clean up the help docs

DESCRIPTION

@@ -15,7 +15,7 @@ BugReports: https://github.com/ICON-in-R/NMA/issues
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3.9000
 Depends:
     R (>= 3.5.0)
 Imports:

R/NMA_run.R

@@ -1,7 +1,8 @@
 
 #' Run network meta-analysis
 #' 
-#' BUGS code is taken from DSU reports and papers.
+#' Calling BUGS an NMA is run using the `nma` object created by `new_NMA()`.
+#' The BUGS code is taken from DSU reports and papers.
 #' 
 #' The survival analysis data used is from the \insertCite{Woods2010}{NMA} model.
 #' 
@@ -10,10 +11,10 @@
 #' @param save Save BUGS output to file? Logical
 #' @importFrom Rdpack reprompt
 #' 
-#' @return \code{res_bugs}
+#' @return `res_bugs`
 #' @export
 #' @name NMA_run
-#' @seealso \code{\link{new_NMA}}, \code{\link{NMA_update}}
+#' @seealso `new_NMA()`, `NMA_update()`
 #' 
 #' @references
 #' \insertAllCited{}

R/NMA_update.R

@@ -1,15 +1,16 @@
 
 #' Update NMA
-#' 
-#' Take an existing analysis and modify it.
-#' 
+#'
+#' Take an existing NMA analysis created with an `nma` object, modify the input
+#' arguments and rerun it.
+#'
 #' @template args-nma
 #' @param ... Additional arguments
 #'
 #' @return
 #' @export
 #' @name NMA_update
-#' @seealso \code{\link{new_NMA}}, \code{\link{NMA_run}}
+#' @seealso `new_NMA()`, `NMA_run()`
 #' 
 NMA_update <- function(nma, ...) {
   UseMethod("NMA_update", nma)

R/bugs_stats.R

@@ -6,7 +6,7 @@
 #' @param effectParam text vector of names
 #' @param random RE or FE
 #'
-#' @return
+#' @return List
 #' @export
 #'
 bugs_stats <- function(dat,

R/check_study_data.R

@@ -1,5 +1,6 @@
 
-#
+#' Check study data
+#' 
 check_study_data <- function(survDataHR = NA,
                              survDataMed = NA,
                              survDataBin = NA,

R/make_labels.R

@@ -1,5 +1,7 @@
 
-#'
+#' Make labels
+#' @return list
+#' 
 make_labels <- function(label) {
 
   # Short label without spaces

R/make_report.R

@@ -1,16 +1,15 @@
 
 #' Make Report
 #' 
-#' Constructs the automated report from the output of the NMA.
-#' 
-#' @param ext A string of text to indicate the extension of the 
-#' resulting output file. Possible options are \code{"pdf"}, \code{"docx"}.
-#' This requires the use of pandoc, knitr and rmarkdown.
-#' @param echo A string (default to \code{FALSE}) to instruct whether
-#' the report should also include the \code{BCEA} commands used to 
-#' produce the analyses. If the optional argument \code{echo} is set
-#' to \code{TRUE} (default = \code{FALSE}), then the commands are also
-#' printed.
+#' Constructs an automated report from the output of the NMA.
+#'
+#' @param 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.
+#' @param 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.
 #' @param ... Additional parameters.
 #' 
 #' @importFrom fs path file_copy
@@ -130,6 +129,7 @@ make_report <- function(nma_model,
 }
 
 #' Allow disabling of the cat messages
+#' 
 #' @param x Object to quietly return
 #' @keywords internal
 #' 

R/my_bugs_summary.R

@@ -1,5 +1,5 @@
 
-#' summStat
+#' Summary statistics
 #' 
 #' @param x x
 #' @param probs Probabilities

R/new_NMA.R

@@ -1,12 +1,15 @@
 
 #' NMA constructor
+#'
+#' 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.
 #' 
-#' Create an \code{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.
+#' @section Different data types: 
 #' 
+#' The data types are split in to two: survival data and other.
+#'
 #' @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
@@ -15,18 +18,17 @@
 #' @param contsData Continuous data input data frame. Optional
 #' @param bugs_params List of BUGS parameters. Optional
 #' @param is_random Random effects model? Logical
-#' @param data_type Vector of names of data formats from
-#'                  "hr_data", "surv_bin_data", "med_data", "bin_data",
-#'                  "count_data", "conts_data"
+#' @param data_type Vector of names of data formats from "hr_data",
+#'   "surv_bin_data", "med_data", "bin_data", "count_data", "conts_data"
 #' @param hyperparams List of hyperparameters
 #' @param refTx Reference treatment; string
 #' @param effectParam Effect parameter
 #' @param label Label
 #' @param endpoint End point name; string
-#' @seealso \code{\link{NMA_run}}, \code{\link{NMA_update}}
+#' @seealso [NMA_run()], [NMA_update()]
 #' @return
 #' @export
-#'
+#' 
 new_NMA <- function(survDataHR = NA,
                     survDataMed = NA,
                     survDataBin = NA,

R/new_NMA_dir.R

@@ -1,10 +1,13 @@
 
 #' Load all input data from a folder
 #'
+#' Rather than script the prepocessing, read in data from a folder containing a
+#' `REFERENCE` file telling R what and where the different input data file are.
+#' 
 #' @param data_dir folder location; string
-#' @return \code{nma} object
+#' @return `nma` object
 #' @importFrom fs path
-#' 
+#'
 #' @export
 #' 
 new_NMA_dir <- function(data_dir = ".") {

R/nma_helper.R

@@ -1,5 +1,5 @@
 
-#' nma helper
+#' nma helper to validate NMA
 #'
 #' @return
 #' @export

R/nma_outputs.R

@@ -1,4 +1,5 @@
 
+#' Diagnostics
 #' @keywords internal
 #' 
 diagnostics <- function(res_bugs,

R/plots_and_tables.R

@@ -1,7 +1,7 @@
 
 #' Write to file multiple NMA plots and tables
 #'
-#' @param dat ist of study data, including subData
+#' @param dat List of study data, including subData
 #'  and possibly survDataBin and survDataMed
 #' @param res_bugs BUGS output
 #' @param effectParam Effect parameter names; string

R/prep_codeData.R

@@ -1,5 +1,5 @@
 
-#' Prepare data used in computation
+#' Prepare data used in NMA computation
 #' 
 #' Create input data for NMA.
 #' Renames the study, base and other fields with appended letter