Added update_documentation to quickly update everything and generate …

R/add_CI.R

@@ -7,7 +7,7 @@
 #'
 #'   No default method is available at the moment.
 #'
-#' @param gg visR object
+#' @param gg A ggplot created with visR
 #' @param ... other arguments passed on to the method to modify \code{\link[ggplot2]{geom_ribbon}}
 #'
 #' @examples
@@ -43,7 +43,6 @@ add_CI <- function(gg, ...){
   UseMethod("add_CI", gg)
 }
 
-#' @param gg A ggplot created with visR
 #' @param alpha aesthetic of ggplot2 \code{\link[ggplot2]{geom_ribbon}}. Default is 0.1.
 #' @param style aesthetic of ggplot2 \code{\link[ggplot2]{geom_ribbon}}. Default is "ribbon". An alternative option is "step" that uses a line to display interval bounds.
 #' @param linetype aesthetic of ggplot2 \code{\link[ggplot2]{geom_ribbon}}.

R/add_CNSR.R

@@ -6,7 +6,7 @@
 #'
 #'   No default method is available at the moment.
 #'
-#' @param gg visR object
+#' @param gg A ggplot created with visR
 #' @param ... other arguments passed on to the method to modify \code{\link[ggplot2]{geom_point}}
 #'
 #' @examples
@@ -39,7 +39,6 @@ add_CNSR <- function(gg, ...){
   UseMethod("add_CNSR", gg)
 }
 
-#' @param gg A ggplot created with visR
 #' @param shape aesthetic of ggplot2 \code{\link[ggplot2]{geom_point}}. Default is 3.
 #' @param size aesthetic of ggplot2 \code{\link[ggplot2]{geom_point}}. Default is 2.
 #'

R/add_highlight.R

@@ -2,7 +2,7 @@
 #'
 #' @description S3 method for highlighting a specific strata by lowering the opacity of all other strata.
 #'
-#' @param gg visR object
+#' @param gg A ggplot created with visR
 #' @param ... other arguments passed on to the method
 #'
 #' @examples
@@ -31,7 +31,6 @@ add_highlight <- function(gg, ...){
   UseMethod("add_highlight", gg)
 }
 
-#' @param gg A ggsurvfit, ideatlly created with visR
 #' @param strata String representing the name and value of the strata to be highlighted as shown in the legend.
 #' @param bg_alpha A numerical value between 0 and 1 that is used to decrease the opacity off all strata not chosen to be highlighted in `strata`. The other strata's existing alpha values are multiplied by `bg_alpha` to decrease their opacity, highlighting the target strata. This works on both `colour` and `fill` properties, as for example present after applying `visR::add_CI()`.
 #'

R/add_quantiles.R

@@ -2,7 +2,7 @@
 #'
 #' @description Method to add quantile lines to a plot.
 #'
-#' @param gg visR object
+#' @param gg A ggplot created with visR
 #' @param ... other arguments passed on to the method to modify \code{\link[ggplot2]{geom_line}}
 #'
 #' @examples
@@ -47,7 +47,6 @@ add_quantiles <- function(gg, ...){
   UseMethod("add_quantiles", gg)
 }
 
-#' @param gg A ggplot created with visR
 #' @param quantiles vector of quantiles to be displayed on the probability scale, default: 0.5
 #' @param linetype string indicating the linetype as described in the aesthetics of ggplot2 \code{\link[ggplot2]{geom_line}}, default: dashed (also supports "mixed" -> horizontal lines are solid, vertical ones are dashed)
 #' @param linecolour string indicating the linetype as described in the aesthetics of ggplot2 \code{\link[ggplot2]{geom_line}}, default: grey, (also supports "strata" -> horizontal lines are grey50, vertical ones are the same colour as the respective strata)

R/add_risktable.R

@@ -14,7 +14,7 @@
 #'        }
 #'     }
 #'
-#' @param gg visR plot of class `ggsurvfit` or `ggtidycmprsk`
+#' @param gg A ggplot created with visR
 #' @param ... other arguments passed on to the method add_risktable
 #'
 #' @rdname add_risktable

