From 0d40e0acbcd3a63181d927df9e8f34f4a96d5166 Mon Sep 17 00:00:00 2001 From: Dr Nathan Green Date: Thu, 9 Nov 2023 08:11:37 +0000 Subject: [PATCH] replaced all subData. with survData. --- R/check_study_data.R | 18 +- R/data.R | 6 +- R/load_input_data.R | 8 +- R/make_report.R | 12 +- R/new_NMA.R | 20 +- R/new_NMA_dir.R | 24 +- R/plotNetwork.R | 4 +- R/plots_and_tables.R | 10 +- R/prep_codeData.R | 42 +- R/setupData.R | 130 ++--- R/write_data_to_file.R | 8 +- _pkgdown.yml | 8 +- docs/articles/dont-build/how-to-use-nma.html | 34 +- docs/articles/dont-build/reference_file.html | 4 +- .../articles/dont-build/run_multiple_nma.html | 10 +- .../how-to-use-nma-survival-test-data.html | 36 +- docs/articles/how-to-use-nma-test-data.html | 34 +- docs/articles/reference-file-test-data.html | 4 +- docs/reference/index.html | 523 +++++++++--------- docs/reference/make_report.html | 339 ++++++------ docs/reference/new_NMA.html | 311 +++++------ docs/reference/plotNetwork.html | 215 +++---- docs/reference/plots_and_tables.html | 271 ++++----- docs/reference/prep_codeData.html | 235 ++++---- docs/reference/setupData.html | 215 +++---- docs/reference/subDataBin.html | 213 +++---- docs/reference/subDataHR.html | 225 ++++---- docs/reference/subDataMed.html | 219 ++++---- docs/sitemap.xml | 6 +- man/make_report.Rd | 12 +- man/new_NMA.Rd | 12 +- man/plotNetwork.Rd | 2 +- man/plots_and_tables.Rd | 2 +- man/prep_codeData.Rd | 12 +- man/setupData.Rd | 6 +- man/subDataBin.Rd | 6 +- man/subDataHR.Rd | 6 +- man/subDataMed.Rd | 6 +- scripts/run_analysis.R | 12 +- scripts/run_analysis_S3.R | 8 +- tests/testthat/test-NMA_run.R | 12 +- .../how-to-use-nma-survival-test-data.Rmd | 22 +- vignettes/reference-file-test-data.Rmd | 4 +- 43 files changed, 1658 insertions(+), 1648 deletions(-) diff --git a/R/check_study_data.R b/R/check_study_data.R index 7dc2f13..9c1baab 100644 --- a/R/check_study_data.R +++ b/R/check_study_data.R @@ -1,31 +1,31 @@ # -check_study_data <- function(subDataHR = NA, - subDataMed = NA, - subDataBin = NA, +check_study_data <- function(survDataHR = NA, + survDataMed = NA, + survDataBin = NA, countData = NA, contsData = NA, binData = NA) { - if (any(!is.na(subDataHR))) { + if (any(!is.na(survDataHR))) { hr_col_names <- c("tx", "base", "study", "Lmean", "Lse", "multi_arm") - hr_missing_cols <- !all(hr_col_names %in% names(subDataHR)) + hr_missing_cols <- !all(hr_col_names %in% names(survDataHR)) if (hr_missing_cols) stop("HR data set is missing columns", call. = FALSE) } - if (any(!is.na(subDataBin))) { + if (any(!is.na(survDataBin))) { bin_col_names <- c("tx", "base", "study", "BinN", "BinR") - bin_missing_cols <- !all(bin_col_names %in% names(subDataBin)) + bin_missing_cols <- !all(bin_col_names %in% names(survDataBin)) if (bin_missing_cols) stop("Binary data set is missing columns", call. = FALSE) } - if (any(!is.na(subDataMed))) { + if (any(!is.na(survDataMed))) { med_col_names <- c("tx", "base", "study", "medN", "medR", "median") - med_missing_cols <- !all(med_col_names %in% names(subDataMed)) + med_missing_cols <- !all(med_col_names %in% names(survDataMed)) if (med_missing_cols) stop("Median data set is missing columns", call. = FALSE) diff --git a/R/data.R b/R/data.R index 7526794..eaeb29b 100644 --- a/R/data.R +++ b/R/data.R @@ -13,7 +13,7 @@ #' \item{Lse}{Standard error of log hazard ratio} #' \item{multi_arm}{Multi-arm trial indicator: 0/1} #' } -"subDataHR" +"survDataHR" #' Study survival binary outcome data @@ -28,7 +28,7 @@ #' \item{BinR}{Count of number of events} #' \item{BinN}{Total sample size} #' } -"subDataBin" +"survDataBin" #' Study median time to event @@ -44,7 +44,7 @@ #' \item{medN}{Sample size} #' \item{medR}{Sample size/2 as estimated number of events} #' } -"subDataMed" +"survDataMed" #' Binary data diff --git a/R/load_input_data.R b/R/load_input_data.R index 64b4c4a..a3cb1b3 100644 --- a/R/load_input_data.R +++ b/R/load_input_data.R @@ -22,14 +22,14 @@ load_input_data <- function(is_med, header = TRUE, as.is = TRUE) - subDataBin <- + survDataBin <- if (is_bin) { read.csv(paste0(file_name, "bin.csv"), header = TRUE, as.is = TRUE) } else {NA} - subDataMed <- + survDataMed <- if (is_med) { read.csv(paste0(file_name, "med.csv"), header = TRUE, @@ -38,7 +38,7 @@ load_input_data <- function(is_med, } else {NA} list(subData = subData, - subDataMed = subDataMed, - subDataBin = subDataBin) + survDataMed = survDataMed, + survDataBin = survDataBin) } diff --git a/R/make_report.R b/R/make_report.R index 3ac5192..f4f9f28 100644 --- a/R/make_report.R +++ b/R/make_report.R @@ -38,19 +38,19 @@ #' #' file_name <- here::here(file.path("inst", "extdata", "survdata_")) #' -#' subDataHR <- +#' survDataHR <- #' read.csv(paste0(file_name, "hr_test.csv"), #' header = TRUE, #' as.is = TRUE) #' -#' subDataBin <- +#' survDataBin <- #' tryCatch( #' read.csv(paste0(file_name, "bin_test.csv"), #' header = TRUE, #' as.is = TRUE), #' error = function(e) NA) #' -#' subDataMed <- +#' survDataMed <- #' tryCatch( #' read.csv(paste0(file_name, "med_test.csv"), #' header = TRUE, @@ -59,9 +59,9 @@ #' error = function(e) NA) #' #' nma_model <- -#' new_NMA(subDataHR = subDataHR, -#' subDataMed = subDataMed, -#' subDataBin = subDataBin, +#' new_NMA(survDataHR = survDataHR, +#' survDataMed = survDataMed, +#' survDataBin = survDataBin, #' bugs_params = bugs_params, #' is_random = RANDOM, #' data_type = data_type, diff --git a/R/new_NMA.R b/R/new_NMA.R index 3109761..9c546a2 100644 --- a/R/new_NMA.R +++ b/R/new_NMA.R @@ -7,9 +7,9 @@ #' the passed data sets. If none given then all of the supplied #' data are assumed. #' -#' @param subDataHR Hazard ratio input data frame. Optional -#' @param subDataMed Median time input data frame. Optional -#' @param subDataBin Survival binary data input data frame. Optional +#' @param survDataHR Hazard ratio input data frame. Optional +#' @param survDataMed Median time input data frame. Optional +#' @param survDataBin Survival binary data input data frame. Optional #' @param binData Binary data input data frame. Optional #' @param countData Count data input data frame. Optional #' @param contsData Continuous data input data frame. Optional @@ -27,9 +27,9 @@ #' @return #' @export #' -new_NMA <- function(subDataHR = NA, - subDataMed = NA, - subDataBin = NA, +new_NMA <- function(survDataHR = NA, + survDataMed = NA, + survDataBin = NA, binData = NA, countData = NA, contsData = NA, @@ -43,9 +43,9 @@ new_NMA <- function(subDataHR = NA, endpoint) { data_lookup <- - c(subDataHR = "hr_data", - subDataMed = "med_data", - subDataBin = "surv_bin_data", + c(survDataHR = "hr_data", + survDataMed = "med_data", + survDataBin = "surv_bin_data", binData = "bin_data", countData = "count_data", contsData = "conts_data") @@ -55,7 +55,7 @@ new_NMA <- function(subDataHR = NA, several.ok = TRUE) nma_datasets <- - tibble::lst(subDataHR, subDataMed, subDataBin, + tibble::lst(survDataHR, survDataMed, survDataBin, binData, countData, contsData) # use all provided data diff --git a/R/new_NMA_dir.R b/R/new_NMA_dir.R index a5d4e70..a4c2996 100644 --- a/R/new_NMA_dir.R +++ b/R/new_NMA_dir.R @@ -13,12 +13,12 @@ new_NMA_dir <- function(data_dir = ".") { analysis_filename <- reference$file[reference$type == "analysis"] bugs_filename <- reference$file[reference$type == "bugs"] - subDataHR_filename <- reference$file[reference$type == "subData"] - subDataBin_filename <- reference$file[reference$type == "subDataBin"] - subDataMed_filename <- reference$file[reference$type == "subDataMed"] + survDataHR_filename <- reference$file[reference$type == "subData"] + survDataBin_filename <- reference$file[reference$type == "survDataBin"] + survDataMed_filename <- reference$file[reference$type == "survDataMed"] subData <- - read.csv(fs::path(data_dir, subDataHR_filename), + read.csv(fs::path(data_dir, survDataHR_filename), stringsAsFactors = FALSE, header = TRUE, as.is = TRUE) @@ -37,17 +37,17 @@ new_NMA_dir <- function(data_dir = ".") { keyval_as_list %>% validate_analysis_param - subDataBin <- - if (length(subDataBin_filename) != 0) { - read.csv(fs::path(data_dir, subDataBin_filename), + survDataBin <- + if (length(survDataBin_filename) != 0) { + read.csv(fs::path(data_dir, survDataBin_filename), stringsAsFactors = FALSE, header = TRUE, as.is = TRUE) } else {NA} - subDataMed <- - if (length(subDataMed_filename) != 0) { - read.csv(fs::path(data_dir, subDataMed_filename), + survDataMed <- + if (length(survDataMed_filename) != 0) { + read.csv(fs::path(data_dir, survDataMed_filename), stringsAsFactors = FALSE, header = TRUE, as.is = TRUE) %>% @@ -57,8 +57,8 @@ new_NMA_dir <- function(data_dir = ".") { NMA_params <- c(analysis_params, list(subData = subData, - subDataBin = subDataBin, - subDataMed = subDataMed, + survDataBin = survDataBin, + survDataMed = survDataMed, bugs_params = bugs_params)) do.call(new_NMA, NMA_params) diff --git a/R/plotNetwork.R b/R/plotNetwork.R index c31428f..b082c1d 100644 --- a/R/plotNetwork.R +++ b/R/plotNetwork.R @@ -2,7 +2,7 @@ #' Plot network diagram #' #' @param dat List of study data, including subData -#' and possibly subDataBin and subDataMed +#' and possibly survDataBin and survDataMed #' @param usecurve Which line to use? Logical #' @param ... Additional arguments #' @export @@ -23,7 +23,7 @@ plotNetwork <- function(dat, plotNetwork.default <- function(dat, usecurve = FALSE, ...) { - keep_dat <- names(dat) %in% c("subDataBin", "subDataMed", "binData") #, "subDataHR" + keep_dat <- names(dat) %in% c("survDataBin", "survDataMed", "binData") #, "survDataHR" study_data <- dat[keep_dat] for (i in seq_along(study_data)) { diff --git a/R/plots_and_tables.R b/R/plots_and_tables.R index eee7a8b..b6c050d 100644 --- a/R/plots_and_tables.R +++ b/R/plots_and_tables.R @@ -2,7 +2,7 @@ #' Write to file multiple NMA plots and tables #' #' @param dat ist of study data, including subData -#' and possibly subDataBin and subDataMed +#' and possibly survDataBin and survDataMed #' @param res_bugs BUGS output #' @param effectParam Effect parameter names; string #' @param labels Labels @@ -110,7 +110,7 @@ plots_and_tables <- function(dat, append = TRUE, col.names = NA) - if (all(!is.na(dat$subDataBin))) { + if (all(!is.na(dat$survDataBin))) { file_name <- paste0("data_", label, "_bin.csv") dataFileLocBin <- file.path(folder, "data", file_name) @@ -129,14 +129,14 @@ plots_and_tables <- function(dat, col.names = NA) write.table( - dat$subDataBin, + dat$survDataBin, file = dataFileLocBin, sep = ",", append = TRUE, col.names = NA) } - if (all(!is.na(dat$subDataMed))) { + if (all(!is.na(dat$survDataMed))) { file_name <- paste0("data_", label, "_med.csv") dataFileLocMed <- file.path(folder, "data", file_name) @@ -154,7 +154,7 @@ plots_and_tables <- function(dat, col.names = NA) write.table( - dat$subDataMed, + dat$survDataMed, file = dataFileLocMed, sep = ",", append = TRUE, diff --git a/R/prep_codeData.R b/R/prep_codeData.R index 10a3fd6..b98e38e 100644 --- a/R/prep_codeData.R +++ b/R/prep_codeData.R @@ -5,9 +5,9 @@ #' Renames the study, base and other fields with appended letter #' depending on type of data. #' -#' @param subDataHR Hazard ratio data frame -#' @param subDataBin Optional data frame. Survival binary data -#' @param subDataMed Optional data frame. Median times +#' @param survDataHR Hazard ratio data frame +#' @param survDataBin Optional data frame. Survival binary data +#' @param survDataMed Optional data frame. Median times #' @param refTx Reference treatment name; string #' @importFrom purrr map map_if #' @import dplyr @@ -16,26 +16,26 @@ #' If no binary of median data empty sub-lists. #' @export #' -prep_codeData <- function(subDataHR = NA, - subDataBin = NA, - subDataMed = NA, +prep_codeData <- function(survDataHR = NA, + survDataBin = NA, + survDataMed = NA, binData = NA, countData = NA, contsData = NA, refTx = NA) { - if (all(is.na(subDataHR))) return() + if (all(is.na(survDataHR))) return() - is_med <- all(!is.na(subDataMed)) - is_bin <- all(!is.na(subDataBin)) + is_med <- all(!is.na(survDataMed)) + is_bin <- all(!is.na(survDataBin)) dat_list <- list() bin_list <- list() med_list <- list() - dat <- list(subDataHR, - subDataMed, - subDataBin) + dat <- list(survDataHR, + survDataMed, + survDataBin) # all treatments in data sets tx_names <- @@ -55,49 +55,49 @@ prep_codeData <- function(subDataHR = NA, study_names <- unique(unlist(map(dat, "study"))) dat_list$dat <- - subDataHR %>% + survDataHR %>% mutate(Ltx = match(tx, tx_names), Lbase = match(base, tx_names), Lstudy = match(study, study_names)) %>% arrange(study, tx) %>% as.data.frame() - dat_list$LnObs <- nrow(subDataHR) + dat_list$LnObs <- nrow(survDataHR) nStudies <- max(dat_list$dat$Lstudy, 2) if (is_bin) { bin_list$dat <- - subDataBin %>% + survDataBin %>% mutate(Btx = match(tx, tx_names), Bbase = match(base, tx_names), Bstudy = match(study, study_names)) %>% arrange(study, tx) %>% as.data.frame() - bin_list$BnObs <- nrow(subDataBin) + bin_list$BnObs <- nrow(survDataBin) nStudies <- max(c(nStudies, bin_list$dat$Bstudy)) } if (is_med) { med_list$dat <- - subDataMed %>% + survDataMed %>% mutate(mediantx = match(tx, tx_names), medianbase = match(base, tx_names), medianstudy = match(study, study_names)) %>% arrange(study, tx) %>% as.data.frame() - med_list$medianNObs <- nrow(subDataMed) + med_list$medianNObs <- nrow(survDataMed) nStudies <- max(c(nStudies, med_list$dat$medianstudy)) } return(list( - subDataHR = dat_list, - subDataMed = med_list, - subDataBin = bin_list, + survDataHR = dat_list, + survDataMed = med_list, + survDataBin = bin_list, nStudies = nStudies, nTx = nTx, refTx = refTx, diff --git a/R/setupData.R b/R/setupData.R index 5079ee0..4dfd72e 100644 --- a/R/setupData.R +++ b/R/setupData.R @@ -28,9 +28,9 @@ rinits <- function(nTx, nStudies, param_names) { #' #' Arrange input data for NMA. #' -#' @param nma_datasets subDataHR: Hazard ratio data. Optional; -#' subDataBin: Survival binary data. Optional; -#' subDataMed: Median time data. Optional; +#' @param nma_datasets survDataHR: Hazard ratio data. Optional; +#' survDataBin: Survival binary data. Optional; +#' survDataMed: Median time data. Optional; #' binData: Binary data. Optional; #' countData: Count data. Optional; #' contsData: Continuous data. Optional @@ -127,19 +127,19 @@ setupData <- function(nma_datasets, bugsData <- list( - Lstudy = input$subDataHR$dat$Lstudy, - Ltx = input$subDataHR$dat$Ltx, - Lbase = input$subDataHR$dat$Lbase, - Lmean = input$subDataHR$dat$Lmean, - Lse = input$subDataHR$dat$Lse, - multi = input$subDataHR$dat$multi_arm, - LnObs = input$subDataHR$LnObs, + Lstudy = input$survDataHR$dat$Lstudy, + Ltx = input$survDataHR$dat$Ltx, + Lbase = input$survDataHR$dat$Lbase, + Lmean = input$survDataHR$dat$Lmean, + Lse = input$survDataHR$dat$Lse, + multi = input$survDataHR$dat$multi_arm, + LnObs = input$survDataHR$LnObs, nTx = input$nTx, nStudies = input$nStudies) return(list( inits = rinits(input$nTx, input$nStudies, param_names), - subDataHR = input$subDataHR$dat, + survDataHR = input$survDataHR$dat, bugsData = bugsData, txList = input$txList)) } @@ -148,26 +148,26 @@ setupData <- function(nma_datasets, bugsData <- list( - Lstudy = input$subDataHR$dat$Lstudy, - Ltx = input$subDataHR$dat$Ltx, - Lbase = input$subDataHR$dat$Lbase, - Lmean = input$subDataHR$dat$Lmean, - Lse = input$subDataHR$dat$Lse, - multi = input$subDataHR$dat$multi, - LnObs = input$subDataHR$LnObs, + Lstudy = input$survDataHR$dat$Lstudy, + Ltx = input$survDataHR$dat$Ltx, + Lbase = input$survDataHR$dat$Lbase, + Lmean = input$survDataHR$dat$Lmean, + Lse = input$survDataHR$dat$Lse, + multi = input$survDataHR$dat$multi, + LnObs = input$survDataHR$LnObs, nTx = input$nTx, nStudies = input$nStudies, - Bstudy = input$subDataBin$dat$Bstudy, - Btx = input$subDataBin$dat$Btx, - Bbase = input$subDataBin$dat$Bbase, - Bn = input$subDataBin$dat$BinN, - Br = input$subDataBin$dat$BinR, - BnObs = input$subDataBin$BnObs) + Bstudy = input$survDataBin$dat$Bstudy, + Btx = input$survDataBin$dat$Btx, + Bbase = input$survDataBin$dat$Bbase, + Bn = input$survDataBin$dat$BinN, + Br = input$survDataBin$dat$BinR, + BnObs = input$survDataBin$BnObs) return(list( inits = rinits(input$nTx, input$nStudies, param_names), - subDataHR = input$subDataHR$dat, - subDataBin = input$subDataBin$dat, + survDataHR = input$survDataHR$dat, + survDataBin = input$survDataBin$dat, bugsData = bugsData, txList = input$txList)) } @@ -176,27 +176,27 @@ setupData <- function(nma_datasets, bugsData <- list( - Lstudy = input$subDataHR$dat$Lstudy, - Ltx = input$subDataHR$dat$Ltx, - Lbase = input$subDataHR$dat$Lbase, - Lmean = input$subDataHR$dat$Lmean, - Lse = input$subDataHR$dat$Lse, - multi = input$subDataHR$dat$multi_arm, - LnObs = input$subDataHR$LnObs, + Lstudy = input$survDataHR$dat$Lstudy, + Ltx = input$survDataHR$dat$Ltx, + Lbase = input$survDataHR$dat$Lbase, + Lmean = input$survDataHR$dat$Lmean, + Lse = input$survDataHR$dat$Lse, + multi = input$survDataHR$dat$multi_arm, + LnObs = input$survDataHR$LnObs, nTx = input$nTx, nStudies = input$nStudies, - medianStudy = input$subDataMed$dat$medianstudy, - medianTx = input$subDataMed$dat$mediantx , - medianBase = input$subDataMed$dat$medianbase, - medianN = input$subDataMed$dat$medN, - medianR = input$subDataMed$dat$medR, - median = input$subDataMed$dat$median, - medianNObs = input$subDataMed$medianNObs) + medianStudy = input$survDataMed$dat$medianstudy, + medianTx = input$survDataMed$dat$mediantx , + medianBase = input$survDataMed$dat$medianbase, + medianN = input$survDataMed$dat$medN, + medianR = input$survDataMed$dat$medR, + median = input$survDataMed$dat$median, + medianNObs = input$survDataMed$medianNObs) return(list( inits = rinits(input$nTx, input$nStudies, param_names), - subDataHR = input$subDataHR$dat, - subDataMed = input$subDataMed$dat, + survDataHR = input$survDataHR$dat, + survDataMed = input$survDataMed$dat, bugsData = bugsData, txList = input$txList)) } @@ -205,34 +205,34 @@ setupData <- function(nma_datasets, bugsData <- list( - Lstudy = input$subDataHR$dat$Lstudy, - Ltx = input$subDataHR$dat$Ltx, - Lbase = input$subDataHR$dat$Lbase, - Lmean = input$subDataHR$dat$Lmean, - Lse = input$subDataHR$dat$Lse, - multi = input$subDataHR$dat$multi_arm, - LnObs = input$subDataHR$LnObs, + Lstudy = input$survDataHR$dat$Lstudy, + Ltx = input$survDataHR$dat$Ltx, + Lbase = input$survDataHR$dat$Lbase, + Lmean = input$survDataHR$dat$Lmean, + Lse = input$survDataHR$dat$Lse, + multi = input$survDataHR$dat$multi_arm, + LnObs = input$survDataHR$LnObs, nTx = input$nTx, nStudies = input$nStudies, - medianStudy = input$subDataMed$dat$medianstudy, - medianTx = input$subDataMed$dat$mediantx , - medianBase = input$subDataMed$dat$medianbase, - Bstudy = input$subDataBin$dat$Bstudy, - Btx = input$subDataBin$dat$Btx, - Bbase = input$subDataBin$dat$Bbase, - medianN = input$subDataMed$dat$medN, - medianR = input$subDataMed$dat$medR, - median = input$subDataMed$dat$median, - medianNObs = input$subDataMed$medianNObs, - Bn = input$subDataBin$dat$BinN, - Br = input$subDataBin$dat$BinR, - BnObs = input$subDataBin$BnObs) + medianStudy = input$survDataMed$dat$medianstudy, + medianTx = input$survDataMed$dat$mediantx , + medianBase = input$survDataMed$dat$medianbase, + Bstudy = input$survDataBin$dat$Bstudy, + Btx = input$survDataBin$dat$Btx, + Bbase = input$survDataBin$dat$Bbase, + medianN = input$survDataMed$dat$medN, + medianR = input$survDataMed$dat$medR, + median = input$survDataMed$dat$median, + medianNObs = input$survDataMed$medianNObs, + Bn = input$survDataBin$dat$BinN, + Br = input$survDataBin$dat$BinR, + BnObs = input$survDataBin$BnObs) return(list( inits = rinits(input$nTx, input$nStudies, param_names), - subDataHR = input$subDataHR$dat, - subDataBin = input$subDataBin$dat, - subDataMed = input$subDataMed$dat, + survDataHR = input$survDataHR$dat, + survDataBin = input$survDataBin$dat, + survDataMed = input$survDataMed$dat, bugsData = bugsData, txList = input$txList)) } diff --git a/R/write_data_to_file.R b/R/write_data_to_file.R index fc52143..ab6c954 100644 --- a/R/write_data_to_file.R +++ b/R/write_data_to_file.R @@ -42,7 +42,7 @@ write_data_to_file.nma <- function(nma, append = TRUE, col.names = NA)) - if (all(!is.na(dat$subDataBin))) { + if (all(!is.na(dat$survDataBin))) { file_name <- paste0("data_", label, "_bin.csv") dir_nameBin <- file.path(folder, "data", file_name) @@ -56,14 +56,14 @@ write_data_to_file.nma <- function(nma, suppressWarnings( write.table( - dat$subDataBin, + dat$survDataBin, file = dir_nameBin, sep = ",", append = TRUE, col.names = NA)) } - if (all(!is.na(dat$subDataMed))) { + if (all(!is.na(dat$survDataMed))) { file_name <- paste0("data_", label, "_med.csv") dir_nameMed <- file.path(folder, "data", file_name) @@ -75,7 +75,7 @@ write_data_to_file.nma <- function(nma, suppressWarnings( write.table( - dat$subDataMed, + dat$survDataMed, file = dir_nameMed, sep = ",", append = TRUE, diff --git a/_pkgdown.yml b/_pkgdown.yml index edf67b1..94c301c 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -41,9 +41,9 @@ reference: - validate_nma - title: Data contents: - - subDataHR - - subDataBin - - subDataMed + - survDataHR + - survDataBin + - survDataMed - binData - countData - contsData @@ -62,4 +62,4 @@ navbar: - text: Using count data href: articles/binary-data.html - \ No newline at end of file + diff --git a/docs/articles/dont-build/how-to-use-nma.html b/docs/articles/dont-build/how-to-use-nma.html index 96243dd..b11d6e4 100644 --- a/docs/articles/dont-build/how-to-use-nma.html +++ b/docs/articles/dont-build/how-to-use-nma.html @@ -124,13 +124,13 @@

