From 8fb47d552eb555d4331b47e3e3425f8abdb175a1 Mon Sep 17 00:00:00 2001 From: unknown Date: Thu, 9 Nov 2023 17:09:50 +0530 Subject: [PATCH] adding join_key changes. --- R/tm_a_gee.R | 6 +++--- R/tm_a_mmrm.R | 6 +++--- R/tm_g_barchart_simple.R | 2 +- R/tm_g_ci.R | 2 +- R/tm_g_forest_rsp.R | 4 ++-- R/tm_g_forest_tte.R | 4 ++-- R/tm_g_ipp.R | 4 ++-- R/tm_g_km.R | 2 +- R/tm_g_lineplot.R | 2 +- R/tm_g_pp_adverse_events.R | 2 +- R/tm_g_pp_patient_timeline.R | 4 ++-- R/tm_g_pp_therapy.R | 2 +- R/tm_g_pp_vitals.R | 2 +- R/tm_t_abnormality.R | 6 +++--- R/tm_t_abnormality_by_worst_grade.R | 4 ++-- R/tm_t_ancova.R | 4 ++-- R/tm_t_binary_outcome.R | 4 ++-- R/tm_t_coxreg.R | 6 +++--- R/tm_t_events.R | 4 ++-- R/tm_t_events_by_grade.R | 6 +++--- R/tm_t_events_patyear.R | 4 ++-- R/tm_t_events_summary.R | 6 +++--- R/tm_t_exposure.R | 6 +++--- R/tm_t_logistic.R | 4 ++-- R/tm_t_mult_events.R | 4 ++-- R/tm_t_pp_basic_info.R | 2 +- R/tm_t_pp_laboratory.R | 2 +- R/tm_t_pp_medical_history.R | 2 +- R/tm_t_pp_prior_medication.R | 2 +- R/tm_t_shift_by_arm.R | 4 ++-- R/tm_t_shift_by_arm_by_worst.R | 4 ++-- R/tm_t_shift_by_grade.R | 4 ++-- R/tm_t_smq.R | 6 +++--- R/tm_t_summary.R | 4 ++-- R/tm_t_summary_by.R | 4 ++-- R/tm_t_tte.R | 4 ++-- man/template_g_lineplot.Rd | 12 +++++------- man/tm_a_gee.Rd | 2 +- man/tm_a_mmrm.Rd | 2 +- man/tm_g_lineplot.Rd | 12 +++++------- man/tm_g_pp_patient_timeline.Rd | 2 +- man/tm_t_abnormality.Rd | 2 +- man/tm_t_coxreg.Rd | 4 ++-- man/tm_t_events_by_grade.Rd | 2 +- man/tm_t_events_summary.Rd | 2 +- man/tm_t_exposure.Rd | 2 +- man/tm_t_smq.Rd | 2 +- 47 files changed, 89 insertions(+), 93 deletions(-) diff --git a/R/tm_a_gee.R b/R/tm_a_gee.R index c975a7f452..e78e91f90f 100644 --- a/R/tm_a_gee.R +++ b/R/tm_a_gee.R @@ -145,7 +145,7 @@ template_a_gee <- function(output_table, #' }) #' datanames <- c("ADSL", "ADQS") #' datanames(data) <- datanames -#' data@join_keys <- cdisc_join_keys(!!!datanames) +#' join_keys(data) <- cdisc_join_keys(!!!datanames) #' #' app <- init( #' data = data, @@ -447,14 +447,14 @@ srv_gee <- function(id, datasets = data, selector_list = selector_list, merge_function = "dplyr::inner_join", - join_keys = teal.data::get_join_keys(data) + join_keys = teal.data::join_keys(data) ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, data_extract = list(arm_var = arm_var), anl_name = "ANL_ADSL", - join_keys = teal.data::get_join_keys(data) + join_keys = teal.data::join_keys(data) ) anl_q <- shiny::reactive({ diff --git a/R/tm_a_mmrm.R b/R/tm_a_mmrm.R index b743eb392a..6614c3d220 100644 --- a/R/tm_a_mmrm.R +++ b/R/tm_a_mmrm.R @@ -476,7 +476,7 @@ template_mmrm_plots <- function(fit_name, #' #' datanames <- c("ADSL", "ADQS") #' datanames(data) <- datanames -#' data@join_keys <- cdisc_join_keys(!!!datanames) +#' join_keys(data) <- cdisc_join_keys(!!!datanames) #' app <- init( #' data = data, #' modules = modules( @@ -920,14 +920,14 @@ srv_mmrm <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, selector_list = selector_list_without_cov, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::inner_join" ) adsl_merge_inputs <- teal.transform::merge_expression_module( datasets = data, data_extract = list(arm_var = arm_var), - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), anl_name = "ANL_ADSL" ) diff --git a/R/tm_g_barchart_simple.R b/R/tm_g_barchart_simple.R index 0d8ca890ca..08604c82e4 100644 --- a/R/tm_g_barchart_simple.R +++ b/R/tm_g_barchart_simple.R @@ -381,7 +381,7 @@ srv_g_barchart_simple <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list ) diff --git a/R/tm_g_ci.R b/R/tm_g_ci.R index e7c4ea1897..6ed37997bd 100644 --- a/R/tm_g_ci.R +++ b/R/tm_g_ci.R @@ -403,7 +403,7 @@ srv_g_ci <- function(id, # nolint anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list ) diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R index 141cfcb3e5..8ea397b378 100644 --- a/R/tm_g_forest_rsp.R +++ b/R/tm_g_forest_rsp.R @@ -521,13 +521,13 @@ srv_g_forest_rsp <- function(id, datasets = data, selector_list = selector_list, merge_function = "dplyr::inner_join", - join_keys = teal.data::get_join_keys(data) + join_keys = teal.data::join_keys(data) ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, data_extract = list(arm_var = arm_var, subgroup_var = subgroup_var, strata_var = strata_var), - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), anl_name = "ANL_ADSL" ) diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R index 2662bbedc6..3eeb82bbe8 100644 --- a/R/tm_g_forest_tte.R +++ b/R/tm_g_forest_tte.R @@ -522,14 +522,14 @@ srv_g_forest_tte <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list, merge_function = "dplyr::inner_join" ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), data_extract = list(arm_var = arm_var, subgroup_var = subgroup_var, strata_var = strata_var), anl_name = "ANL_ADSL" ) diff --git a/R/tm_g_ipp.R b/R/tm_g_ipp.R index 580b12a1a5..37dc7875fa 100644 --- a/R/tm_g_ipp.R +++ b/R/tm_g_ipp.R @@ -499,12 +499,12 @@ srv_g_ipp <- function(id, datasets = data, selector_list = selector_list, merge_function = "dplyr::inner_join", - join_keys = teal.data::get_join_keys(data) + join_keys = teal.data::join_keys(data) ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), data_extract = list(arm_var = arm_var, id_var = id_var), anl_name = "ANL_ADSL" ) diff --git a/R/tm_g_km.R b/R/tm_g_km.R index 9de6059fd0..1bbf08c4b5 100644 --- a/R/tm_g_km.R +++ b/R/tm_g_km.R @@ -656,7 +656,7 @@ srv_g_km <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list, merge_function = "dplyr::inner_join" ) diff --git a/R/tm_g_lineplot.R b/R/tm_g_lineplot.R index ea24026228..1e4d4e6e8a 100644 --- a/R/tm_g_lineplot.R +++ b/R/tm_g_lineplot.R @@ -555,7 +555,7 @@ srv_g_lineplot <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list, merge_function = "dplyr::inner_join" ) diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R index 05d3829a34..2772d39963 100644 --- a/R/tm_g_pp_adverse_events.R +++ b/R/tm_g_pp_adverse_events.R @@ -496,7 +496,7 @@ srv_g_adverse_events <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, selector_list = selector_list, - join_keys = teal.data::get_join_keys(data) + join_keys = teal.data::join_keys(data) ) anl_q <- shiny::reactive( diff --git a/R/tm_g_pp_patient_timeline.R b/R/tm_g_pp_patient_timeline.R index 25b23f9135..ddb503e9cf 100644 --- a/R/tm_g_pp_patient_timeline.R +++ b/R/tm_g_pp_patient_timeline.R @@ -375,7 +375,7 @@ template_patient_timeline <- function(dataname = "ANL", #' }) #' #' datanames(data) <- c("ADSL", "ADAE", "ADCM") -#' data@join_keys <- join_keys( +#' join_keys(data) <- join_keys( #' join_key("ADSL", keys = get_cdisc_keys("ADSL")), #' join_key("ADAE", keys = get_cdisc_keys("ADAE")), #' join_key("ADCM", keys = adcm_keys), @@ -772,7 +772,7 @@ srv_g_patient_timeline <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list ) diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R index 9ecf0071f6..3460b7f399 100644 --- a/R/tm_g_pp_therapy.R +++ b/R/tm_g_pp_therapy.R @@ -613,7 +613,7 @@ srv_g_therapy <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list, merge_function = "dplyr::left_join" ) diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R index 67905939a6..dcd7f64605 100644 --- a/R/tm_g_pp_vitals.R +++ b/R/tm_g_pp_vitals.R @@ -429,7 +429,7 @@ srv_g_vitals <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list, merge_function = "dplyr::left_join" ) diff --git a/R/tm_t_abnormality.R b/R/tm_t_abnormality.R index 96fb2f1666..e9e11a243b 100644 --- a/R/tm_t_abnormality.R +++ b/R/tm_t_abnormality.R @@ -251,7 +251,7 @@ template_abnormality <- function(parentname, #' }) #' datanames <- c("ADSL", "ADLB") #' datanames(data) <- datanames -#' data@join_keys <- cdisc_join_keys(!!!datanames) +#' join_keys(data) <- cdisc_join_keys(!!!datanames) #' #' app <- init( #' data = data, @@ -542,14 +542,14 @@ srv_t_abnormality <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list, merge_function = "dplyr::inner_join" ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), data_extract = list(arm_var = arm_var), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_abnormality_by_worst_grade.R b/R/tm_t_abnormality_by_worst_grade.R index e49738ef0d..14dbceecab 100644 --- a/R/tm_t_abnormality_by_worst_grade.R +++ b/R/tm_t_abnormality_by_worst_grade.R @@ -534,13 +534,13 @@ srv_t_abnormality_by_worst_grade <- function(id, # nolint anl_inputs <- teal.transform::merge_expression_srv( selector_list = selector_list, datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::inner_join" ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), data_extract = list(arm_var = arm_var), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_ancova.R b/R/tm_t_ancova.R index 172e4ecd07..52664149a4 100644 --- a/R/tm_t_ancova.R +++ b/R/tm_t_ancova.R @@ -730,7 +730,7 @@ srv_ancova <- function(id, anl_inputs <- teal.transform::merge_expression_srv( selector_list = selector_list, datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::inner_join" ) @@ -738,7 +738,7 @@ srv_ancova <- function(id, datasets = data, data_extract = list(arm_var = arm_var), anl_name = "ANL_ADSL", - join_keys = teal.data::get_join_keys(data) + join_keys = teal.data::join_keys(data) ) anl_q <- shiny::reactive({ diff --git a/R/tm_t_binary_outcome.R b/R/tm_t_binary_outcome.R index 15fad4ff25..d114ec3846 100644 --- a/R/tm_t_binary_outcome.R +++ b/R/tm_t_binary_outcome.R @@ -792,13 +792,13 @@ srv_t_binary_outcome <- function(id, datasets = data, selector_list = selector_list, merge_function = "dplyr::inner_join", - join_keys = teal.data::get_join_keys(data) + join_keys = teal.data::join_keys(data) ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, data_extract = list(arm_var = arm_var, strata_var = strata_var), - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_coxreg.R b/R/tm_t_coxreg.R index 6b7b1c6a71..1e751d5c7c 100644 --- a/R/tm_t_coxreg.R +++ b/R/tm_t_coxreg.R @@ -371,7 +371,7 @@ template_coxreg_m <- function(dataname, #' }) #' datanames <- c("ADSL", "ADTTE") #' datanames(data) <- datanames -#' data@join_keys <- cdisc_join_keys(!!!datanames) +#' join_keys(data) <- cdisc_join_keys(!!!datanames) #' #' app <- init( #' data = data, @@ -439,7 +439,7 @@ template_coxreg_m <- function(dataname, #' #' datanames <- c("ADSL", "ADTTE") #' datanames(data) <- datanames -#' data@join_keys <- cdisc_join_keys(!!!datanames) +#' join_keys(data) <- cdisc_join_keys(!!!datanames) #' #' ## Teal application #' ## ================ @@ -790,7 +790,7 @@ srv_t_coxreg <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list, merge_function = "dplyr::inner_join" ) diff --git a/R/tm_t_events.R b/R/tm_t_events.R index c97d917609..955df7a834 100644 --- a/R/tm_t_events.R +++ b/R/tm_t_events.R @@ -679,7 +679,7 @@ srv_t_events_byterm <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list, merge_function = "dplyr::inner_join" ) @@ -688,7 +688,7 @@ srv_t_events_byterm <- function(id, datasets = data, data_extract = list(arm_var = arm_var), anl_name = "ANL_ADSL", - join_keys = teal.data::get_join_keys(data) + join_keys = teal.data::join_keys(data) ) anl_q <- shiny::reactive({ diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R index 405dea497e..eac648d84e 100644 --- a/R/tm_t_events_by_grade.R +++ b/R/tm_t_events_by_grade.R @@ -794,7 +794,7 @@ template_events_col_by_grade <- function(dataname, #' #' datanames <- c("ADSL", "ADAE") #' datanames(data) <- datanames -#' data@join_keys <- cdisc_join_keys(!!!datanames) +#' join_keys(data) <- cdisc_join_keys(!!!datanames) #' #' app <- init( #' data = data, @@ -1046,14 +1046,14 @@ srv_t_events_by_grade <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, selector_list = selector_list, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::inner_join" ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, data_extract = list(arm_var = arm_var), - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_events_patyear.R b/R/tm_t_events_patyear.R index 1d0bc4ed93..564ca517cc 100644 --- a/R/tm_t_events_patyear.R +++ b/R/tm_t_events_patyear.R @@ -443,14 +443,14 @@ srv_events_patyear <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, selector_list = selector_list, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::inner_join" ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, data_extract = list(arm_var = arm_var), - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_events_summary.R b/R/tm_t_events_summary.R index 9c432a4dab..2bbe7fd053 100644 --- a/R/tm_t_events_summary.R +++ b/R/tm_t_events_summary.R @@ -538,7 +538,7 @@ template_events_summary <- function(anl_name, #' #' datanames <- c("ADSL", "ADAE") #' datanames(data) <- datanames -#' data@join_keys <- cdisc_join_keys(!!!datanames) +#' join_keys(data) <- cdisc_join_keys(!!!datanames) #' #' app <- init( #' data = data, @@ -824,14 +824,14 @@ srv_t_events_summary <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, selector_list = selector_list, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::inner_join" ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, data_extract = Filter(Negate(is.null), list(arm_var = arm_var, dthfl_var = dthfl_var, dcsreas_var = dcsreas_var)), - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_exposure.R b/R/tm_t_exposure.R index 2e0e391628..1f92836935 100644 --- a/R/tm_t_exposure.R +++ b/R/tm_t_exposure.R @@ -246,7 +246,7 @@ template_exposure <- function(parentname, #' #' datanames <- c("ADSL", "ADEX") #' datanames(data) <- datanames -#' data@join_keys <- cdisc_join_keys(!!!datanames) +#' join_keys(data) <- cdisc_join_keys(!!!datanames) #' #' app <- init( #' data = data, @@ -528,13 +528,13 @@ srv_t_exposure <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, selector_list = selector_list, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::inner_join" ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), data_extract = list(col_by_var = col_by_var), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_logistic.R b/R/tm_t_logistic.R