diff --git a/.lintr b/.lintr index 34473d2738..0a0bb22f32 100644 --- a/.lintr +++ b/.lintr @@ -1,5 +1,6 @@ linters: linters_with_defaults( line_length_linter = line_length_linter(120), cyclocomp_linter = NULL, - object_usage_linter = NULL + object_usage_linter = NULL, + indentation_linter = NULL ) diff --git a/R/tm_a_gee.R b/R/tm_a_gee.R index 8d1784418c..838da724b4 100644 --- a/R/tm_a_gee.R +++ b/R/tm_a_gee.R @@ -547,14 +547,15 @@ srv_gee <- function(id, title = label ) + ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Generalized Estimating Equations (GEE) Analysis Table") - card$append_text("Generalized Estimating Equations (GEE) Analysis Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Generalized Estimating Equations (GEE) Analysis Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) table_type <- switch(input$output_table, "t_gee_cov" = "Residual Covariance Matrix Estimate", "t_gee_coef" = "Model Coefficients", diff --git a/R/tm_a_mmrm.R b/R/tm_a_mmrm.R index a174338f0e..d6dc606fc1 100644 --- a/R/tm_a_mmrm.R +++ b/R/tm_a_mmrm.R @@ -239,11 +239,10 @@ template_mmrm_tables <- function(parentname, layout_list <- add_expr( layout_list, substitute( - expr = - rtables::add_overall_col(total_label) %>% - rtables::split_rows_by(visit_var) %>% - tern.mmrm::summarize_lsmeans(arms = FALSE) %>% - rtables::append_topleft(paste0(" ", paramcd)), + expr = rtables::add_overall_col(total_label) %>% + rtables::split_rows_by(visit_var) %>% + tern.mmrm::summarize_lsmeans(arms = FALSE) %>% + rtables::append_topleft(paste0(" ", paramcd)), env = list( total_label = total_label, visit_var = visit_var, @@ -1432,20 +1431,17 @@ srv_mmrm <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("MMRM") - card$append_text("Mixed Model Repeated Measurements (MMRM) Analysis", "header2") - card$append_text( - paste( + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Mixed Model Repeated Measurements (MMRM) Analysis", + label = label, + description = paste( "Mixed Models procedure analyzes results from repeated measures designs", "in which the outcome is continuous and measured at fixed time points" ), - "header3" + with_filter = with_filter, + filter_panel_api = filter_panel_api ) - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } if (!is.null(table_r())) { card$append_text("Table", "header3") card$append_table(table_r()) diff --git a/R/tm_g_barchart_simple.R b/R/tm_g_barchart_simple.R index f3279ebd8d..5419e8a4fa 100644 --- a/R/tm_g_barchart_simple.R +++ b/R/tm_g_barchart_simple.R @@ -538,13 +538,13 @@ srv_g_barchart_simple <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Barchart Plot") - card$append_text("Barchart Plot", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Barchart Plot", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Plot", "header3") card$append_plot(plot_r(), dim = pws$dim()) if (!comment == "") { diff --git a/R/tm_g_ci.R b/R/tm_g_ci.R index 3fc44aaaf3..17f69b5d00 100644 --- a/R/tm_g_ci.R +++ b/R/tm_g_ci.R @@ -483,14 +483,14 @@ srv_g_ci <- function(id, # nolint ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("CI Plot") - card$append_text("CI Plot", "header2") - card$append_text("Confidence Interval Plot", "header3") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "CI Plot", + label = label, + description = "Confidence Interval Plot", + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Plot", "header3") card$append_plot(plot_r(), dim = pws$dim()) if (!comment == "") { diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R index 4f5b9b5747..24f2a5b899 100644 --- a/R/tm_g_forest_rsp.R +++ b/R/tm_g_forest_rsp.R @@ -718,13 +718,13 @@ srv_g_forest_rsp <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Forest Response Plot") - card$append_text("Forest Response Plot", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Forest Response Plot", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Plot", "header3") card$append_plot(plot_r(), dim = pws$dim()) if (!comment == "") { diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R index 89b366a91d..e87bb051f2 100644 --- a/R/tm_g_forest_tte.R +++ b/R/tm_g_forest_tte.R @@ -652,13 +652,13 @@ srv_g_forest_tte <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Forest Survival Plot") - card$append_text("Forest Survival Plot", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Forest Survival Plot", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Plot", "header3") card$append_plot(plot_r(), dim = pws$dim()) if (!comment == "") { diff --git a/R/tm_g_ipp.R b/R/tm_g_ipp.R index 4a9918c829..c8e51e2935 100644 --- a/R/tm_g_ipp.R +++ b/R/tm_g_ipp.R @@ -611,13 +611,13 @@ srv_g_ipp <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Individual Patient