Read in datasets

The trials data consist of up to 3 separate data frames. A main table, subData, and optional tables for median event time -and binary data, subDataMed and subDataBin +and binary data, survDataMed and survDataBin respectively. Lets read in the each data set separately. In another article we will show how to do this in one function call by including a Reference file in the data folder which contains the meta data of how to read in the study data. If there is no binary or median data used in the -NMA then the variables subDataBin and -subDataMed are assigned NA.

+NMA then the variables survDataBin and +survDataMed are assigned NA.

 file_name <- paste0(here::here("inst", "extdata"), "/survdata_", endpoint, "_")
 
@@ -139,14 +139,14 @@ 
Read in datasets= TRUE,
            as.is = TRUE)
 
-subDataBin <-
+survDataBin <-
   if (is_bin) {
     read.csv(paste0(file_name, "bin.csv"),
              header = TRUE,
              as.is = TRUE)
   } else {NA}
 
-subDataMed <-
+survDataMed <-
   if (is_med) {
     read.csv(paste0(file_name, "med.csv"),
              header = TRUE,
@@ -164,8 +164,8 @@ 
Build model
 nma_model <-
   new_NMA(subData = subData,
-          subDataMed = subDataMed,
-          subDataBin = subDataBin,
+          survDataMed = survDataMed,
+          survDataBin = survDataBin,
           bugs_params = bugs_params,
           is_random = RANDOM,
           refTx = REFTX ,
@@ -173,9 +173,9 @@ 
Build model= "totresdev",
           label = label_name,
           endpoint = endpoint)
-#> Warning in if (!is.na(subDataBin)) {: the condition has length > 1 and only the
+#> Warning in if (!is.na(survDataBin)) {: the condition has length > 1 and only the
 #> first element will be used
-#> Warning in if (!is.na(subDataMed)) {: the condition has length > 1 and only the
+#> Warning in if (!is.na(survDataMed)) {: the condition has length > 1 and only the
 #> first element will be used
 
 nma_model
@@ -251,12 +251,12 @@ 
Build model#> 27  0.15700375 0.1967513         0   3     2     12
 #> 28 -0.51082562 0.3536465         0   1    18     21
 #> 
-#> $dat$subDataBin
+#> $dat$survDataBin
 #>                     study    base      tx BinR BinN Btx Bbase Bstudy
 #> 1 NCT01039948 (Mok, 2016) ERL/GEF ERL/GEF   34   38   1     1     33
 #> 2 NCT01039948 (Mok, 2016) ERL/GEF GEF+FIC   27   33  14     1     33
 #> 
-#> $dat$subDataMed
+#> $dat$survDataMed
 #>                                     study          base            tx median
 #> 1                                 An 2016       ERL/GEF       ERL/GEF   14.0
 #> 2                                 An 2016       ERL/GEF       GEF+PEM   18.0
@@ -444,11 +444,11 @@ 
Build model#> attr(,"CALL")$subData
 #> subData
 #> 
-#> attr(,"CALL")$subDataMed
-#> subDataMed
+#> attr(,"CALL")$survDataMed
+#> survDataMed
 #> 
-#> attr(,"CALL")$subDataBin
-#> subDataBin
+#> attr(,"CALL")$survDataBin
+#> survDataBin
 #> 
 #> attr(,"CALL")$bugs_params
 #> bugs_params
@@ -532,9 +532,9 @@ 
Reconfigure modelnma_model2 <-
   NMA_update(nma_model,
              is_random = TRUE)
-#> Warning in if (!is.na(subDataBin)) {: the condition has length > 1 and only the
+#> Warning in if (!is.na(survDataBin)) {: the condition has length > 1 and only the
 #> first element will be used
-#> Warning in if (!is.na(subDataMed)) {: the condition has length > 1 and only the
+#> Warning in if (!is.na(survDataMed)) {: the condition has length > 1 and only the
 #> first element will be used
 
 nma_res2 <- NMA_run(nma_model2, save = FALSE)
diff --git a/docs/articles/dont-build/reference_file.html b/docs/articles/dont-build/reference_file.html
index 76d567d..4246da5 100644
--- a/docs/articles/dont-build/reference_file.html
+++ b/docs/articles/dont-build/reference_file.html
@@ -111,12 +111,12 @@ 
Reference fileLmean, Lse, multi_arm
 
 
  • 
-subDataBin: Optional binary data. Required column
+survDataBin: Optional binary data. Required column
 headings of tx, base, study,
 BinN, BinR
 
    • 
 
  • 
-subDataMed: Optional median time data. Required column
+survDataMed: Optional median time data. Required column
 headings of tx, base, study,
 medN, medR, median
 
    • 
diff --git a/docs/articles/dont-build/run_multiple_nma.html b/docs/articles/dont-build/run_multiple_nma.html
index 801071e..23ebc94 100644
--- a/docs/articles/dont-build/run_multiple_nma.html
+++ b/docs/articles/dont-build/run_multiple_nma.html
@@ -121,20 +121,20 @@ 
    Settings
 
 
-
+
 
 
 
 
 
 
-
+
 
 
 
 
 
-
+
 
 
 
@@ -147,8 +147,8 @@ 
    Settings
 
 
-
-
+
+
 
 
 
diff --git a/docs/articles/how-to-use-nma-survival-test-data.html b/docs/articles/how-to-use-nma-survival-test-data.html
index 97b008e..45c605a 100644
--- a/docs/articles/how-to-use-nma-survival-test-data.html
+++ b/docs/articles/how-to-use-nma-survival-test-data.html
@@ -124,29 +124,29 @@ 
    Read in datasets
 
    The trials data consist of up to 3 separate data frames. A main
 table, subData, and optional tables for median event time
-and binary data, subDataMed and subDataBin
+and binary data, survDataMed and survDataBin
 respectively. Lets read in the each data set separately. In another
 article we will show how to do this in one function call by including a
 Reference file in the data folder which contains the meta data
 of how to read in the study data. If there is no binary or median data
-used in the NMA then the variables subDataBin and
-subDataMed are assigned NA.
    
+used in the NMA then the variables survDataBin and
+survDataMed are assigned NA.
    
 
     file_name <- here::here(file.path("inst", "extdata", "survdata_"))
 
-subDataHR <-
+survDataHR <-
   read.csv(paste0(file_name, "hr_test.csv"),
            header = TRUE,
            as.is = TRUE)
 
-subDataBin <-
+survDataBin <-
   tryCatch(
     read.csv(paste0(file_name, "bin_test.csv"),
              header = TRUE,
              as.is = TRUE),
     error = function(e) NA)
 
-subDataMed <-
+survDataMed <-
   tryCatch(
     read.csv(paste0(file_name, "med_test.csv"),
              header = TRUE,
@@ -290,9 +290,9 @@ 
    Build model
     nma_model <-
-  new_NMA(subDataHR = subDataHR,
-          subDataMed = subDataMed,
-          subDataBin = subDataBin,
+  new_NMA(survDataHR = survDataHR,
+          survDataMed = survDataMed,
+          survDataBin = survDataBin,
           bugs_params = bugs_params,
           is_random = RANDOM,
           data_type = data_type,
@@ -317,18 +317,18 @@ 
    Build model#> <bytecode: 0x0000000016dbfe30>
 #> <environment: 0x0000000016db6850>
 #> 
-#> $dat$subDataHR
+#> $dat$survDataHR
 #>   study base tx      Lmean       Lse multi_arm Ltx Lbase Lstudy
 #> 1     A    X  Y -0.5259393 0.1275307         0   2     1      1
 #> 2     B    Y  Z -0.7133499 0.1437422         0   3     2      2
 #> 3     C    Z  X -0.3011051 0.1758496         0   1     3      3
 #> 
-#> $dat$subDataBin
+#> $dat$survDataBin
 #>   study base tx BinR BinN Btx Bbase Bstudy
 #> 1     A    X  X   34   38   1     1      1
 #> 2     B    X  Y   27   33   2     1      2
 #> 
-#> $dat$subDataMed
+#> $dat$survDataMed
 #>   study base tx median medN medR mediantx medianbase medianstudy
 #> 1     A    X  Y   14.0   45   22        2          1           1
 #> 2     B    Y  Z   18.0   45   22        3          2           2
@@ -472,14 +472,14 @@ 
    Build model#> attr(,"class")
 #> [1] "nma"
 #> attr(,"CALL")
-#> attr(,"CALL")$subDataHR
-#> subDataHR
+#> attr(,"CALL")$survDataHR
+#> survDataHR
 #> 
-#> attr(,"CALL")$subDataMed
-#> subDataMed
+#> attr(,"CALL")$survDataMed
+#> survDataMed
 #> 
-#> attr(,"CALL")$subDataBin
-#> subDataBin
+#> attr(,"CALL")$survDataBin
+#> survDataBin
 #> 
 #> attr(,"CALL")$bugs_params
 #> bugs_params
diff --git a/docs/articles/how-to-use-nma-test-data.html b/docs/articles/how-to-use-nma-test-data.html
index 75e4444..9c6032f 100644
--- a/docs/articles/how-to-use-nma-test-data.html
+++ b/docs/articles/how-to-use-nma-test-data.html
@@ -121,29 +121,29 @@ 
    Read in datasets
 
    The trials data consist of up to 3 separate data frames. A main
 table, subData, and optional tables for median event time
-and binary data, subDataMed and subDataBin
+and binary data, survDataMed and survDataBin
 respectively. Lets read in the each data set separately. In another
 article we will show how to do this in one function call by including a
 Reference file in the data folder which contains the meta data
 of how to read in the study data. If there is no binary or median data
-used in the NMA then the variables subDataBin and
-subDataMed are assigned NA.
    
