diff --git a/R/asr_dataprep.R b/R/asr_dataprep.R index 25f26aa..b0bc864 100644 --- a/R/asr_dataprep.R +++ b/R/asr_dataprep.R @@ -183,6 +183,8 @@ asr_dataprep <- function(data names(data)[names(data) == var_trt] <- "trt" if(tx_var){ names(data)[names(data) == var_tx] <- "intervention" + }else{ + data <- data[,!names(data) %in% "intervention"] } ## relevant variables exist diff --git a/R/asr_safety_summary.R b/R/asr_safety_summary.R index d3de81a..64c8ee7 100644 --- a/R/asr_safety_summary.R +++ b/R/asr_safety_summary.R @@ -51,10 +51,15 @@ asr_safety_summary <- function(data, period_data, trial_type, n_pat_e, n_per_arm trial_type <- match.arg(trial_type, c("imp", "medical device", "other","trp")) - ## display unique values in the trt variable - check <- unique(data$trt) - if(!all(check %in% names(n_per_arm))) warning("The treatment groups are not present in the treatment variable in the data set.") + ## check whether the intervention variable has been defined + if("intervention" %in% names(data)){ + check <- unique(data$intervention) + ## Check whether the treatment are defined correctly in the trt variable + if(all(!is.na(n_per_arm))) + if(!all(check %in% names(n_per_arm))) stop("The treatment groups in the data do not match those in 'n_par_arm'. \n", + "Please define the names of the treatment groups in the 'var_tx' variable or set 'n_par_arm' to NA.") + } if(trial_type == "imp"){ # FOR IMP TRIALS @@ -85,8 +90,7 @@ asr_safety_summary <- function(data, period_data, trial_type, n_pat_e, n_per_arm 'Suspected Unexpected Serious Adverse Reactions, SUSARs (only for IMPs)'), stringsAsFactors = FALSE) - if(all(!is.na(n_per_arm))) - if(!all(check %in% names(n_per_arm))){ + if("intervention" %in% names(data)){ ### define the values for the two interventional groups grp <- names(n_per_arm) @@ -186,7 +190,7 @@ asr_safety_summary <- function(data, period_data, trial_type, n_pat_e, n_per_arm 'Safety and protective measures taken in Switzerland and abroad.'), stringsAsFactors = FALSE) - if(all(!is.na(n_per_arm))){ + if("intervention" %in% names(data)){ ### define the values for the two interventional groups grp <- names(n_per_arm) @@ -255,7 +259,7 @@ asr_safety_summary <- function(data, period_data, trial_type, n_pat_e, n_per_arm 'Other SAEs where a causality to the intervention cannot be excluded'), stringsAsFactors = FALSE) - if(all(!is.na(n_per_arm))){ + if("intervention" %in% names(data)){ ### define the values for the two interventional groups grp <- names(n_per_arm) @@ -328,7 +332,7 @@ asr_safety_summary <- function(data, period_data, trial_type, n_pat_e, n_per_arm 'Serious Adverse Drug Reactions, SADRs', 'Suspected Unexpected Serious Adverse Reactions, SUSARs'), stringsAsFactors = FALSE) - if(all(!is.na(n_per_arm))){ + if("intervention" %in% names(data)){ grp <- names(n_per_arm)