index ea3250f093..b85792f005 100644 --- a/R/tm_t_logistic.R +++ b/R/tm_t_logistic.R @@ -523,13 +523,13 @@ srv_t_logistic <- function(id, anl_inputs <- teal.transform::merge_expression_srv( selector_list = selector_list, datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::inner_join" ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), data_extract = list(arm_var = arm_var), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_mult_events.R b/R/tm_t_mult_events.R index 9d433c9263..c5aaf4291d 100644 --- a/R/tm_t_mult_events.R +++ b/R/tm_t_mult_events.R @@ -488,7 +488,7 @@ srv_t_mult_events_byterm <- function(id, anl_merge_inputs <- teal.transform::merge_expression_srv( id = "anl_merge", datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list, merge_function = "dplyr::inner_join" ) @@ -496,7 +496,7 @@ srv_t_mult_events_byterm <- function(id, adsl_merge_inputs <- teal.transform::merge_expression_module( id = "adsl_merge", datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), data_extract = list(arm_var = arm_var), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_pp_basic_info.R b/R/tm_t_pp_basic_info.R index e3232d167b..6ea4d5fa74 100644 --- a/R/tm_t_pp_basic_info.R +++ b/R/tm_t_pp_basic_info.R @@ -219,7 +219,7 @@ srv_t_basic_info <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list, merge_function = "dplyr::left_join" ) diff --git a/R/tm_t_pp_laboratory.R b/R/tm_t_pp_laboratory.R index 989a726fc3..3e790017a0 100644 --- a/R/tm_t_pp_laboratory.R +++ b/R/tm_t_pp_laboratory.R @@ -381,7 +381,7 @@ srv_g_laboratory <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list ) diff --git a/R/tm_t_pp_medical_history.R b/R/tm_t_pp_medical_history.R index 8c57b5402d..66b5a66157 100644 --- a/R/tm_t_pp_medical_history.R +++ b/R/tm_t_pp_medical_history.R @@ -282,7 +282,7 @@ srv_t_medical_history <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list, merge_function = "dplyr::left_join" ) diff --git a/R/tm_t_pp_prior_medication.R b/R/tm_t_pp_prior_medication.R index 57c7a192f8..1f297be6d8 100644 --- a/R/tm_t_pp_prior_medication.R +++ b/R/tm_t_pp_prior_medication.R @@ -298,7 +298,7 @@ srv_t_prior_medication <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, selector_list = selector_list, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::left_join" ) diff --git a/R/tm_t_shift_by_arm.R b/R/tm_t_shift_by_arm.R index 2586b31f6e..a881eda4d9 100644 --- a/R/tm_t_shift_by_arm.R +++ b/R/tm_t_shift_by_arm.R @@ -430,14 +430,14 @@ srv_shift_by_arm <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list, merge_function = "dplyr::inner_join" ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), data_extract = list(arm_var = arm_var), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_shift_by_arm_by_worst.R b/R/tm_t_shift_by_arm_by_worst.R index a6fe6b1f6e..7172783191 100644 --- a/R/tm_t_shift_by_arm_by_worst.R +++ b/R/tm_t_shift_by_arm_by_worst.R @@ -454,13 +454,13 @@ srv_shift_by_arm_by_worst <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, selector_list = selector_list, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::inner_join" ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), data_extract = list(arm_var = arm_var), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_shift_by_grade.R b/R/tm_t_shift_by_grade.R index 93388139fb..6e5a3b46a1 100644 --- a/R/tm_t_shift_by_grade.R +++ b/R/tm_t_shift_by_grade.R @@ -790,14 +790,14 @@ srv_t_shift_by_grade <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), selector_list = selector_list, merge_function = "dplyr::inner_join" ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), data_extract = list(arm_var = arm_var), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_smq.R b/R/tm_t_smq.R index 9f862e9bc8..9cb55278fd 100644 --- a/R/tm_t_smq.R +++ b/R/tm_t_smq.R @@ -340,7 +340,7 @@ template_smq <- function(dataname, #' #' datanames <- c("ADSL", "ADAE") #' datanames(data) <- datanames -#' data@join_keys <- cdisc_join_keys(!!!datanames) +#' join_keys(data) <- cdisc_join_keys(!!!datanames) #' #' app <- init( #' data = data, @@ -570,13 +570,13 @@ srv_t_smq <- function(id, anl_inputs <- teal.transform::merge_expression_srv( datasets = data, selector_list = selector_list, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::inner_join" ) adsl_inputs <- teal.transform::merge_expression_module( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), data_extract = list(arm_var = arm_var), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_summary.R b/R/tm_t_summary.R index ab2ef229cc..71704fc2e7 100644 --- a/R/tm_t_summary.R +++ b/R/tm_t_summary.R @@ -454,7 +454,7 @@ srv_summary <- function(id, id = "anl_merge", datasets = data, selector_list = selector_list, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::inner_join" ) @@ -462,7 +462,7 @@ srv_summary <- function(id, id = "adsl_merge", datasets = data, data_extract = list(arm_var = arm_var), - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_summary_by.R b/R/tm_t_summary_by.R index 51ff1b6b41..0b07a51130 100644 --- a/R/tm_t_summary_by.R +++ b/R/tm_t_summary_by.R @@ -630,14 +630,14 @@ srv_summary_by <- function(id, anl_inputs <- teal.transform::merge_expression_srv( selector_list = selector_list, datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::inner_join" ) adsl_inputs <- teal.transform::merge_expression_module( id = "adsl_merge", datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), data_extract = list(arm_var = arm_var), anl_name = "ANL_ADSL" ) diff --git a/R/tm_t_tte.R b/R/tm_t_tte.R index 7b04542ec8..f73461eeaf 100644 --- a/R/tm_t_tte.R +++ b/R/tm_t_tte.R @@ -796,13 +796,13 @@ srv_t_tte <- function(id, anl_merge_inputs <- teal.transform::merge_expression_srv( datasets = data, selector_list = selector_list, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), merge_function = "dplyr::inner_join" ) adsl_merge_inputs <- teal.transform::merge_expression_module( datasets = data, - join_keys = teal.data::get_join_keys(data), + join_keys = teal.data::join_keys(data), data_extract = list(arm_var = arm_var, strata_var = strata_var), anl_name = "ANL_ADSL" ) diff --git a/man/template_g_lineplot.Rd b/man/template_g_lineplot.Rd index 5c1e8881b8..149a4fc47e 100644 --- a/man/template_g_lineplot.Rd +++ b/man/template_g_lineplot.Rd @@ -30,7 +30,7 @@ template_g_lineplot( \item{dataname}{(\code{character})\cr analysis data used in teal module.} -\item{strata}{(\code{character} or \code{NA})\cr deprecated - group variable name.} +\item{strata}{(\code{character} or \code{NA})\cr strata variable name.} \item{x}{(\code{character})\cr x variable name.} @@ -49,13 +49,11 @@ and be of a \code{double} or \code{numeric} type vector of length one.} \item{interval}{(\code{character} or \code{NULL})\cr names of the statistics that will be plotted as intervals. All the statistics indicated in \code{interval} variable must be present in the object returned by \code{sfun}, -and be of a \code{double} or \code{numeric} type vector of length two. Set \code{interval = NULL} if intervals should not be -added to the plot.