+used in the NMA then the variables survDataBin and
+survDataMed are assigned NA.
    
 
     file_name <- here::here(file.path("inst", "extdata", "survdata_"))
 
-subDataHR <-
+survDataHR <-
   read.csv(paste0(file_name, "hr_test.csv"),
            header = TRUE,
            as.is = TRUE)
 
-subDataBin <-
+survDataBin <-
   tryCatch(
     read.csv(paste0(file_name, "bin_test.csv"),
              header = TRUE,
              as.is = TRUE),
     error = function(e) NA)
 
-subDataMed <-
+survDataMed <-
   tryCatch(
     read.csv(paste0(file_name, "med_test.csv"),
              header = TRUE,
@@ -287,9 +287,9 @@ 
    Build model
     nma_model <-
-  new_NMA(subDataHR = subDataHR,
-          subDataMed = subDataMed,
-          subDataBin = subDataBin,
+  new_NMA(survDataHR = survDataHR,
+          survDataMed = survDataMed,
+          survDataBin = survDataBin,
           bugs_params = bugs_params,
           is_random = RANDOM,
           data_type = data_type,
@@ -317,12 +317,12 @@ 
    Build model#> 2     B    Y  Z -0.7133499 0.1437422         0   3     2      2
 #> 3     C    Z  X -0.3011051 0.1758496         0   1     3      3
 #> 
-#> $dat$subDataBin
+#> $dat$survDataBin
 #>   study base tx BinR BinN Btx Bbase Bstudy
 #> 1     A    X  X   34   38   1     1      1
 #> 2     B    X  Y   27   33   2     1      2
 #> 
-#> $dat$subDataMed
+#> $dat$survDataMed
 #>   study base tx median medN medR mediantx medianbase medianstudy
 #> 1     A    X  Y   14.0   45   22        2          1           1
 #> 2     B    Y  Z   18.0   45   22        3          2           2
@@ -466,14 +466,14 @@ 
    Build model#> attr(,"class")
 #> [1] "nma"
 #> attr(,"CALL")
-#> attr(,"CALL")$subDataHR
-#> subDataHR
+#> attr(,"CALL")$survDataHR
+#> survDataHR
 #> 
-#> attr(,"CALL")$subDataMed
-#> subDataMed
+#> attr(,"CALL")$survDataMed
+#> survDataMed
 #> 
-#> attr(,"CALL")$subDataBin
-#> subDataBin
+#> attr(,"CALL")$survDataBin
+#> survDataBin
 #> 
 #> attr(,"CALL")$bugs_params
 #> bugs_params
diff --git a/docs/articles/reference-file-test-data.html b/docs/articles/reference-file-test-data.html
index a71f44b..0fdf078 100644
--- a/docs/articles/reference-file-test-data.html
+++ b/docs/articles/reference-file-test-data.html
@@ -113,12 +113,12 @@ 
    Reference fileLmean, Lse, multi_arm
 
 
  • 
-subDataBin: Optional binary data. Required column
+survDataBin: Optional binary data. Required column
 headings of tx, base, study,
 BinN, BinR
 
    • 
 
  • 
-subDataMed: Optional median time data. Required column
+survDataMed: Optional median time data. Required column
 headings of tx, base, study,
 medN, medR, median
 
    • 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index a790bd4..c29fbd6 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,261 +1,262 @@
-
-Function reference • NMA
-        Skip to contents
-    
-
-    
    
-
    
-  
    
-      
    Function reference
    
-    
    
-
-    
    
-      
    NMA functions
    
-      
-      
-
-      
-    
    
-      
-      
-      
-
-      
    
-          
-          NMA_run() 
-        
    
-        
    Run network meta-analysis
    
-      
    
-          
-          NMA_update() 
-        
    
-        
    Update NMA
    
-      
    
-          
-          new_NMA() 
-        
    
-        
    NMA constructor
    
-      
    
-          
-          new_NMA_dir() 
-        
    
-        
    Load all input data from a folder
    
-      
    
-      
    BUGS functions
    
-      
-      
-
-      
-    
    
-      
-      
-      
-
-      
    
-          
-          bugs_stats() 
-        
    
-        
    BUGS statistics
    
-      
    
-          
-          make_bugs_filename() 
-        
    
-        
    Make BUGS model file name
    
-      
    
-          
-          my_bugs_summary() 
-        
    
-        
    BUGS summary
    
-      
    
-          
-          save_bugs_files() 
-        
    
-        
    Save BUGS files
    
-      
    
-      
    Plotting and tables
    
-      
-      
-
-      
-    
    
-      
-      
-      
-
-      
    
-          
-          diagnostic_plots() 
-        
    
-        
    WinBUGS diagnostic plots
    
-      
    
-          
-          pairwiseTable() 
-        
    
-        
    Pairwise table
    
-      
    
-          
-          plotNetwork() 
-        
    
-        
    Plot network diagram
    
-      
    
-          
-          plots_and_tables() plots_and_tables() 
-        
    
-        
    Write to file multiple NMA plots and tables
    
-      
    
-          
-          rankProbPlot() 
-        
    
-        
    Rank probability plot
    
-      
    
-          
-          txEffectPlot() 
-        
    
-        
    Treatment effect plot
    
-      
    
-          
-          varPlot() 
-        
    
-        
    Study network diagram
    
-      
    
-      
    Other functions
    
-      
-      
-
-      
-    
    
-      
-      
-      
-
-      
    
-          
-          load_input_data() 
-        
    
-        
    Load input data
    
-      
    
-          
-          nma_outputs() 
-        
    
-        
    All output functions
    
-      
    
-          
-          prep_codeData() 
-        
    
-        
    Prepare data used in computation
    
-      
    
-          
-          setupData() 
-        
    
-        
    Set-up study data
    
-      
    
-          
-          validate_nma() 
-        
    
-        
    nma validator
    
-      
    
-      
    Data
    
-      
-      
-
-      
-    
    
-      
-      
-      
-
-      
    
-          
-          subDataHR 
-        
    
-        
    Study log hazard ratios and standard errors
    
-      
    
-          
-          subDataBin 
-        
    
-        
    Study survival binary outcome data
    
-      
    
-          
-          subDataMed 
-        
    
-        
    Study median time to event
    
-      
    
-          
-          binData 
-        
    
-        
    Binary data
    
-      
    
-          
-          countData 
-        
    
-        
    Counts data
    
-      
    
-          
-          contsData 
-        
    
-        
    Continuous data
    
-      
    
-  
    
-
-
-    
    
-  
    Developed by Nathan Green.
    
-
    
-
-
    
-  
    Site built with pkgdown

-2.0.2.
    
-
    
-
-    
    
-
-  
-
-  
-
-  
-
+
+Function reference • NMA
+    Skip to contents
+    
+
+    
    
+
    
+  
    
+      
    Function reference
    
+    
    
+
+    
    
+      
    NMA functions
    
+      
+      
+
+      
+    
    
+      
+      
+      
+
+      
    
+          
+          NMA_run() 
+        
    
+        
    Run network meta-analysis
    
+      
    
+          
+          NMA_update() 
+        
    
+        
    Update NMA
    
+      
    
+          
+          new_NMA() 
+        
    
+        
    NMA constructor
    
+      
    
+          
+          new_NMA_dir() 
+        
    
+        
    Load all input data from a folder
    
+      
    
+      
    BUGS functions
    
+      
+      
+
+      
+    
    
+      
+      
+      
+
+      
    
+          
+          bugs_stats() 
+        
    
+        
    BUGS statistics
    
+      
    
+          
+          make_bugs_filename() 
+        
    
+        
    Make BUGS model file name
    
+      
    
+          
+          my_bugs_summary() 
+        
    
+        
    BUGS summary
    
+      
    
+          
+          save_bugs_files() 
+        
    
+        
    Save BUGS files
    
+      
    
+      
    Plotting and tables
    
+      
+      
+
+      
+    
    
+      
+      
+      
+
+      
    
+          
+          diagnostic_plots() 
+        
    
+        
    WinBUGS diagnostic plots
    
+      
    
+          
+          pairwiseTable() 
+        
    
+        
    Pairwise table
    
+      
    
+          
+          plotNetwork() 
+        
    
+        
    Plot network diagram
    
+      
    
+          
+          plots_and_tables() plots_and_tables() 
+        
    
+        
    Write to file multiple NMA plots and tables
    
+      
    
+          
+          rankProbPlot() 
+        
    
+        
    Rank probability plot
    
+      
    
+          
+          txEffectPlot() 
+        
    
+        
    Treatment effect plot
    
+      
    
+          
+          varPlot() 
+        
    
+        
    Study network diagram
    
+      
    
+      
    Other functions
    
+      
+      
+
+      
+    
    
+      
+      
+      
+
+      
    
+          
+          load_input_data() 
+        
    
+        
    Load input data
    
+      
    
+          
+          nma_outputs() 
+        
    
+        
    All output functions
    
+      
    
+          
+          prep_codeData() 
+        
    
+        
    Prepare data used in computation
    
+      
    
+          
+          setupData() 
+        
    
+        
    Set-up study data
    
+      
    
+          
+          validate_nma() 
+        
    
+        
    nma validator
    
+      
    
+      
    Data
    
+      
+      
+
+      
+    
    
+      
+      
+      
+
+      
    
+          
+          survDataHR 
+        
    
+        
    Study log hazard ratios and standard errors
    
+      
    
+          
+          survDataBin 
+        
    
+        
    Study survival binary outcome data
    
+      
    
+          
+          survDataMed 
+        
    
+        
    Study median time to event
    
+      
    
+          
+          binData 
+        
    
+        
    Binary data
    
+      
    
+          
+          countData 
+        
    
+        
    Counts data
    
+      
    
+          
+          contsData 
+        
    
+        
    Continuous data
    
+      
    
+  
    
+
+
+    
    
+  
    Developed by Nathan Green.
    
+
    
+
+
    
+  
    Site built with pkgdown
+
+2.0.2.
    
