fix documentation for describe lists

R/anlz_hmpreport.R

@@ -14,33 +14,33 @@
 #'
 #' Columns in the output are as follows:
 #'
-#' \itemize{
-#'  \item{year: }{Year of the assessment}
-#'  \item{metric :}{Habitat type assessed}
-#'  \item{Acres: }{Coverage estimate for the year}
-#'  \item{lacres: }{Coverage estimate for the previous set of available data}
-#'  \item{lyr: }{Year for the previous set of available data}
-#'  \item{category: }{Strata for the habitat type}
-#'  \item{Target: }{2030 target for the habitat type from the Habitat Master Plan}
-#'  \item{Goal: }{2050 goal for the habitat type from the Habitat Master Plan}
-#'  \item{acresdiff: }{Difference in acres for the current year and the previous set of available data}
-#'  \item{yeardiff: }{Difference in years for the current year and the previous set of available data}
-#'  \item{changerate: }{Acreage change per year for the current year relative to the previous set of available data}
-#'  \item{targetrate: }{Annual rate required to achieve the 2030 target}
-#'  \item{goalrate: }{Annual rate required to achieve the 2050 goal}
-#'  \item{targetprop: }{Proportion of target met for the current year}
-#'  \item{goalprop: }{Proportion of goal met for the current year}
-#'  \item{targeteval: }{A number indicating target status of the current year for the report card}
-#'  \item{goaleval: }{A number indicating goal status of the current year for the report card}
+#' \describe{
+#'  \item{year}{Year of the assessment}
+#'  \item{metric}{Habitat type assessed}
+#'  \item{Acres}{Coverage estimate for the year}
+#'  \item{lacres}{Coverage estimate for the previous set of available data}
+#'  \item{lyr}{Year for the previous set of available data}
+#'  \item{category}{Strata for the habitat type}
+#'  \item{Target}{2030 target for the habitat type from the Habitat Master Plan}
+#'  \item{Goal}{2050 goal for the habitat type from the Habitat Master Plan}
+#'  \item{acresdiff}{Difference in acres for the current year and the previous set of available data}
+#'  \item{yeardiff}{Difference in years for the current year and the previous set of available data}
+#'  \item{changerate}{Acreage change per year for the current year relative to the previous set of available data}
+#'  \item{targetrate}{Annual rate required to achieve the 2030 target}
+#'  \item{goalrate}{Annual rate required to achieve the 2050 goal}
+#'  \item{targetprop}{Proportion of target met for the current year}
+#'  \item{goalprop}{Proportion of goal met for the current year}
+#'  \item{targeteval}{A number indicating target status of the current year for the report card}
+#'  \item{goaleval}{A number indicating goal status of the current year for the report card}
 #' }
 #'
 #' The numbers in \code{targeteval} and \code{goaleval} are one of four values as -1, 0, 0.5, and 1. These numbers define the status for the assessment year:
 #'
-#' \itemize{
-#'  \item{-1: }{target or goal not met, trending below}
-#'  \item{0: }{target or goal met, trending below}
-#'  \item{0.5: }{target or goal not met, trending above}
-#'  \item{1: }{target or goal met, trending above}
+#' \describe{
+#'  \item{-1}{target or goal not met, trending below}
+#'  \item{0}{target or goal met, trending below}
+#'  \item{0.5}{target or goal not met, trending above}
+#'  \item{1}{target or goal met, trending above}
 #' }
 #'
 #' @export

R/read_importwq.R

@@ -7,7 +7,7 @@
 #'
 #' @details Loads the "RWMDataSpreadsheet" worksheet from the file located at \code{xlsx}.  The file is downloaded from \url{https://epcbocc.sharepoint.com/:x:/s/Share/EYXZ5t16UlFGk1rzIU91VogBa8U37lh8z_Hftf2KJISSHg?e=8r1SUL&download=1}.  The files can be viewed at \url{https://epcbocc.sharepoint.com/:f:/s/Share/EiypSSYdsEFCi84Sv_6-t7kBUYaXiIqN0B1n2w57Z_V3kQ?e=NdZQcU}.
 #'
-#' Water quality parameters returned by default are total nitrogen (\code{tn}), Secchi depth (\code{sd}), chlorophyll-a (\code{chla}), salinity (top, mid, and bottom depths, \code{Sal_} prefix), water temperature (top, mid, and bottom depths, {\code{Temp_Water_} prefix}), turbidity (\code{Turbidity_JTU-NTU}), and water color (\code{Color_345_F45}).  Additional qualifier columns for each that include the \code{_Q} suffix are also returned, excluding salinity and water temperature.  All other water quality parameters and qualifiers can be returned by setting \code{all = T}.
+#' Water quality parameters returned by default are total nitrogen (\code{tn}), Secchi depth (\code{sd}), chlorophyll-a (\code{chla}), salinity (top, mid, and bottom depths, \code{Sal_} prefix), water temperature (top, mid, and bottom depths, \code{Temp_Water_} prefix), turbidity (\code{Turbidity_JTU-NTU}), and water color (\code{Color_345_F45}).  Additional qualifier columns for each that include the \code{_Q} suffix are also returned, excluding salinity and water temperature.  All other water quality parameters and qualifiers can be returned by setting \code{all = T}.
 #'
 #' @export
 #'

R/show_ratab.R

@@ -23,11 +23,21 @@
 #'
 #' @examples
 #' show_ratab(epcdata, yrsel = 2023, bay_segment = 'OTB')
-show_ratab <- function(epcdata, yrsel, bay_segment = c('OTB', 'HB', 'MTB', 'LTB', 'RALTB'), partialyr = F, outtxt1 = 'All years below threshold so far, not necessary for NMC Actions 2-5', outtxt2 = "All years met threshold, not necessary for NMC Actions 3-5", outtxt3 = "Not necessary due to observed water quality and seagrass conditions in the bay segment", outtxt45 = "Not necessary when chlorophyll-*a* threshold met", txtsz = 13, width = NULL){
+show_ratab <- function(epcdata, yrsel, bay_segment = c('OTB', 'HB', 'MTB', 'LTB', 'RALTB'), partialyr = F, outtxt1 = NULL, outtxt2 = NULL, outtxt3 = NULL, outtxt45 = NULL, txtsz = 13, width = NULL){
 
   if(!requireNamespace('ftExtra', quietly = TRUE))
     stop("Package \"ftExtra\" needed for this function to work. Please install it.", call. = FALSE)
 
+  # defaults for text
+  if(is.null(outtxt1))
+    outtxt1 <- 'All years below threshold so far, not necessary for NMC Actions 2-5'
+  if(is.null(outtxt2))
+    outtxt2 <- "All years met threshold, not necessary for NMC Actions 3-5"
+  if(is.null(outtxt3))
+    outtxt3 <- "Not necessary due to observed water quality and seagrass conditions in the bay segment"
+  if(is.null(outtxt45))
+    outtxt45 <- "Not necessary when chlorophyll-*a* threshold met"
+
   # segment
   bay_segment <- match.arg(bay_segment)