R/apply_theme.R

@@ -13,20 +13,26 @@
 #'
 #' @examples
 #'
-#' theme <- visR::define_theme(strata = list("SEX" = list("F" = "red",
-#'                                                        "M" = "blue"),
-#'                                           "TRTA" = list("Placebo" = "cyan",
-#'                                                         "Xanomeline High Dose" = "purple",
-#'                                                         "Xanomeline Low Dose" = "brown")),
-#'                             fontsizes = list("axis" = 12,
-#'                                              "ticks" = 10,
-#'                                              "legend_title" = 10,
-#'                                              "legend_text" = 8),
-#'                             fontfamily = "Helvetica",
-#'                             grid = list("major" = FALSE,
-#'                                         "minor" = FALSE),
-#'                             bg = "transparent",
-#'                             legend_position = "top")
+#' theme <- visR::define_theme(
+#'   strata = list("SEX" = list("F" = "red",
+#'                              "M" = "blue"
+#'                            ),
+#'                "TRTA" = list("Placebo" = "cyan",
+#'                              "Xanomeline High Dose" = "purple",
+#'                              "Xanomeline Low Dose" = "brown"
+#'                            )
+#'             ),
+#'   fontsizes = list("axis" = 12,
+#'                    "ticks" = 10,
+#'                    "legend_title" = 10,
+#'                    "legend_text" = 8),
+#'   fontfamily = "Helvetica",
+#'   grid = list("major" = FALSE,
+#'               "minor" = FALSE
+#'              ),
+#'   bg = "transparent",
+#'   legend_position = "top"
+#')
 #'
 #' @export
 

R/get_COX_HR.R

@@ -6,7 +6,7 @@
 #'
 #' @seealso \code{\link[survival]{coxph}} \code{\link[stats]{update.formula}}
 #'
-#' @param x S3 object
+#' @param x An object of class \code{survfit}
 #' @param ... other arguments passed on to the method survival::coxph
 #' 
 #' @rdname get_COX_HR
@@ -17,7 +17,6 @@ get_COX_HR <- function(x, ...){
 } 
 
 
-#' @param x An object of class \code{survfit}
 #' @param update_formula Template which specifies how to update the formula of the survfit object \code{\link[stats]{update.formula}}
 #'
 #' @examples 

R/get_quantile.R

@@ -5,7 +5,7 @@
 #' 
 #' @seealso \code{\link[survival]{quantile.survfit}}
 #' 
-#' @param x S3 object
+#' @param x An object of class \code{survfit}
 #' @param ... other arguments passed on to the method
 #' 
 #' @examples

R/get_risktable.R

@@ -5,7 +5,7 @@
 #'
 #' @seealso \code{\link[survival]{summary.survfit}}
 #'
-#' @param x object to be passed on to the method
+#' @param x an object of class `survfit` or `tidycuminc`
 #' @param ... other arguments passed on to the method
 #' @return return list of attributes the form the risk table i.e.
 #'   number of patients at risk per strata
@@ -17,7 +17,6 @@ get_risktable <- function(x, ...){
   UseMethod("get_risktable")
 }
 
-#' @param x an object of class `survfit` or `tidycuminc`
 #' @param times Numeric vector indicating the times at which the risk set, censored subjects, events are calculated.
 #' @param statlist Character vector indicating which summary data to present. Current choices are "n.risk" "n.event"
 #'   "n.censor", "cum.event", "cum.censor".

R/get_summary.R

@@ -3,7 +3,7 @@
 #' @description S3 method for extracting descriptive statistics across strata.
 #'     No default method is available at the moment.
 #'
-#' @param x S3 object
+#' @param x An object of class `survfit`
 #' @param ... other arguments passed on to the method
 #'
 #' @rdname get_summary
@@ -14,7 +14,6 @@ get_summary <- function(x, ...){
   UseMethod("get_summary", x)
 }
 
-#' @param x An object of class `survfit`
 #' @param statlist Character vector containing the desired information to be displayed. The order of the arguments determines the order in which
 #'    they are displayed in the final result. Default is the strata ("strata"), number of subjects ("records"), number of events ("events"),
 #'    the median survival time ("median"), the Confidence Interval ("CI"), the Lower Confidence Limit ("UCL") and the Upper Confidence Limit ("UCL").

R/tidyme.R

@@ -7,7 +7,7 @@
 #'
 #' @seealso \code{\link[broom]{tidy}}
 #'
-#' @param x S3 object
+#' @param x An S3 object
 #' @param ... other arguments passed on to the method
 #'
 #' @examples