+
    
+
+    
    
+
+  
+
+  
+
+  
+
diff --git a/docs/reference/make_report.html b/docs/reference/make_report.html
index 694e5c2..8261012 100644
--- a/docs/reference/make_report.html
+++ b/docs/reference/make_report.html
@@ -1,169 +1,170 @@
-
-Make Report — make_report • NMA
-    Skip to contents
-    
-
-    
    
-
    
-  
    
-      
    Make Report
    
-      Source: R/make_report.R
-      
    make_report.Rd
    
-    
    
-
-    
    
-    
    Constructs the automated report from the output of the NMA.
    
-    
    
-
-    
    
-    
    Usage
    
-    
    make_report(nma_model, ext = "pdf", echo = FALSE, ...)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    ext
    
-
    A string of text to indicate the extension of the
-resulting output file. Possible options are "pdf", "docx".
-This requires the use of pandoc, knitr and rmarkdown.
    
-
    echo
    
-
    A string (default to FALSE) to instruct whether
-the report should also include the BCEA commands used to
-produce the analyses. If the optional argument echo is set
-to TRUE (default = FALSE), then the commands are also
-printed.
    
-
    ...
    
-
    Additional parameters.
    
-
    
-    
    
-    
    References
    
-    
-
-
-    
    
-
-    
    
-    
    Examples
    
-    
    
-if (FALSE) {
-bugs_params <-
-list(
-  PROG = "openBugs",  # which version of BUGS to use to run the MCMC
-  N.BURNIN = 10,#00,  # number of steps to throw away
-  N.SIMS = 150,#0,    # total number of simulations
-  N.CHAINS = 2,       # number of chains
-  N.THIN = 1,         # thinning rate
-  PAUSE = TRUE)
-
-RANDOM <- FALSE             # is this a random effects model?
-REFTX <- "X"                # reference treatment
-data_type <- c("hr_data", "surv_bin_data", "med_data") # which type of data to use
-label_name <- "label_name"
-
-file_name <- here::here(file.path("inst", "extdata", "survdata_"))
-
-subDataHR <-
-  read.csv(paste0(file_name, "hr_test.csv"),
-           header = TRUE,
-           as.is = TRUE)
-
-subDataBin <-
-  tryCatch(
-    read.csv(paste0(file_name, "bin_test.csv"),
-             header = TRUE,
-             as.is = TRUE),
-    error = function(e) NA)
-
-subDataMed <-
-  tryCatch(
-    read.csv(paste0(file_name, "med_test.csv"),
-             header = TRUE,
-             as.is = TRUE) %>% 
-      mutate(medR = floor(medR)),
-    error = function(e) NA)
-
-nma_model <-
-  new_NMA(subDataHR = subDataHR,
-          subDataMed = subDataMed,
-          subDataBin = subDataBin,
-          bugs_params = bugs_params,
-          is_random = RANDOM,
-          data_type = data_type,
-          refTx = REFTX ,
-          effectParam = "beta",
-          label = "",
-          endpoint = "")
-
-nma_model
-
-make_report(nma_model, ext = "docx")
-
-
-}
-
-
    
-    
    
-  
    
-
-
-    
    
-  
    Developed by Nathan Green.
    
-
    
-
-
    
-  
    Site built with pkgdown

-2.0.2.
    
-
    
-
-    
    
-
-  
-
-  
-
-  
-
+
+Make Report — make_report • NMA
+    Skip to contents
+    
+
+    
    
+
    
+  
    
+      
    Make Report
    
+      Source: R/make_report.R
+      
    make_report.Rd
    
+    
    
+
+    
    
+    
    Constructs the automated report from the output of the NMA.
    
+    
    
+
+    
    
+    
    Usage
    
+    
    make_report(nma_model, ext = "pdf", echo = FALSE, ...)
    
+    
    
+
+    
    
+    
    Arguments
    
+    
    ext
    
+
    A string of text to indicate the extension of the
+resulting output file. Possible options are "pdf", "docx".
+This requires the use of pandoc, knitr and rmarkdown.
    
+
    echo
    
+
    A string (default to FALSE) to instruct whether
+the report should also include the BCEA commands used to
+produce the analyses. If the optional argument echo is set
+to TRUE (default = FALSE), then the commands are also
+printed.
    
+
    ...
    
+
    Additional parameters.
    
+
    
+    
    
+    
    References
    
+    
+
+
+    
    
+
+    
    
+    
    Examples
    
+    
    
+if (FALSE) {
+bugs_params <-
+list(
+  PROG = "openBugs",  # which version of BUGS to use to run the MCMC
+  N.BURNIN = 10,#00,  # number of steps to throw away
+  N.SIMS = 150,#0,    # total number of simulations
+  N.CHAINS = 2,       # number of chains
+  N.THIN = 1,         # thinning rate
+  PAUSE = TRUE)
+
+RANDOM <- FALSE             # is this a random effects model?
+REFTX <- "X"                # reference treatment
+data_type <- c("hr_data", "surv_bin_data", "med_data") # which type of data to use
+label_name <- "label_name"
+
+file_name <- here::here(file.path("inst", "extdata", "survdata_"))
+
+survDataHR <-
+  read.csv(paste0(file_name, "hr_test.csv"),
+           header = TRUE,
+           as.is = TRUE)
+
+survDataBin <-
+  tryCatch(
+    read.csv(paste0(file_name, "bin_test.csv"),
+             header = TRUE,
+             as.is = TRUE),
+    error = function(e) NA)
+
+survDataMed <-
+  tryCatch(
+    read.csv(paste0(file_name, "med_test.csv"),
+             header = TRUE,
+             as.is = TRUE) %>% 
+      mutate(medR = floor(medR)),
+    error = function(e) NA)
+
+nma_model <-
+  new_NMA(survDataHR = survDataHR,
+          survDataMed = survDataMed,
+          survDataBin = survDataBin,
+          bugs_params = bugs_params,
+          is_random = RANDOM,
+          data_type = data_type,
+          refTx = REFTX ,
+          effectParam = "beta",
+          label = "",
+          endpoint = "")
+
+nma_model
+
+make_report(nma_model, ext = "docx")
+
+
+}
+
+
    
+    
    
+  
    
+
+
+    
    
+  
    Developed by Nathan Green.
    
+
    
+
+
    
+  
    Site built with pkgdown
+
+2.0.2.
    
+
    
+
+    
    
+
+  
+
+  
+
+  
+
diff --git a/docs/reference/new_NMA.html b/docs/reference/new_NMA.html
index 77c7ead..e2111f5 100644
--- a/docs/reference/new_NMA.html
+++ b/docs/reference/new_NMA.html
@@ -1,155 +1,156 @@
-
-NMA constructor — new_NMA • NMA
-    Skip to contents
-    
-
-    
    
-
    
-  
    
-      
    NMA constructor
    
-      Source: R/new_NMA.R
-      
    new_NMA.Rd
    
-    
    
-
-    
    
-    
    Create an nma class object to use in an analysis.
-All of the data types are optional but at least one needs to be
-passed to the function. The data_type must be a subset of
-the passed data sets. If none given then all of the supplied
-data are assumed.
    
-    
    
-
-    
    
-    
    Usage
    
-    
    new_NMA(
-  subDataHR = NA,
-  subDataMed = NA,
-  subDataBin = NA,
-  binData = NA,
-  countData = NA,
-  contsData = NA,
-  bugs_params = NA,
-  is_random = TRUE,
-  data_type = NA,
-  hyperparams = list(),
-  refTx = NA,
-  effectParam = NA,
-  label,
-  endpoint
-)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    subDataHR
    
-
    Hazard ratio input data frame. Optional
    
-
    subDataMed
    
-
    Median time input data frame. Optional
    
-
    subDataBin
    
-
    Survival binary data input data frame. Optional
    
-
    binData
    
-
    Binary data input data frame. Optional
    
-
    countData
    
-
    Count data input data frame. Optional
    
-
    contsData
    
-
    Continuous data input data frame. Optional
    
-
    bugs_params
    
-
    List of BUGS parameters. Optional
    
-
    is_random
    
-
    Random effects model? Logical
    
-
    data_type
    
-
    Vector of names of data formats from
-"hr_data", "surv_bin_data", "med_data", "bin_data",
-"count_data", "conts_data"
    
-
    hyperparams
    
-
    List of hyperparameters
    
-
    refTx
    
-
    Reference treatment; string
    
-
    effectParam
    
-
    Effect parameter
    
-
    label
    
-
    Label
    
-
    endpoint
    
-
    End point name; string
    
-
    
-    
    
-    
    Value
    
-    
-    
    
-    
    
-    
    See also
    
-    
    NMA_run, NMA_update
    
-    
    
-
-  
    
-
-
-    
    
-  
    Developed by Nathan Green.
    
-
    
-
-
    
-  
    Site built with pkgdown

-2.0.2.
    
-
    
-
-    
    
-
-  
-
-  
-
-  
-
+
+NMA constructor — new_NMA • NMA
+    Skip to contents
+    
+
+    
    
+
    
+  
    
+      
    NMA constructor
    
+      Source: R/new_NMA.R
+      
    new_NMA.Rd
    
+    
    
+
+    
    
+    
    Create an nma class object to use in an analysis.
+All of the data types are optional but at least one needs to be
+passed to the function. The data_type must be a subset of
+the passed data sets. If none given then all of the supplied
+data are assumed.
    
+    
    
+
+    
    
+    
    Usage
    
+    
    new_NMA(
+  survDataHR = NA,
+  survDataMed = NA,
+  survDataBin = NA,
+  binData = NA,
+  countData = NA,
+  contsData = NA,
+  bugs_params = NA,
+  is_random = TRUE,
+  data_type = NA,
+  hyperparams = list(),
+  refTx = NA,
+  effectParam = NA,
+  label,
+  endpoint
+)
    
+    
    
+
+    
    
+    
    Arguments
    
+    
    survDataHR
    
+
    Hazard ratio input data frame. Optional
    
+
    survDataMed
    
+
    Median time input data frame. Optional
    
+
    survDataBin
    
+
    Survival binary data input data frame. Optional
    
+
    binData
    
+
    Binary data input data frame. Optional
    
+
    countData
    
+
    Count data input data frame. Optional
    
+
    contsData
    
+
    Continuous data input data frame. Optional
    
+
    bugs_params
    
+
    List of BUGS parameters. Optional
    
+
    is_random
    
+
    Random effects model? Logical
    
+
    data_type
    
+
    Vector of names of data formats from
+"hr_data", "surv_bin_data", "med_data", "bin_data",
+"count_data", "conts_data"
    
+
    hyperparams
    
+
    List of hyperparameters
    
+
    refTx
    
+
    Reference treatment; string
    
+
    effectParam
    
+
    Effect parameter
    
+
    label
    
+
    Label
    
+
    endpoint
    
+
    End point name; string
    
+
    
+    
    
+    
    Value
    
+    
+    
    
+    
    
+    
    See also
    
+    
    NMA_run, NMA_update
    
+    
    
+
+  
    
+
+
+    
    
+  
    Developed by Nathan Green.
    
+
    
+
+
    
+  
    Site built with pkgdown
+
+2.0.2.
    
