames(data) <- c("ADSL", "ADCM")
#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
#' adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
#' join_keys(data)["ADCM", "ADCM"] <- adcm_keys
#'
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