R/utils_general.R

@@ -14,3 +14,47 @@
            width = 6,
            scientific = FALSE)
 }
+
+#' @title Update documentation
+#' 
+#' @description This functions generates the documentation for a package if both /man and /documentation folders exist within the project:
+#'   \itemize{
+#'     \item{devtools::document(pkg=pkg) is used to generate Rd files}
+#'     \item{Rd files are rendered using ?'anyfunction' eg ?visR}
+#'     \item{Documentation is collected within 'pkg'.pdf. This pdf is written to the documentation folder}
+#'     }
+#'
+#' @usage update_documentation(pkg = "~/visR")
+#' 
+#' @param pkg Path to package.
+#'
+#' @return .Rd files inside man/ folder and an updated pdf within the documentation folder.
+#' @noRd
+#' 
+#' @examples
+#' \dontrun{
+#'   update_documentation(pkg = "~/visR")
+#'  }
+
+update_documentation <- function(pkg = "~/visR", fileNm="visR")
+  {
+
+    ## Create Rd files document ####
+    devtools::document(pkg = pkg)
+
+    ## Look for exported functions
+    tmp <- data.frame(lines = trimws(suppressWarnings(readLines(paste0(pkg, "/NAMESPACE"))), which=("both")), stringsAsFactors = F)
+    tmp <- data.frame(lines = tmp$lines[which(grepl("export", tmp$lines) == "TRUE")], stringsAsFactors = F)
+    tmp <- data.frame(lines = gsub("export(", "", tmp$lines, fixed = TRUE))
+    fcts <- as.vector(gsub(")", "", tmp$lines, fixed = TRUE))
+
+    ## Render Rd files
+    for (j in 1:length(fcts)){
+      eval(parse(text=paste0("?",fcts[j])))
+      writeLines(paste0("?",fcts[j]))
+    }
+
+   ## create pdf
+   system(paste0("R CMD Rd2pdf  ", pkg, "/man --force --no-preview --output='", pkg, "/documentation/", fileNm, ".pdf'"))
+}
+

R/utils_visr.R

@@ -2,26 +2,32 @@
 #'
 #' @description This function aligns multiple \code{ggplot} graphs by making them the same width by taking into account the legend width.
 #'
-#' @param pltlist A list of plots (TODO: provide more detail)
+#' @param pltlist A list of plots
 #'
 #' @return List of \code{ggplot} with equal width.
 #'
-#' @references \url{https://stackoverflow.com/questions/26159495/align-multiple-ggplot-graphs-with-and-without-legends}
+#' @references \url{https://stackoverflow.com/questions/26159495/align-multiple-ggplot-
+#'                  graphs-with-and-without-legends}
 #'
 #' @examples
 #' \donttest{
 #'
 #' ## create 2 graphs
 #' p1 <- ggplot2::ggplot(adtte, ggplot2::aes(x = as.numeric(AGE), fill = "Age")) +
 #'   ggplot2::geom_histogram(bins = 15)
+#'   
 #' p2 <- ggplot2::ggplot(adtte, ggplot2::aes(x = as.numeric(AGE))) +
 #'  ggplot2::geom_histogram(bins = 15)
 #'
 #' ## default alignment does not take into account legend size
-#' cowplot::plot_grid(plotlist = list(p1,p2), align = "none", nrow=2)
+#' cowplot::plot_grid(plotlist = list(p1,p2),
+#'                    align = "none",
+#'                    nrow=2)
 #'
 #' ## align_plots() takes into account legend width
-#' cowplot::plot_grid(plotlist = visR::align_plots(pltlist = list(p1, p2)), align = "none", nrow=2)
+#' cowplot::plot_grid(plotlist = visR::align_plots(pltlist = list(p1, p2)),
+#'                    align = "none",
+#'                    nrow=2)
 #' }
 #' @export
 

R/visr.R

@@ -5,7 +5,8 @@
 #'
 #' @seealso \code{\link[ggplot2]{ggplot}}
 #'
-#' @param x object to be passed on to the method
+#' @param x Object of class `survfit`, `attritiontable` or `visr.tidycuminc`
+
 #' @param ... other arguments passed on to the method
 #'
 #' @rdname visr
@@ -24,7 +25,6 @@ visr.default <- function(x, ...){
   graphics::plot(x)
 }
 
-#' @param x Object of class `survfit`
 #' @param x_label \code{character} Label for the x-asis. When not specified,
 #'   the algorithm will look for "PARAM" information inside the list structure
 #'   of the `survfit` object.
@@ -332,8 +332,6 @@ visr.survfit <- function(
 
 }
 
-#' @param x Object of class `attritiontable` with each row corresponding to an
-#'   inclusion step in the cohort and minimally a description and a count column
 #' @param description_column_name \code{character} Name of the column containing
 #'   the inclusion descriptions
 #' @param value_column_name \code{character} Name of the column containing the
@@ -365,9 +363,13 @@ visr.survfit <- function(
 #' attrition %>%
 #'   visr("Criteria", "Remaining N")
 #'
-#' # Adding more detailed complement descriptions to the "exclusion" part of the CONSORT diagram
+#' # Add detailed complement descriptions to the "exclusion" part of the CONSORT diagram
 #' # Step 1. Add new column to attrition dataframe
-#' attrition$Complement <- c("NA", "Placebo Group", "Younger than 75 years", "Non-White", "Male")
+#' attrition$Complement <- c("NA",
+#'                           "Placebo Group",
+#'                           "Younger than 75 years",
+#'                           "Non-White",
+#'                           "Male")
 #'
 #' # Step 2. Define the name of the column in the call to the plotting function
 #' attrition %>%