+
    
+
+    
    
+
+  
+
+  
+
+  
+
diff --git a/docs/reference/plotNetwork.html b/docs/reference/plotNetwork.html
index c0fa20a..449581f 100644
--- a/docs/reference/plotNetwork.html
+++ b/docs/reference/plotNetwork.html
@@ -1,107 +1,108 @@
-
-Plot network diagram — plotNetwork • NMA
-    Skip to contents
-    
-
-    
    
-
    
-  
    
-      
    Plot network diagram
    
-      Source: R/plotNetwork.R
-      
    plotNetwork.Rd
    
-    
    
-
-    
    
-    
    Plot network diagram
    
-    
    
-
-    
    
-    
    Usage
    
-    
    plotNetwork(dat, usecurve = FALSE)
-
-# S3 method for default
-plotNetwork(dat, usecurve = FALSE, ...)
-
-# S3 method for nma
-plotNetwork(dat, usecurve = FALSE, ...)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    dat
    
-
    List of study data, including subData
-and possibly subDataBin and subDataMed
    
-
    usecurve
    
-
    Which line to use? Logical
    
-
    ...
    
-
    Additional arguments
    
-
    
-    
    
-    
    Value
    
-    
-    
    
-
-  
    
-
-
-    
    
-  
    Developed by Nathan Green.
    
-
    
-
-
    
-  
    Site built with pkgdown

-2.0.2.
    
-
    
-
-    
    
-
-  
-
-  
-
-  
-
+
+Plot network diagram — plotNetwork • NMA
+    Skip to contents
+    
+
+    
    
+
    
+  
    
+      
    Plot network diagram
    
+      Source: R/plotNetwork.R
+      
    plotNetwork.Rd
    
+    
    
+
+    
    
+    
    Plot network diagram
    
+    
    
+
+    
    
+    
    Usage
    
+    
    plotNetwork(dat, usecurve = FALSE)
+
+# S3 method for default
+plotNetwork(dat, usecurve = FALSE, ...)
+
+# S3 method for nma
+plotNetwork(dat, usecurve = FALSE, ...)
    
+    
    
+
+    
    
+    
    Arguments
    
+    
    dat
    
+
    List of study data, including subData
+and possibly survDataBin and survDataMed
    
+
    usecurve
    
+
    Which line to use? Logical
    
+
    ...
    
+
    Additional arguments
    
+
    
+    
    
+    
    Value
    
+    
+    
    
+
+  
    
+
+
+    
    
+  
    Developed by Nathan Green.
    
+
    
+
+
    
+  
    Site built with pkgdown
+
+2.0.2.
    
+
    
+
+    
    
+
+  
+
+  
+
+  
+
diff --git a/docs/reference/plots_and_tables.html b/docs/reference/plots_and_tables.html
index cc1d80d..720ab9a 100644
--- a/docs/reference/plots_and_tables.html
+++ b/docs/reference/plots_and_tables.html
@@ -1,135 +1,136 @@
-
-Write to file multiple NMA plots and tables — plots_and_tables • NMA
-    Skip to contents
-    
-
-    
    
-
    
-  
    
-      
    Write to file multiple NMA plots and tables
    
-      Source: R/plots_and_tables.R, R/plots_and_tables_tmp.R
-      
    plots_and_tables.Rd
    
-    
    
-
-    
    
-    
    Write to file multiple NMA plots and tables
    
-
    Write to file multiple NMA plots and tables
    
-    
    
-
-    
    
-    
    Usage
    
-    
    plots_and_tables(
-  nma,
-  res_bugs,
-  effectParam = NA,
-  label = "",
-  endpoint = NULL,
-  folder = "output",
-  save = FALSE
-)
-
-plots_and_tables(
-  nma,
-  res_bugs,
-  effectParam = NA,
-  label = "",
-  endpoint = NULL,
-  folder = "output",
-  save = FALSE
-)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    nma
    
-
    Object of class nma
    
-
    res_bugs
    
-
    BUGS output
    
-
    effectParam
    
-
    Effect parameter names; string
    
-
    label
    
-
    Label
    
-
    endpoint
    
-
    End point names; string
    
-
    folder
    
-
    Output folder name; string
    
-
    save
    
-
    Logical
    
-
    dat
    
-
    ist of study data, including subData
-and possibly subDataBin and subDataMed
    
-
    labels
    
-
    Labels
    
-
    
-    
    
-    
    Value
    
-    
    res_bugs
-res_bugs
    
-    
    
-
-  
    
-
-
-    
    
-  
    Developed by Nathan Green.
    
-
    
-
-
    
-  
    Site built with pkgdown

-2.0.2.
    
-
    
-
-    
    
-
-  
-
-  
-
-  
-
+
+Write to file multiple NMA plots and tables — plots_and_tables • NMA
+    Skip to contents
+    
+
+    
    
+
    
+  
    
+      
    Write to file multiple NMA plots and tables
    
+      Source: R/plots_and_tables.R, R/plots_and_tables_tmp.R
+      
    plots_and_tables.Rd
    
+    
    
+
+    
    
+    
    Write to file multiple NMA plots and tables
    
+
    Write to file multiple NMA plots and tables
    
+    
    
+
+    
    
+    
    Usage
    
+    
    plots_and_tables(
+  nma,
+  res_bugs,
+  effectParam = NA,
+  label = "",
+  endpoint = NULL,
+  folder = "output",
+  save = FALSE
+)
+
+plots_and_tables(
+  nma,
+  res_bugs,
+  effectParam = NA,
+  label = "",
+  endpoint = NULL,
+  folder = "output",
+  save = FALSE
+)
    
+    
    
+
+    
    
+    
    Arguments
    
+    
    nma
    
+
    Object of class nma
    
+
    res_bugs
    
+
    BUGS output
    
+
    effectParam
    
+
    Effect parameter names; string
    
+
    label
    
+
    Label
    
+
    endpoint
    
+
    End point names; string
    
+
    folder
    
+
    Output folder name; string
    
+
    save
    
+
    Logical
    
+
    dat
    
+
    ist of study data, including subData
+and possibly survDataBin and survDataMed
    
+
    labels
    
+
    Labels
    
+
    
+    
    
+    
    Value
    
+    
    res_bugs
+res_bugs
    
+    
    
+
+  
    
+
+
+    
    
+  
    Developed by Nathan Green.
    
+
    
+
+
    
+  
    Site built with pkgdown
+
+2.0.2.
    
+
    
+
+    
    
+
+  
+
+  
+
+  
+
diff --git a/docs/reference/prep_codeData.html b/docs/reference/prep_codeData.html
index 0edaad6..53af111 100644
--- a/docs/reference/prep_codeData.html
+++ b/docs/reference/prep_codeData.html
@@ -1,117 +1,118 @@
-
-Prepare data used in computation — prep_codeData • NMA
-    Skip to contents
-    
-
-    
    
-
    
-  
    
-      
    Prepare data used in computation
    
-      Source: R/prep_codeData.R
-      
    prep_codeData.Rd
    
-    
    
-
-    
    
-    
    Create input data for NMA.
-Renames the study, base and other fields with appended letter
-depending on type of data.
    
-    
    
-
-    
    
-    
    Usage
    
-    
    prep_codeData(
-  subDataHR = NA,
-  subDataBin = NA,
-  subDataMed = NA,
-  binData = NA,
-  countData = NA,
-  contsData = NA,
-  refTx = NA
-)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    subDataHR
    
-
    Hazard ratio data frame
    
-
    subDataBin
    
-
    Optional data frame. Survival binary data
    
-
    subDataMed
    
-
    Optional data frame. Median times
    
-
    refTx
    
-
    Reference treatment name; string
    
-
    
-    
    
-    
    Value
    
-    
    List of data and statistics.
-If no binary of median data empty sub-lists.
    
-    
    
-
-  
    
-
-
-    
    
-  
    Developed by Nathan Green.
    
-
    
-
-
    
-  
    Site built with pkgdown

-2.0.2.
    
-
    
-
-    
    
-
-  
-
-  
-
-  
-
+
+Prepare data used in computation — prep_codeData • NMA
+    Skip to contents
+    
+
+    
    
+
    
+  
    
+      
    Prepare data used in computation
    
+      Source: R/prep_codeData.R
+      
    prep_codeData.Rd
    
+    
    
+
+    
    
+    
    Create input data for NMA.
+Renames the study, base and other fields with appended letter
+depending on type of data.
    
+    
    
+
+    
    
+    
    Usage
    
+    
    prep_codeData(
+  survDataHR = NA,
+  survDataBin = NA,
+  survDataMed = NA,
+  binData = NA,
+  countData = NA,
+  contsData = NA,
+  refTx = NA
+)
    
+    
    
+
+    
    
+    
    Arguments
    
+    
    survDataHR
    
+
    Hazard ratio data frame
    
+
    survDataBin
    
+
    Optional data frame. Survival binary data
    
+
    survDataMed
    
+
    Optional data frame. Median times
    
+
    refTx
    
+
    Reference treatment name; string
    
+
    
+    
    
+    
    Value
    
+    
    List of data and statistics.
+If no binary of median data empty sub-lists.
    
+    
    
+
+  
    
+
+
+    
    
+  
    Developed by Nathan Green.
    
+
    
+
+
    
+  
    Site built with pkgdown
+
+2.0.2.
    
+
    
+
+    
    
+
+  
+
+  
+
+  
+
diff --git a/docs/reference/setupData.html b/docs/reference/setupData.html
index d19ee84..ba0a013 100644
--- a/docs/reference/setupData.html
+++ b/docs/reference/setupData.html
@@ -1,107 +1,108 @@
-
-Set-up study data — setupData • NMA
-    Skip to contents
-    
-
-    
    
-
    
-  
    
-      
    Set-up study data
    
-      Source: R/setupData.R
-      
    setupData.Rd
    
-    
    
-
-    
    
-    
    Arrange input data for NMA.
    
-    
    
-
-    
    
-    
    Usage
    
-    
    setupData(nma_datasets, data_type = NA, refTx = NA, is_random = TRUE)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    nma_datasets
    
-
    subDataHR: Hazard ratio data. Optional;
-subDataBin: Survival binary data. Optional;
-subDataMed: Median time data. Optional;
-binData: Binary data. Optional;
-countData: Count data. Optional;
-contsData: Continuous data. Optional
    
-
    data_type
    
-
    Data type
    
-
    refTx
    
-
    Reference treatment name
    
-
    is_random
    
-
    Is this a random effects model? Logical
    
-
    
-    
    
-    
    Value
    
-    
    list
    
-    
    
-
-  
    
-
-
-    
    
-  
    Developed by Nathan Green.
    
-
    
-
-
    
-  
    Site built with pkgdown

-2.0.2.
    
-
    
-
-    
    
-
-  
-
-  
-
-  
-
+
+Set-up study data — setupData • NMA
+    Skip to contents
+    
+
+    
    
+
    
+  
    
+      
    Set-up study data
    
+      Source: R/setupData.R
+      
    setupData.Rd
    
+    
    
+
+    
    
+    
    Arrange input data for NMA.
    
+    
    
+
+    
    
+    
    Usage
    
+    
    setupData(nma_datasets, data_type = NA, refTx = NA, is_random = TRUE)
    
+    
    
+
+    
    
+    
    Arguments
    
+    
    nma_datasets
    
+
    survDataHR: Hazard ratio data. Optional;
+survDataBin: Survival binary data. Optional;
+survDataMed: Median time data. Optional;
+binData: Binary data. Optional;
+countData: Count data. Optional;
+contsData: Continuous data. Optional
    
+
    data_type
    
+
    Data type
    
+
    refTx
    
+
    Reference treatment name
    
+
    is_random
    
+
    Is this a random effects model? Logical
    
+
    
+    
    
+    
    Value
    
+    
    list
    
+    
    
+
+  
    
+
+
+    
    
+  
    Developed by Nathan Green.
    
+
    
+
+
    
+  
    Site built with pkgdown
+
+2.0.2.
    
