Merge pull request #86 from ldecicco-USGS/main

weekly colors

DESCRIPTION

@@ -67,4 +67,4 @@ BuildVignettes: true
 LazyLoad: yes
 LazyData: yes
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

R/frequency_analysis.R

@@ -674,6 +674,9 @@ weekly_frequency_table <- function(gw_level_dv,
 #' @param y_axis_label the label used for the y-axis of the plot.
 #' @param flip logical. If \code{TRUE}, flips the y axis so that the smallest number is on top.
 #' Default is \code{FALSE}.
+#' @param percentile_colors Optional argument to provide a vector of 5 colors
+#' used to fill the percentile bars in order from lowest percentile bin to the
+#' highest percentile bin. Default behavior (NA) is to use legacy plot colors.
 #' @return a ggplot object with rectangles representing the historical weekly percentiles,
 #' and points representing the historical median and daily values
 #'
@@ -716,7 +719,8 @@ weekly_frequency_plot <- function(gw_level_dv,
                                   plot_title = "",
                                   subtitle = "U.S. Geological Survey",
                                   y_axis_label = "",
-                                  flip = FALSE) {
+                                  flip = FALSE,
+                                  percentile_colors = NA) {
 
   data_list <- set_up_data(gw_level_dv = gw_level_dv,
                            gwl_data = gwl_data,
@@ -818,11 +822,22 @@ weekly_frequency_plot <- function(gw_level_dv,
                           ordered = TRUE))
 
   # Assign colors and shapes
-  rectangle_colors <- c("5 - 10" = "palevioletred2",
-                        "10 - 25" = "rosybrown1",
-                        "25 - 75" = "darkolivegreen1",
-                        "75 - 90" = "lightskyblue2",
-                        "90 - 95" = "skyblue3")
+  groups <- c("5 - 10", "10 - 25", "25 - 75", "75 - 90", "90 - 95")
+  color_list <- c("palevioletred2", "rosybrown1", "darkolivegreen1", "lightskyblue2",
+                                  "skyblue3")
+
+  if (length(percentile_colors) >= 5) {
+    color_list <- percentile_colors
+  }
+  else if (is.na(percentile_colors) == FALSE) {
+    warning(paste0("percentile_colors argument was provided but was invalid,",
+                   " should be a vector of length 5 in which each item in",
+                   " the vector represents a color."))
+  }
+
+  rectangle_colors <- c(`5 - 10` = color_list[1], `10 - 25` = color_list[2],
+                        `25 - 75` = color_list[3], `75 - 90` = color_list[4],
+                        `90 - 95` = color_list[5])
   point_shapes <- c("Historical weekly median" = 17,
                     "Provisional daily value" = 16,
                     "Approved daily value" = 16)

R/included_data.R

@@ -115,7 +115,7 @@ NULL
 .onAttach <- function(libname, pkgname) {
   packageStartupMessage(
     paste(strwrap('More information:
-https://rconnect.usgs.gov/HASP_docs/', width = 40),
+https://doi-usgs.github.io/HASP/', width = 40),
           collapse='\n'))
 }
 
@@ -141,8 +141,9 @@ https://rconnect.usgs.gov/HASP_docs/', width = 40),
 #'
 #' @name HASP-package
 #' @docType package
-#' @keywords Groundwater levels
-NULL
+#' @keywords internal 
+"_PACKAGE"
+
 
 utils::globalVariables(c("lev_dt", "nYears","minMed", "maxMed", "name", "value",
                          "group", "plot_month_med", "p50", "sl_lev_va", "plot_month_last",

README.Rmd

@@ -24,6 +24,7 @@ knitr::opts_chunk$set(echo = TRUE,
 [![R build status](https://code.usgs.gov/water/stats/hasp/badges/main/pipeline.svg)](https://code.usgs.gov/water/stats/hasp/pipelines)
 [![status](https://img.shields.io/badge/USGS-Documentation-blue.svg)](https://rconnect.usgs.gov/HASP_docs/)
 [![status](https://img.shields.io/badge/USGS-Source-orange.svg)](https://code.usgs.gov/water/stats/hasp)
+[![status](https://img.shields.io/badge/Release-Full-blue.svg)](https://code.usgs.gov/water/stats/hasp/-/tree/1.0.0)
 
 *H*ydrologic *A*naly*S*is *P*ackage
 
@@ -163,6 +164,13 @@ plot_composite_data(aquifer_data, num_years)
 plot_normalized_data(aquifer_data, num_years)
 ```
 
+## Citing HASP
+
+
+```{r cite}
+citation(package = "HASP")
+```
+
 
 ## Installation of R and RStudio
 

README.md

@@ -4,6 +4,7 @@
 status](https://code.usgs.gov/water/stats/hasp/badges/main/pipeline.svg)](https://code.usgs.gov/water/stats/hasp/pipelines)
 [![status](https://img.shields.io/badge/USGS-Documentation-blue.svg)](https://rconnect.usgs.gov/HASP_docs/)
 [![status](https://img.shields.io/badge/USGS-Source-orange.svg)](https://code.usgs.gov/water/stats/hasp)
+[![status](https://img.shields.io/badge/Release-Full-blue.svg)](https://code.usgs.gov/water/stats/hasp/-/tree/1.0.0)
 
 *H*ydrologic *A*naly*S*is *P*ackage
 
@@ -182,6 +183,31 @@ plot_normalized_data(aquifer_data, num_years)
 
 ![](man/figures/README-example-2.png)<!-- -->
 
+## Citing HASP
+
+``` r
+citation(package = "HASP")
+#> To cite HASP in publications, please use:
+#> 
+#>   DeCicco, L.A., Prinos, S.T., Eslick-Huff, P.J., Hopkins, C.B., 2022,
+#>   HASP: Hydrologic AnalySis Package, v1.0.0.,
+#>   https://code.usgs.gov/water/stats/hasp, doi:10.5066/P9BUN5GV
+#> 
+#> A BibTeX entry for LaTeX users is
+#> 
+#>   @Manual{,
+#>     author = {Laura DeCicco and Scott Prinos and Patrick Eslick-Huff and Candice Hopkins and Tara Root},
+#>     title = {HASP: Hydrologic AnalySis Package},
+#>     publisher = {U.S. Geological Survey},
+#>     address = {Reston, VA},
+#>     version = {1.0.0},
+#>     institution = {U.S. Geological Survey},
+#>     year = {2022},
+#>     doi = {10.5066/P9BUN5GV},
+#>     url = {https://code.usgs.gov/water/stats/hasp},
+#>   }
+```
+
 ## Installation of R and RStudio
 
 To use the HASP package, you will need to have R and RStudio installed
@@ -193,10 +219,9 @@ Instructions](https://owi.usgs.gov/R/training-curriculum/installr/)
 
 Useful links:
 
--   [Download R Windows](https://cran.r-project.org/bin/windows/base/)
--   [Download R Mac](https://cran.r-project.org/bin/macosx/)
--   [Download
-    RStudio](https://www.rstudio.com/products/rstudio/download/)
+- [Download R Windows](https://cran.r-project.org/bin/windows/base/)
+- [Download R Mac](https://cran.r-project.org/bin/macosx/)
+- [Download RStudio](https://www.rstudio.com/products/rstudio/download/)
 
 ## Running the apps