} +and be of a \code{double} or \code{numeric} type vector of length two.} -\item{whiskers}{(\code{character})\cr names of the interval whiskers that will be plotted. Names must match names -of the list element \code{interval} that will be returned by \code{sfun} (e.g. \code{mean_ci_lwr} element of -\code{sfun(x)[["mean_ci"]]}). It is possible to specify one whisker only, or to suppress all whiskers by setting -\code{interval = NULL}.} +\item{whiskers}{(\code{character})\cr names of the interval whiskers that will be plotted. Must match the \code{names} +attribute of the \code{interval} element in the list returned by \code{sfun}. It is possible to specify one whisker only, +lower or upper.} \item{table}{(\code{character} or \code{NULL})\cr names of the statistics that will be displayed in the table below the plot. All the statistics indicated in \code{table} variable must be present in the object returned by \code{sfun}.} diff --git a/man/tm_a_gee.Rd b/man/tm_a_gee.Rd index bc11ecd355..25bcbf95ea 100644 --- a/man/tm_a_gee.Rd +++ b/man/tm_a_gee.Rd @@ -106,7 +106,7 @@ data <- within(data, { }) datanames <- c("ADSL", "ADQS") datanames(data) <- datanames -data@join_keys <- cdisc_join_keys(!!!datanames) +join_keys(data) <- cdisc_join_keys(!!!datanames) app <- init( data = data, diff --git a/man/tm_a_mmrm.Rd b/man/tm_a_mmrm.Rd index e89b816fdd..2b99e70ae4 100644 --- a/man/tm_a_mmrm.Rd +++ b/man/tm_a_mmrm.Rd @@ -148,7 +148,7 @@ data <- within(data, { datanames <- c("ADSL", "ADQS") datanames(data) <- datanames -data@join_keys <- cdisc_join_keys(!!!datanames) +join_keys(data) <- cdisc_join_keys(!!!datanames) app <- init( data = data, modules = modules( diff --git a/man/tm_g_lineplot.Rd b/man/tm_g_lineplot.Rd index 2cd5994f18..fc51cc68eb 100644 --- a/man/tm_g_lineplot.Rd +++ b/man/tm_g_lineplot.Rd @@ -47,7 +47,7 @@ analysis data used in teal module.} \item{parentname}{(\code{character})\cr parent analysis data used in teal module, usually this refers to \code{ADSL}.} -\item{strata}{(\code{character} or \code{NA})\cr deprecated - group variable name.} +\item{strata}{(\code{character} or \code{NA})\cr strata variable name.} \item{x}{(\code{character})\cr x variable name.} @@ -65,17 +65,15 @@ value for the confidence level within the range of (0, 1).} \item{interval}{(\code{character} or \code{NULL})\cr names of the statistics that will be plotted as intervals. All the statistics indicated in \code{interval} variable must be present in the object returned by \code{sfun}, -and be of a \code{double} or \code{numeric} type vector of length two. Set \code{interval = NULL} if intervals should not be -added to the plot.} +and be of a \code{double} or \code{numeric} type vector of length two.} \item{mid}{(\code{character} or \code{NULL})\cr names of the statistics that will be plotted as midpoints. All the statistics indicated in \code{mid} variable must be present in the object returned by \code{sfun}, and be of a \code{double} or \code{numeric} type vector of length one.} -\item{whiskers}{(\code{character})\cr names of the interval whiskers that will be plotted. Names must match names -of the list element \code{interval} that will be returned by \code{sfun} (e.g. \code{mean_ci_lwr} element of -\code{sfun(x)[["mean_ci"]]}). It is possible to specify one whisker only, or to suppress all whiskers by setting -\code{interval = NULL}.