+
    
+
+    
    
+
+  
+
+  
+
+  
+
diff --git a/docs/reference/subDataBin.html b/docs/reference/subDataBin.html
index ddef6e1..8e1ad70 100644
--- a/docs/reference/subDataBin.html
+++ b/docs/reference/subDataBin.html
@@ -1,106 +1,107 @@
-
-Study survival binary outcome data — subDataBin • NMA
-    Skip to contents
-    
-
-    
    
-
    
-  
    
-      
    Study survival binary outcome data
    
-      Source: R/data.R
-      
    subDataBin.Rd
    
-    
    
-
-    
    
-    
    A dataset containing the pair comparisons for studies.
    
-    
    
-
-    
    
-    
    Usage
    
-    
    subDataBin
    
-    
    
-
-    
    
-    
    Format
    
-    
    A data frame with 5 variables:
    study
    
-
    Study name
    
-
-
    base
    
-
    Reference treatment name
    
-
-
    tx
    
-
    Comparison treatment name
    
-
-
    BinR
    
-
    Count of number of events
    
-
-
    BinN
    
-
    Total sample size
    
-
-
-
    
-
-  
    
-
-
-    
    
-  
    Developed by Nathan Green.
    
-
    
-
-
    
-  
    Site built with pkgdown

-2.0.2.
    
-
    
-
-    
    
-
-  
-
-  
-
-  
-
+
+Study survival binary outcome data — subDataBin • NMA
+    Skip to contents
+    
+
+    
    
+
    
+  
    
+      
    Study survival binary outcome data
    
+      Source: R/data.R
+      
    survDataBin.Rd
    
+    
    
+
+    
    
+    
    A dataset containing the pair comparisons for studies.
    
+    
    
+
+    
    
+    
    Usage
    
+    
    survDataBin
    
+    
    
+
+    
    
+    
    Format
    
+    
    A data frame with 5 variables:
    study
    
+
    Study name
    
+
+
    base
    
+
    Reference treatment name
    
+
+
    tx
    
+
    Comparison treatment name
    
+
+
    BinR
    
+
    Count of number of events
    
+
+
    BinN
    
+
    Total sample size
    
+
+
+
    
+
+  
    
+
+
+    
    
+  
    Developed by Nathan Green.
    
+
    
+
+
    
+  
    Site built with pkgdown
+
+2.0.2.
    
+
    
+
+    
    
+
+  
+
+  
+
+  
+
diff --git a/docs/reference/subDataHR.html b/docs/reference/subDataHR.html
index e5a5167..04cb087 100644
--- a/docs/reference/subDataHR.html
+++ b/docs/reference/subDataHR.html
@@ -1,112 +1,113 @@
-
-Study log hazard ratios and standard errors — subDataHR • NMA
-    Skip to contents
-    
-
-    
    
-
    
-  
    
-      
    Study log hazard ratios and standard errors
    
-      Source: R/data.R
-      
    subDataHR.Rd
    
-    
    
-
-    
    
-    
    A dataset containing the pair comparisons for studies.
-Woods NMA allows data on HR on the log scale.
    
-    
    
-
-    
    
-    
    Usage
    
-    
    subDataHR
    
-    
    
-
-    
    
-    
    Format
    
-    
    A data frame with 6 variables:
    study
    
-
    Study name
    
-
-
    base
    
-
    Reference treatment name
    
-
-
    tx
    
-
    Comparison treatment name
    
-
-
    Lmean
    
-
    Log hazard ratio
    
-
-
    Lse
    
-
    Standard error of log hazard ratio
    
-
-
    multi_arm
    
-
    Multi-arm trial indicator: 0/1
    
-
-
-
    
-
-  
    
-
-
-    
    
-  
    Developed by Nathan Green.
    
-
    
-
-
    
-  
    Site built with pkgdown

-2.0.2.
    
-
    
-
-    
    
-
-  
-
-  
-
-  
-
+
+Study log hazard ratios and standard errors — survDataHR • NMA
+    Skip to contents
+    
+
+    
    
+
    
+  
    
+      
    Study log hazard ratios and standard errors
    
+      Source: R/data.R
+      
    survDataHR.Rd
    
+    
    
+
+    
    
+    
    A dataset containing the pair comparisons for studies.
+Woods NMA allows data on HR on the log scale.
    
+    
    
+
+    
    
+    
    Usage
    
+    
    survDataHR
    
+    
    
+
+    
    
+    
    Format
    
+    
    A data frame with 6 variables:
    study
    
+
    Study name
    
+
+
    base
    
+
    Reference treatment name
    
+
+
    tx
    
+
    Comparison treatment name
    
+
+
    Lmean
    
+
    Log hazard ratio
    
+
+
    Lse
    
+
    Standard error of log hazard ratio
    
+
+
    multi_arm
    
+
    Multi-arm trial indicator: 0/1
    
+
+
+
    
+
+  
    
+
+
+    
    
+  
    Developed by Nathan Green.
    
+
    
+
+
    
+  
    Site built with pkgdown
+
+2.0.2.
    
+
    
+
+    
    
+
+  
+
+  
+
+  
+
diff --git a/docs/reference/subDataMed.html b/docs/reference/subDataMed.html
index e7e31b1..5076060 100644
--- a/docs/reference/subDataMed.html
+++ b/docs/reference/subDataMed.html
@@ -1,109 +1,110 @@
-
-Study median time to event — subDataMed • NMA
-    Skip to contents
-    
-
-    
    
-
    
-  
    
-      
    Study median time to event
    
-      Source: R/data.R
-      
    subDataMed.Rd
    
-    
    
-
-    
    
-    
    A dataset containing the pair comparisons for studies.
    
-    
    
-
-    
    
-    
    Usage
    
-    
    subDataMed
    
-    
    
-
-    
    
-    
    Format
    
-    
    A data frame with 6 variables:
    study
    
-
    Study name
    
-
-
    base
    
-
    Reference treatment name
    
-
-
    tx
    
-
    Comparison treatment name
    
-
-
    median
    
-
    Median time
    
-
-
    medN
    
-
    Sample size
    
-
-
    medR
    
-
    Sample size/2 as estimated number of events
    
-
-
-
    
-
-  
    
-
-
-    
    
-  
    Developed by Nathan Green.
    
-
    
-
-
    
-  
    Site built with pkgdown

-2.0.2.
    
-
    
-
-    
    
-
-  
-
-  
-
-  
-
+
+Study median time to event — subDataMed • NMA
+    Skip to contents
+    
+
+    
    
+
    
+  
    
+      
    Study median time to event
    
+      Source: R/data.R
+      
    survDataMed.Rd
    
+    
    
+
+    
    
+    
    A dataset containing the pair comparisons for studies.
    
+    
    
+
+    
    
+    
    Usage
    
+    
    survDataMed
    
+    
    
+
+    
    
+    
    Format
    
+    
    A data frame with 6 variables:
    study
    
+
    Study name
    
+
+
    base
    
+
    Reference treatment name
    
+
+
    tx
    
+
    Comparison treatment name
    
+
+
    median
    
+
    Median time
    
+
+
    medN
    
+
    Sample size
    
+
+
    medR
    
+
    Sample size/2 as estimated number of events
    
+
+
+
    
+
+  
    
+
+
+    
    
+  
    Developed by Nathan Green.
    
+
    
+
+
    
+  
    Site built with pkgdown
+
+2.0.2.
    
+
    
+
+    
    
+
+  
+
+  
+
+  
+
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 6eabe5e..0f73d7c 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -145,13 +145,13 @@
     https://icon-in-r.github.io/NMA/reference/subData.html
   
   
-    https://icon-in-r.github.io/NMA/reference/subDataBin.html
+    https://icon-in-r.github.io/NMA/reference/survDataBin.html
   
   
-    https://icon-in-r.github.io/NMA/reference/subDataHR.html
+    https://icon-in-r.github.io/NMA/reference/survDataHR.html
   
   
-    https://icon-in-r.github.io/NMA/reference/subDataMed.html
+    https://icon-in-r.github.io/NMA/reference/survDataMed.html
   
   
     https://icon-in-r.github.io/NMA/reference/summStat.html
diff --git a/man/make_report.Rd b/man/make_report.Rd
index dd8111a..542b593 100644
--- a/man/make_report.Rd
+++ b/man/make_report.Rd
@@ -41,19 +41,19 @@ label_name <- "label_name"
 
 file_name <- here::here(file.path("inst", "extdata", "survdata_"))
 
-subDataHR <-
+survDataHR <-
   read.csv(paste0(file_name, "hr_test.csv"),
            header = TRUE,
            as.is = TRUE)
 
-subDataBin <-
+survDataBin <-
   tryCatch(
     read.csv(paste0(file_name, "bin_test.csv"),
              header = TRUE,
              as.is = TRUE),
     error = function(e) NA)
 
-subDataMed <-
+survDataMed <-
   tryCatch(
     read.csv(paste0(file_name, "med_test.csv"),
              header = TRUE,
@@ -62,9 +62,9 @@ subDataMed <-
     error = function(e) NA)
 
 nma_model <-
-  new_NMA(subDataHR = subDataHR,
-          subDataMed = subDataMed,
-          subDataBin = subDataBin,
+  new_NMA(survDataHR = survDataHR,
+          survDataMed = survDataMed,
+          survDataBin = survDataBin,
           bugs_params = bugs_params,
           is_random = RANDOM,
           data_type = data_type,
diff --git a/man/new_NMA.Rd b/man/new_NMA.Rd
index 5066c3c..5304b0e 100644
--- a/man/new_NMA.Rd
+++ b/man/new_NMA.Rd
@@ -5,9 +5,9 @@
 \title{NMA constructor}
 \usage{
 new_NMA(
-  subDataHR = NA,
-  subDataMed = NA,
-  subDataBin = NA,
+  survDataHR = NA,
+  survDataMed = NA,
+  survDataBin = NA,
   binData = NA,
   countData = NA,
   contsData = NA,
@@ -22,11 +22,11 @@ new_NMA(
 )
 }
 \arguments{
-\item{subDataHR}{Hazard ratio input data frame. Optional}
+\item{survDataHR}{Hazard ratio input data frame. Optional}
 
-\item{subDataMed}{Median time input data frame. Optional}
+\item{survDataMed}{Median time input data frame. Optional}
 
-\item{subDataBin}{Survival binary data input data frame. Optional}
+\item{survDataBin}{Survival binary data input data frame. Optional}
 
 \item{binData}{Binary data input data frame. Optional}
 
diff --git a/man/plotNetwork.Rd b/man/plotNetwork.Rd
index 59b44bc..24df45f 100644
--- a/man/plotNetwork.Rd
+++ b/man/plotNetwork.Rd
@@ -14,7 +14,7 @@ plotNetwork(dat, usecurve = FALSE)
 }
 \arguments{
 \item{dat}{List of study data, including subData
-and possibly subDataBin and subDataMed}
+and possibly survDataBin and survDataMed}
 
 \item{usecurve}{Which line to use? Logical}
 
diff --git a/man/plots_and_tables.Rd b/man/plots_and_tables.Rd
index f86e43d..2af4532 100644
--- a/man/plots_and_tables.Rd
+++ b/man/plots_and_tables.Rd
@@ -40,7 +40,7 @@ plots_and_tables(
 \item{save}{Logical}
 
 \item{dat}{ist of study data, including subData
-and possibly subDataBin and subDataMed}
+and possibly survDataBin and survDataMed}
 