Plot") - card$append_text("Individual Patient Plot", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Individual Patient Plot", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Plot", "header3") card$append_plot(plot_r(), dim = pws$dim()) if (!comment == "") { diff --git a/R/tm_g_km.R b/R/tm_g_km.R index fd544eacf2..874f361ced 100644 --- a/R/tm_g_km.R +++ b/R/tm_g_km.R @@ -773,14 +773,14 @@ srv_g_km <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Kaplan Meier Plot") - card$append_text("Kaplan Meier Plot", "header2") - card$append_text("Non-parametric method used to estimate the survival function from lifetime data", "header3") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Kaplan Meier Plot", + label = label, + description = "Non-parametric method used to estimate the survival function from lifetime data", + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Plot", "header3") card$append_plot(plot_r(), dim = pws$dim()) if (!comment == "") { diff --git a/R/tm_g_lineplot.R b/R/tm_g_lineplot.R index 4d7bbbebc9..fced62f2a1 100644 --- a/R/tm_g_lineplot.R +++ b/R/tm_g_lineplot.R @@ -648,13 +648,13 @@ srv_g_lineplot <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Line Plot") - card$append_text("Line Plot", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Line Plot", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Plot", "header3") card$append_plot(plot_r(), dim = pws$dim()) if (!comment == "") { diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R index ea37176a7e..bd2243b965 100644 --- a/R/tm_g_pp_adverse_events.R +++ b/R/tm_g_pp_adverse_events.R @@ -575,13 +575,13 @@ srv_g_adverse_events <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Patient Profile Adverse Events") - card$append_text("Patient Profile Adverse Events", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Patient Profile Adverse Events Plot", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(teal.code::dev_suppress(all_q()[["table"]])) card$append_text("Plot", "header3") diff --git a/R/tm_g_pp_patient_timeline.R b/R/tm_g_pp_patient_timeline.R index 19c558204a..5655454b56 100644 --- a/R/tm_g_pp_patient_timeline.R +++ b/R/tm_g_pp_patient_timeline.R @@ -831,8 +831,10 @@ srv_g_patient_timeline <- function(id, shiny::validate( shiny::need( !input$relday_x_axis || - (sum(stats::complete.cases(p_time_data_pat[, c(aerelday_start_name, aerelday_end_name)])) > 0 || - sum(stats::complete.cases(p_time_data_pat[, c(dsrelday_start_name, dsrelday_end_name)])) > 0), + ( + sum(stats::complete.cases(p_time_data_pat[, c(aerelday_start_name, aerelday_end_name)])) > 0 || + sum(stats::complete.cases(p_time_data_pat[, c(dsrelday_start_name, dsrelday_end_name)])) > 0 + ), "Selected patient is not in dataset (either due to filtering or missing values). Consider relaxing filters." ) ) @@ -894,13 +896,13 @@ srv_g_patient_timeline <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Patient Profile Timeline Plot") - card$append_text("Patient Profile Timeline Plot", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Patient Profile Timeline Plot", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Plot", "header3") card$append_plot(plot_r(), dim = pws$dim()) if (!comment == "") { diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R index adf42b587d..9617eca52d 100644 --- a/R/tm_g_pp_therapy.R +++ b/R/tm_g_pp_therapy.R @@ -696,13 +696,13 @@ srv_g_therapy <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Patient Profile Therapy") - card$append_text("Patient Profile Therapy", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Patient Profile Therapy", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(teal.code::dev_suppress(all_q()[["therapy_table"]])) card$append_text("Plot", "header3") diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R index 1b91b4b3b8..e092a57afc 100644 --- a/R/tm_g_pp_vitals.R +++ b/R/tm_g_pp_vitals.R @@ -528,13 +528,13 @@ srv_g_vitals <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Patient Profile Vitals Plot") - card$append_text("Patient Profile Vitals Plot", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Patient Profile Vitals Plot", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Plot", "header3") card$append_plot(plot_r(), dim = pws$dim()) if (!comment == "") { diff --git a/R/tm_t_abnormality.R b/R/tm_t_abnormality.R index 8f789993fa..ba732508a4 100644 --- a/R/tm_t_abnormality.R +++ b/R/tm_t_abnormality.R @@ -647,13 +647,13 @@ srv_t_abnormality <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Abnormality Summary Table") - card$append_text("Abnormality Summary Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Abnormality Summary Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_abnormality_by_worst_grade.R