diff --git a/R/data_spec.R b/R/data_spec.R index 7860b08..dcca673 100644 --- a/R/data_spec.R +++ b/R/data_spec.R @@ -7,8 +7,8 @@ new_DataSpec <- function( pheno_fname, cohort, patient_id_col, - pfs_col, - progression_col, + time_to_event_col, + event_col, ipi_col, ipi_feat_cols, gene_id_col, @@ -22,8 +22,8 @@ new_DataSpec <- function( stopifnot(is.character(pheno_fname)) stopifnot(is.null(cohort) | is.character(cohort)) stopifnot(is.character(patient_id_col)) - stopifnot(is.character(pfs_col)) - stopifnot(is.character(progression_col)) + stopifnot(is.character(time_to_event_col)) + stopifnot(is.character(event_col)) stopifnot(is.character(ipi_col)) stopifnot(is.character(ipi_feat_cols) | is.null(ipi_feat_cols)) stopifnot(is.character(gene_id_col)) @@ -50,8 +50,8 @@ new_DataSpec <- function( "pheno_fname" = pheno_fname, "cohort" = cohort, "patient_id_col" = patient_id_col, - "pfs_col" = pfs_col, - "progression_col" = progression_col, + "time_to_event_col" = time_to_event_col, + "event_col" = event_col, "ipi_col" = ipi_col, "ipi_feat_cols" = ipi_feat_cols, "gene_id_col" = gene_id_col, @@ -93,10 +93,10 @@ ipi_feat_cols_default <- c( #' throw an error. #' @param patient_id_col string. The name of the column in the pheno data that holds #' the patient identifiers. Default is `"patient_id"`. -#' @param pfs_col string. The name of the column in the pheno data that holds the -#' progression-free survival (PFS) values. Default is `"pfs_years"`. -#' @param progression_col string. The name of the column in the pheno data that holds -#' the progression status encoded as 1 = progression, 0 = no progression. Default is +#' @param time_to_event_col string. The name of the column in the pheno data that holds the +#' time-to-event values. Default is `"pfs_years"`. +#' @param event_col string. The name of the column in the pheno data that holds +#' the event status encoded as 1 = occurrence, 0 = censoring. Default is #' `"progression"`. #' @param ipi_col string. The name of the column in the pheno data that holds the #' International Prognostic Index (IPI) values. Default is `"ipi"`. @@ -128,8 +128,8 @@ DataSpec <- function( pheno_fname = "pheno.csv", cohort = NULL, patient_id_col = "patient_id", - pfs_col = "pfs_years", - progression_col = "progression", + time_to_event_col = "pfs_years", + event_col = "progression", ipi_col = "ipi", ipi_feat_cols = c( "age" = "age", @@ -153,8 +153,8 @@ DataSpec <- function( pheno_fname = pheno_fname, cohort = cohort, patient_id_col = patient_id_col, - pfs_col = pfs_col, - progression_col = progression_col, + time_to_event_col = time_to_event_col, + event_col = event_col, ipi_col = ipi_col, ipi_feat_cols = ipi_feat_cols, gene_id_col = gene_id_col, diff --git a/man/DataSpec.Rd b/man/DataSpec.Rd index 256f5ce..7cb186e 100644 --- a/man/DataSpec.Rd +++ b/man/DataSpec.Rd @@ -13,8 +13,8 @@ DataSpec( pheno_fname = "pheno.csv", cohort = NULL, patient_id_col = "patient_id", - pfs_col = "pfs_years", - progression_col = "progression", + time_to_event_col = "pfs_years", + event_col = "progression", ipi_col = "ipi", ipi_feat_cols = c(age = "age", stage = "ann_arbor_stage", ldh_ratio = "ldh_ratio", performance_status = "ecog_performance_status", n_extranodal_sites = @@ -51,11 +51,11 @@ throw an error.} \item{patient_id_col}{string. The name of the column in the pheno data that holds the patient identifiers. Default is \code{"patient_id"}.} -\item{pfs_col}{string. The name of the column in the pheno data that holds the -progression-free survival (PFS) values. Default is \code{"pfs_years"}.} +\item{time_to_event_col}{string. The name of the column in the pheno data that holds the +time-to-event values. Default is \code{"pfs_years"}.} -\item{progression_col}{string. The name of the column in the pheno data that holds -the progression status encoded as 1 = progression, 0 = no progression. Default is +\item{event_col}{string. The name of the column in the pheno data that holds +the event status encoded as 1 = occurrence, 0 = censoring. Default is \code{"progression"}.} \item{ipi_col}{string. The name of the column in the pheno data that holds the