} +\item{whiskers}{(\code{character})\cr names of the interval whiskers that will be plotted. Must match the \code{names} +attribute of the \code{interval} element in the list returned by \code{sfun}. It is possible to specify one whisker only, +lower or upper.} \item{table}{(\code{character} or \code{NULL})\cr names of the statistics that will be displayed in the table below the plot. All the statistics indicated in \code{table} variable must be present in the object returned by \code{sfun}.} diff --git a/man/tm_g_pp_patient_timeline.Rd b/man/tm_g_pp_patient_timeline.Rd index fdbeb5c27e..fa34ea85ee 100644 --- a/man/tm_g_pp_patient_timeline.Rd +++ b/man/tm_g_pp_patient_timeline.Rd @@ -127,7 +127,7 @@ data <- within(data, { }) datanames(data) <- c("ADSL", "ADAE", "ADCM") -data@join_keys <- join_keys( +join_keys(data) <- join_keys( join_key("ADSL", keys = get_cdisc_keys("ADSL")), join_key("ADAE", keys = get_cdisc_keys("ADAE")), join_key("ADCM", keys = adcm_keys), diff --git a/man/tm_t_abnormality.Rd b/man/tm_t_abnormality.Rd index 4f69b03f8d..83e0165c0b 100644 --- a/man/tm_t_abnormality.Rd +++ b/man/tm_t_abnormality.Rd @@ -122,7 +122,7 @@ data <- within(data, { }) datanames <- c("ADSL", "ADLB") datanames(data) <- datanames -data@join_keys <- cdisc_join_keys(!!!datanames) +join_keys(data) <- cdisc_join_keys(!!!datanames) app <- init( data = data, diff --git a/man/tm_t_coxreg.Rd b/man/tm_t_coxreg.Rd index 5c120d9281..bd9194e80a 100644 --- a/man/tm_t_coxreg.Rd +++ b/man/tm_t_coxreg.Rd @@ -151,7 +151,7 @@ data <- within(data, { }) datanames <- c("ADSL", "ADTTE") datanames(data) <- datanames -data@join_keys <- cdisc_join_keys(!!!datanames) +join_keys(data) <- cdisc_join_keys(!!!datanames) app <- init( data = data, @@ -219,7 +219,7 @@ data <- within(data, { datanames <- c("ADSL", "ADTTE") datanames(data) <- datanames -data@join_keys <- cdisc_join_keys(!!!datanames) +join_keys(data) <- cdisc_join_keys(!!!datanames) ## Teal application ## ================ diff --git a/man/tm_t_events_by_grade.Rd b/man/tm_t_events_by_grade.Rd index cbe361cf01..b9d8051aeb 100644 --- a/man/tm_t_events_by_grade.Rd +++ b/man/tm_t_events_by_grade.Rd @@ -100,7 +100,7 @@ data <- within(data, { datanames <- c("ADSL", "ADAE") datanames(data) <- datanames -data@join_keys <- cdisc_join_keys(!!!datanames) +join_keys(data) <- cdisc_join_keys(!!!datanames) app <- init( data = data, diff --git a/man/tm_t_events_summary.Rd b/man/tm_t_events_summary.Rd index a42c143362..b30a16f00b 100644 --- a/man/tm_t_events_summary.Rd +++ b/man/tm_t_events_summary.Rd @@ -152,7 +152,7 @@ data <- within(data, { datanames <- c("ADSL", "ADAE") datanames(data) <- datanames -data@join_keys <- cdisc_join_keys(!!!datanames) +join_keys(data) <- cdisc_join_keys(!!!datanames) app <- init( data = data, diff --git a/man/tm_t_exposure.Rd b/man/tm_t_exposure.Rd index 315a26e62c..3a456bb966 100644 --- a/man/tm_t_exposure.Rd +++ b/man/tm_t_exposure.Rd @@ -123,7 +123,7 @@ data <- within(data, { datanames <- c("ADSL", "ADEX") datanames(data) <- datanames -data@join_keys <- cdisc_join_keys(!!!datanames) +join_keys(data) <- cdisc_join_keys(!!!datanames) app <- init( data = data, diff --git a/man/tm_t_smq.Rd b/man/tm_t_smq.Rd index 9bb06a04a8..1d815447c4 100644 --- a/man/tm_t_smq.Rd +++ b/man/tm_t_smq.Rd @@ -116,7 +116,7 @@ data <- within(data, { datanames <- c("ADSL", "ADAE") datanames(data) <- datanames -data@join_keys <- cdisc_join_keys(!!!datanames) +join_keys(data) <- cdisc_join_keys(!!!datanames) app <- init( data = data,