b/R/tm_t_abnormality_by_worst_grade.R index 65cffd439e..e0b4512ee2 100644 --- a/R/tm_t_abnormality_by_worst_grade.R +++ b/R/tm_t_abnormality_by_worst_grade.R @@ -664,14 +664,14 @@ srv_t_abnormality_by_worst_grade <- function(id, # nolint ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Laboratory Test Results Table") - card$append_text("Laboratory Test Results Table", "header2") - card$append_text("Laboratory test results with highest grade post-baseline Table", "header3") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Laboratory Test Results Table", + label = label, + description = "Laboratory test results with highest grade post-baseline Table", + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_ancova.R b/R/tm_t_ancova.R index 11ef31b14d..dcc31fb95a 100644 --- a/R/tm_t_ancova.R +++ b/R/tm_t_ancova.R @@ -945,14 +945,14 @@ srv_ancova <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("ANCOVA") - card$append_text("ANCOVA", "header2") - card$append_text("Analysis of Covariance", "header3") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "ANCOVA", + label = label, + description = "Analysis of Covariance", + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_binary_outcome.R b/R/tm_t_binary_outcome.R index 6de0b8ab18..2ce52bab7d 100644 --- a/R/tm_t_binary_outcome.R +++ b/R/tm_t_binary_outcome.R @@ -1008,13 +1008,13 @@ srv_t_binary_outcome <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Binary Outcome Table") - card$append_text("Binary Outcome Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Binary Outcome Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_coxreg.R b/R/tm_t_coxreg.R index bf9468f78c..518b1d9654 100644 --- a/R/tm_t_coxreg.R +++ b/R/tm_t_coxreg.R @@ -1062,13 +1062,13 @@ srv_t_coxreg <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Cox Regression Table") - card$append_text("Cox Regression Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Cox Regression Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_events.R b/R/tm_t_events.R index e89ace16a8..0eb62ab54e 100644 --- a/R/tm_t_events.R +++ b/R/tm_t_events.R @@ -228,26 +228,25 @@ template_events <- function(dataname, layout_list <- add_expr( layout_list, substitute( - expr = - rtables::split_rows_by( - hlt, - child_labels = "visible", - nested = FALSE, - indent_mod = -1L, - split_fun = split_fun, - label_pos = "topleft", - split_label = formatters::var_labels(dataname[hlt]) + expr = rtables::split_rows_by( + hlt, + child_labels = "visible", + nested = FALSE, + indent_mod = -1L, + split_fun = split_fun, + label_pos = "topleft", + split_label = formatters::var_labels(dataname[hlt]) + ) %>% + summarize_num_patients( + var = "USUBJID", + .stats = c("unique", "nonunique"), + .labels = c( + unique = unique_label, + nonunique = nonunique_label + ) ) %>% - summarize_num_patients( - var = "USUBJID", - .stats = c("unique", "nonunique"), - .labels = c( - unique = unique_label, - nonunique = nonunique_label - ) - ) %>% - count_occurrences(vars = llt, .indent_mods = c(count_fraction = 1L)) %>% - append_varlabels(dataname, llt, indent = 1L), + count_occurrences(vars = llt, .indent_mods = c(count_fraction = 1L)) %>% + append_varlabels(dataname, llt, indent = 1L), env = list( dataname = as.name(dataname), hlt = hlt, @@ -793,13 +792,13 @@ srv_t_events_byterm <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Events by Term Table") - card$append_text("Events by Term Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Events by Term Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R index 7bf74176fb..bf3e1a6c94 100644 --- a/R/tm_t_events_by_grade.R +++ b/R/tm_t_events_by_grade.R @@ -1193,13 +1193,13 @@ srv_t_events_by_grade <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Events by Grade Table") - card$append_text("Events by Grade Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Events by Grade Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_events_patyear.R b/R/tm_t_events_patyear.R index 1dfa6b9809..1c5c6661ac 100644 --- a/R/tm_t_events_patyear.R +++ b/R/tm_t_events_patyear.R @@ -555,13 +555,13 @@ srv_events_patyear <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Event Rates Adjusted For Patient-Years Table") - card$append_text("Event Rates Adjusted For Patient-Years Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Event Rates Adjusted For Patient-Years Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_events_summary.R b/R/tm_t_events_summary.R index 901652efc1..2a86d6c01a 100644 --- a/R/tm_t_events_summary.R +++ b/R/tm_t_events_summary.R @@ -965,13 +965,13 @@ srv_t_events_summary <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Adverse Events Summary Table") - card$append_text("Adverse Events