 \item{labels}{Labels}
 }
diff --git a/man/prep_codeData.Rd b/man/prep_codeData.Rd
index bf305c7..f9349a5 100644
--- a/man/prep_codeData.Rd
+++ b/man/prep_codeData.Rd
@@ -5,9 +5,9 @@
 \title{Prepare data used in computation}
 \usage{
 prep_codeData(
-  subDataHR = NA,
-  subDataBin = NA,
-  subDataMed = NA,
+  survDataHR = NA,
+  survDataBin = NA,
+  survDataMed = NA,
   binData = NA,
   countData = NA,
   contsData = NA,
@@ -15,11 +15,11 @@ prep_codeData(
 )
 }
 \arguments{
-\item{subDataHR}{Hazard ratio data frame}
+\item{survDataHR}{Hazard ratio data frame}
 
-\item{subDataBin}{Optional data frame. Survival binary data}
+\item{survDataBin}{Optional data frame. Survival binary data}
 
-\item{subDataMed}{Optional data frame. Median times}
+\item{survDataMed}{Optional data frame. Median times}
 
 \item{refTx}{Reference treatment name; string}
 }
diff --git a/man/setupData.Rd b/man/setupData.Rd
index 999d52f..3da1158 100644
--- a/man/setupData.Rd
+++ b/man/setupData.Rd
@@ -7,9 +7,9 @@
 setupData(nma_datasets, data_type = NA, refTx = NA, is_random = TRUE)
 }
 \arguments{
-\item{nma_datasets}{subDataHR: Hazard ratio data. Optional;
-subDataBin: Survival binary data. Optional;
-subDataMed: Median time data. Optional;
+\item{nma_datasets}{survDataHR: Hazard ratio data. Optional;
+survDataBin: Survival binary data. Optional;
+survDataMed: Median time data. Optional;
 binData: Binary data. Optional;
 countData: Count data. Optional;
 contsData: Continuous data. Optional}
diff --git a/man/subDataBin.Rd b/man/subDataBin.Rd
index 36aa374..567cdf7 100644
--- a/man/subDataBin.Rd
+++ b/man/subDataBin.Rd
@@ -1,8 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/data.R
 \docType{data}
-\name{subDataBin}
-\alias{subDataBin}
+\name{survDataBin}
+\alias{survDataBin}
 \title{Study survival binary outcome data}
 \format{
 A data frame with 5 variables:
@@ -15,7 +15,7 @@ A data frame with 5 variables:
 }
 }
 \usage{
-subDataBin
+survDataBin
 }
 \description{
 A dataset containing the pair comparisons for studies.
diff --git a/man/subDataHR.Rd b/man/subDataHR.Rd
index d310538..6b98f1b 100644
--- a/man/subDataHR.Rd
+++ b/man/subDataHR.Rd
@@ -1,8 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/data.R
 \docType{data}
-\name{subDataHR}
-\alias{subDataHR}
+\name{survDataHR}
+\alias{survDataHR}
 \title{Study log hazard ratios and standard errors}
 \format{
 A data frame with 6 variables:
@@ -16,7 +16,7 @@ A data frame with 6 variables:
 }
 }
 \usage{
-subDataHR
+survDataHR
 }
 \description{
 A dataset containing the pair comparisons for studies.
diff --git a/man/subDataMed.Rd b/man/subDataMed.Rd
index c085aa2..590c308 100644
--- a/man/subDataMed.Rd
+++ b/man/subDataMed.Rd
@@ -1,8 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/data.R
 \docType{data}
-\name{subDataMed}
-\alias{subDataMed}
+\name{survDataMed}
+\alias{survDataMed}
 \title{Study median time to event}
 \format{
 A data frame with 6 variables:
@@ -16,7 +16,7 @@ A data frame with 6 variables:
 }
 }
 \usage{
-subDataMed
+survDataMed
 }
 \description{
 A dataset containing the pair comparisons for studies.
diff --git a/scripts/run_analysis.R b/scripts/run_analysis.R
index 36cf3b9..aa534c6 100644
--- a/scripts/run_analysis.R
+++ b/scripts/run_analysis.R
@@ -62,14 +62,14 @@ subData <-
            as.is = TRUE)
 
 if (is_bin) {
-  subDataBin <-
+  survDataBin <-
     read.csv(paste0(file_name, "bin.csv"),
              header = TRUE,
              as.is = TRUE)
 }
 
 if (is_med) {
-  subDataMed <-
+  survDataMed <-
     read.csv(paste0(file_name, "med.csv"),
              header = TRUE,
              as.is = TRUE) %>% 
@@ -79,8 +79,8 @@ if (is_med) {
   
 nma_res <-
   setupData(subData = subData,
-            subDataMed = subDataMed,
-            subDataBin = subDataBin,
+            survDataMed = survDataMed,
+            survDataBin = survDataBin,
             is_random = RANDOM,
             refTx = REFTX) %>% 
   NMA(dat = .,
@@ -101,8 +101,8 @@ nma_res <-
 library(sna)
 dat <- 
   setupData(subData = subData,
-            subDataMed = subDataMed,
-            subDataBin = subDataBin,
+            survDataMed = survDataMed,
+            survDataBin = survDataBin,
             is_random = RANDOM,
             refTx = REFTX) 
 
diff --git a/scripts/run_analysis_S3.R b/scripts/run_analysis_S3.R
index 5f69edf..d665d89 100644
--- a/scripts/run_analysis_S3.R
+++ b/scripts/run_analysis_S3.R
@@ -58,14 +58,14 @@ subData <-
            header = TRUE,
            as.is = TRUE)
 
-subDataBin <-
+survDataBin <-
   if (is_bin) {
     read.csv(paste0(file_name, "bin.csv"),
              header = TRUE,
              as.is = TRUE)
   } else {NA}
 
-subDataMed <-
+survDataMed <-
   if (is_med) {
     read.csv(paste0(file_name, "med.csv"),
              header = TRUE,
@@ -79,8 +79,8 @@ subDataMed <-
 ## build model
 nma_model <-
   new_NMA(subData = subData,
-          subDataMed = subDataMed,
-          subDataBin = subDataBin,
+          survDataMed = survDataMed,
+          survDataBin = survDataBin,
           bugs_params = bugs_params,
           is_random = RANDOM,
           hyperparams = hyperparams,
diff --git a/tests/testthat/test-NMA_run.R b/tests/testthat/test-NMA_run.R
index 77a5c97..0d8a01d 100644
--- a/tests/testthat/test-NMA_run.R
+++ b/tests/testthat/test-NMA_run.R
@@ -16,17 +16,17 @@ test_that("new_NMA", {
   file_name <- system.file("extdata", package = "NMA")
   # file_name <- "C:/Users/n8tha/Documents/R/NMA/inst/extdata/survdata_"
   
-  subDataHR <-
+  survDataHR <-
     read.csv(file.path(file_name, "survdata_hr_test.csv"),
              header = TRUE,
              as.is = TRUE)
   
-  subDataBin <-
+  survDataBin <-
     read.csv(file.path(file_name, "survdata_bin_test.csv"),
              header = TRUE,
              as.is = TRUE)
   
-  subDataMed <-
+  survDataMed <-
     read.csv(file.path(file_name, "survdata_med_test.csv"),
              header = TRUE,
              as.is = TRUE) %>% 
@@ -47,9 +47,9 @@ test_that("new_NMA", {
     for (j in seq_along(datasets)) {
       
       nma_model[[as.character(i)]][[j]] <-
-        new_NMA(subDataHR = subDataHR,
-                subDataMed = subDataMed,
-                subDataBin = subDataBin,
+        new_NMA(survDataHR = survDataHR,
+                survDataMed = survDataMed,
+                survDataBin = survDataBin,
                 bugs_params = bugs_params,
                 is_random = i,
                 data_type = datasets[[j]],
diff --git a/vignettes/how-to-use-nma-survival-test-data.Rmd b/vignettes/how-to-use-nma-survival-test-data.Rmd
index 094be5c..0681752 100644
--- a/vignettes/how-to-use-nma-survival-test-data.Rmd
+++ b/vignettes/how-to-use-nma-survival-test-data.Rmd
@@ -60,27 +60,27 @@ label_name <- "label_name"
 ### Read in datasets
 
 The trials data consist of up to 3 separate data frames.
-A main table, `subData`, and optional tables for median event time and binary data, `subDataMed` and `subDataBin` respectively.
+A main table, `subData`, and optional tables for median event time and binary data, `survDataMed` and `survDataBin` respectively.
 Lets read in the each data set separately.
 In another article we will show how to do this in one function call by including a _Reference_ file in the data folder which contains the meta data of how to read in the study data.
-If there is no binary or median data used in the NMA then the variables `subDataBin` and `subDataMed` are assigned `NA`.
+If there is no binary or median data used in the NMA then the variables `survDataBin` and `survDataMed` are assigned `NA`.
 
 ```{r}
 file_name <- here::here(file.path("inst", "extdata", "survdata_"))
 
-subDataHR <-
+survDataHR <-
   read.csv(paste0(file_name, "hr_test.csv"),
            header = TRUE,
            as.is = TRUE)
 
-subDataBin <-
+survDataBin <-
   tryCatch(
     read.csv(paste0(file_name, "bin_test.csv"),
              header = TRUE,
              as.is = TRUE),
     error = function(e) NA)
 
-subDataMed <-
+survDataMed <-
   tryCatch(
     read.csv(paste0(file_name, "med_test.csv"),
              header = TRUE,
@@ -93,19 +93,19 @@ The format of the data should be fairly self-explanatory and looks like the foll
 For the hazard ratio data
 
 ```{r echo=FALSE}
-knitr::kable(subDataHR)
+knitr::kable(survDataHR)
 ```
 
 For the binary data
 
 ```{r echo=FALSE}
-knitr::kable(subDataBin)
+knitr::kable(survDataBin)
 ```
 
 and for the median time data
 
 ```{r echo=FALSE}
-knitr::kable(subDataMed)
+knitr::kable(survDataMed)
 ```
 
 More information about these data is available in the help documentation which can be accessed with e.g. `help(subData)`.
@@ -149,9 +149,9 @@ This then means that we can perform modified fits but we don't have to redo any
 
 ```{r warning=FALSE, message=FALSE}
 nma_model <-
-  new_NMA(subDataHR = subDataHR,
-          subDataMed = subDataMed,
-          subDataBin = subDataBin,
+  new_NMA(survDataHR = survDataHR,
+          survDataMed = survDataMed,
+          survDataBin = survDataBin,
           bugs_params = bugs_params,
           is_random = RANDOM,
           data_type = data_type,
diff --git a/vignettes/reference-file-test-data.Rmd b/vignettes/reference-file-test-data.Rmd
index 96044d6..0bde588 100644
--- a/vignettes/reference-file-test-data.Rmd
+++ b/vignettes/reference-file-test-data.Rmd
@@ -37,8 +37,8 @@ Rows in the `type` column must contain one of the following keywords:
 * `bugs`: File containing the BUGS input parameters for MCMC
 * `analysis`: File containing the scenario information
 * `subData`: Mandatory NMA data. Required column headings of `tx`, `base`, `study`, `Lmean`, `Lse`, `multi_arm`
-* `subDataBin`: Optional binary data. Required column headings of `tx`, `base`, `study`, `BinN`, `BinR`
-* `subDataMed`: Optional median time data. Required column headings of `tx`, `base`, `study`, `medN`, `medR`, `median`
+* `survDataBin`: Optional binary data. Required column headings of `tx`, `base`, `study`, `BinN`, `BinR`
+* `survDataMed`: Optional median time data. Required column headings of `tx`, `base`, `study`, `medN`, `medR`, `median`
 
 `type` | `file`
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