Summary Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Adverse Events Summary Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_exposure.R b/R/tm_t_exposure.R index 60e118e255..ef2b2a3b98 100644 --- a/R/tm_t_exposure.R +++ b/R/tm_t_exposure.R @@ -645,13 +645,13 @@ srv_t_exposure <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Exposure for Risk Management Plan Table") - card$append_text("Exposure for Risk Management Plan Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Exposure for Risk Management Plan Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_logistic.R b/R/tm_t_logistic.R index 89cf28802a..8afbde897e 100644 --- a/R/tm_t_logistic.R +++ b/R/tm_t_logistic.R @@ -492,8 +492,10 @@ srv_t_logistic <- function(id, iv$add_validator(iv_arco) # Conditional validator for interaction values. iv_int <- shinyvalidate::InputValidator$new() - iv_int$condition(~ length(input$interaction_var) > 0L && - is.numeric(merged$anl_q()[["ANL"]][[input$interaction_var]])) + iv_int$condition( + ~ length(input$interaction_var) > 0L && + is.numeric(merged$anl_q()[["ANL"]][[input$interaction_var]]) + ) iv_int$add_rule("interaction_values", shinyvalidate::sv_required( "If interaction is specified the level should be entered." )) @@ -713,13 +715,13 @@ srv_t_logistic <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Logistic Regression Table") - card$append_text("Logistic Regression Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Logistic Regression Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_mult_events.R b/R/tm_t_mult_events.R index 24adfd1869..809a0b7d50 100644 --- a/R/tm_t_mult_events.R +++ b/R/tm_t_mult_events.R @@ -148,9 +148,8 @@ template_mult_events <- function(dataname, layout_list <- add_expr( layout_list, substitute( - expr = - count_occurrences(vars = llt, .indent_mods = -1L) %>% - append_varlabels(dataname, llt, indent = 0L), + expr = count_occurrences(vars = llt, .indent_mods = -1L) %>% + append_varlabels(dataname, llt, indent = 0L), env = list( dataname = as.name(dataname), llt = llt ) @@ -203,18 +202,17 @@ template_mult_events <- function(dataname, layout_list <- add_expr( layout_list, substitute( - expr = - summarize_num_patients( - var = "USUBJID", - count_by = seq_var, - .stats = c("unique", "nonunique"), - .labels = c( - unique = unique_label, - nonunique = nonunique_label - ) - ) %>% - count_occurrences(vars = llt, .indent_mods = -1L) %>% - append_varlabels(dataname, llt, indent = indent_space), + expr = summarize_num_patients( + var = "USUBJID", + count_by = seq_var, + .stats = c("unique", "nonunique"), + .labels = c( + unique = unique_label, + nonunique = nonunique_label + ) + ) %>% + count_occurrences(vars = llt, .indent_mods = -1L) %>% + append_varlabels(dataname, llt, indent = indent_space), env = list( dataname = as.name(dataname), llt = llt, unique_label = unique_label, nonunique_label = nonunique_label, @@ -591,13 +589,13 @@ srv_t_mult_events_byterm <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Multiple Events by Term Table") - card$append_text("Multiple Events by Term Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Multiple Events by Term Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_pp_basic_info.R b/R/tm_t_pp_basic_info.R index d6a112f223..d9e45950cb 100644 --- a/R/tm_t_pp_basic_info.R +++ b/R/tm_t_pp_basic_info.R @@ -279,13 +279,13 @@ srv_t_basic_info <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Patient Profile Basic Info Table") - card$append_text("Patient Profile Basic Info Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Patient Profile Basic Info Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_pp_laboratory.R b/R/tm_t_pp_laboratory.R index 16f7f301d1..1773bd1d72 100644 --- a/R/tm_t_pp_laboratory.R +++ b/R/tm_t_pp_laboratory.R @@ -452,13 +452,13 @@ srv_g_laboratory <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Patient Profile Laboratory Table") - card$append_text("Patient Profile Laboratory Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Patient Profile Laboratory Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()$raw) if (!comment == "") { diff --git a/R/tm_t_pp_medical_history.R b/R/tm_t_pp_medical_history.R index 917ca2127c..2fa4ca639f 100644 --- a/R/tm_t_pp_medical_history.R +++ b/R/tm_t_pp_medical_history.R @@ -342,13 +342,13 @@ srv_t_medical_history <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Patient Medical History Table") - card$append_text("Patient Medical History Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Patient Medical History Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_pp_prior_medication.R b/R/tm_t_pp_prior_medication.R index 4d3c2ab862..8e009acbfc 100644 --- a/R/tm_t_pp_prior_medication.R +++ b/R/tm_t_pp_prior_medication.R @@ -344,13 +344,13 @@ srv_t_prior_medication <- function(id, ) if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Patient Prior Medication Table") - card$append_text("Patient Prior Medication Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Patient Prior Medication Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_shift_by_arm.R b/R/tm_t_shift_by_arm.R index 810fc93c5d..ab78b47ea2 100644 --- a/R/tm_t_shift_by_arm.R +++ b/R/tm_t_shift_by_arm.R @@ -528,13 +528,13 @@ srv_shift_by_arm <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Shift by Arm Table") - card$append_text("Shift by Arm Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Shift by Arm Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_shift_by_arm_by_worst.R b/R/tm_t_shift_by_arm_by_worst.R index de3ed6f797..403a13b22e 100644 --- a/R/tm_t_shift_by_arm_by_worst.R +++ b/R/tm_t_shift_by_arm_by_worst.R @@ -566,13 +566,13 @@ srv_shift_by_arm_by_worst <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Shift by Arm by Worst Table") - card$append_text("Shift by Arm by Worst Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Shift by Arm by Worst Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_shift_by_grade.R b/R/tm_t_shift_by_grade.R index d5b2a0fab2..79bc855906 100644 --- a/R/tm_t_shift_by_grade.R +++ b/R/tm_t_shift_by_grade.R @@ -886,13 +886,13 @@ srv_t_shift_by_grade <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Grade Summary Table") - card$append_text("Grade Summary Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Grade Summary Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_smq.R b/R/tm_t_smq.R index c8c90533bc..6f787dc92f 100644 --- a/R/tm_t_smq.R +++ b/R/tm_t_smq.R @@ -658,13 +658,13 @@ srv_t_smq <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("SMQ Table") - card$append_text("Adverse Events Table by Standardized `MedDRA` Query (SMQ)", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Adverse Events Table by Standardized `MedDRA` Query (SMQ)", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_summary.R b/R/tm_t_summary.R index 191a9a57aa..37a9fabc45 100644 --- a/R/tm_t_summary.R +++ b/R/tm_t_summary.R @@ -576,13 +576,13 @@ srv_summary <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Summary Table") - card$append_text("Summary Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Summary Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_summary_by.R b/R/tm_t_summary_by.R index c4dbbeaba7..88c4a7ad96 100644 --- a/R/tm_t_summary_by.R +++ b/R/tm_t_summary_by.R @@ -733,13 +733,13 @@ srv_summary_by <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Summarize Variables by Row Groups Table") - card$append_text("Summarize Variables by Row Groups Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Summarize Variables by Row Groups Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/tm_t_tte.R b/R/tm_t_tte.R index be82cec62b..40d8bd0dc7 100644 --- a/R/tm_t_tte.R +++ b/R/tm_t_tte.R @@ -10,20 +10,21 @@ #' parameters for comparison, specified using [tern::control_surv_timepoint()]. #' @keywords internal #' -control_tte <- function(surv_time = list( - conf_level = 0.95, - conf_type = "plain", - quantiles = c(0.25, 0.75) - ), - coxph = list( - pval_method = "log-rank", - ties = "efron", - conf_level = 0.95 - ), - surv_timepoint = control_surv_timepoint( - conf_level = 0.95, - conf_type = c("plain", "none", "log", "log-log") - )) { +control_tte <- function( + surv_time = list( + conf_level = 0.95, + conf_type = "plain", + quantiles = c(0.25, 0.75) + ), + coxph = list( + pval_method = "log-rank", + ties = "efron", + conf_level = 0.95 + ), + surv_timepoint = control_surv_timepoint( + conf_level = 0.95, + conf_type = c("plain", "none", "log", "log-log") + )) { list( surv_time = do.call("control_surv_time", surv_time), coxph = do.call("control_coxph", coxph), @@ -926,13 +927,13 @@ srv_t_tte <- function(id, ### REPORTER if (with_reporter) { - card_fun <- function(comment) { - card <- teal::TealReportCard$new() - card$set_name("Time To Event Table") - card$append_text("Time To Event Table", "header2") - if (with_filter) { - card$append_fs(filter_panel_api$get_filter_state()) - } + card_fun <- function(comment, label) { + card <- teal::report_card_template( + title = "Time To Event Table", + label = label, + with_filter = with_filter, + filter_panel_api = filter_panel_api + ) card$append_text("Table", "header3") card$append_table(table_r()) if (!comment == "") { diff --git a/R/utils.R b/R/utils.R index 2b9cd61d0a..130b97c1c4 100644 --- a/R/utils.R +++ b/R/utils.R @@ -821,7 +821,6 @@ clean_description <- function(x) { x } - #' Utility function for extracting `paramcd` for forest plots #' #' Utility function for extracting `paramcd` for forest plots