Merge branch 'dev' into master

.Rbuildignore

@@ -13,3 +13,4 @@
 ^.rvt$
 
 R/rvn_rvi_process_visplot
+^\.github$

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          # - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          # - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          # upload-snapshots: true
+          error-on: '"error"'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,46 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

NAMESPACE

@@ -3,6 +3,7 @@
 export("%>%")
 export("%notin%")
 export(cmax)
+export(hhmmss2dec)
 export(rvn_annual_peak)
 export(rvn_annual_peak_error)
 export(rvn_annual_peak_event)
@@ -61,12 +62,14 @@ export(rvn_rvh_subbasin_visnetwork_plot)
 export(rvn_rvh_summarize)
 export(rvn_rvh_write)
 export(rvn_rvh_write_subbasingroup)
+export(rvn_rvi_commandupdate)
 export(rvn_rvi_connections)
 export(rvn_rvi_getparams)
 export(rvn_rvi_process_diagrammer)
 export(rvn_rvi_process_ggplot)
 export(rvn_rvi_read)
 export(rvn_rvi_write_template)
+export(rvn_rvp_calib_template)
 export(rvn_rvp_fill_template)
 export(rvn_rvt_read)
 export(rvn_rvt_tidyhydat)

R/rvn_apply_wyearly.R

@@ -11,6 +11,8 @@
 #' mm and dd indicate the end of the water year period (i.e. mm=9 and dd=30 indicates
 #' a new water year on Oct 1).
 #'
+#' Note that if using \code{FUN=mean}, please use \code{FUN=colMeans} instead.
+#'
 #' @param x xts vector to calculate FUN for
 #' @param FUN the function to be applied
 #' @param ... optional arguments to FUN
@@ -22,11 +24,11 @@
 #' # use sample forcing data (or use forcings_read to read in ForcingFunctions.csv)
 #' data(rvn_forcing_data)
 #'
-#' # apply mean as FUN to daily average temperature
-#' rvn_apply_wyearly(rvn_forcing_data$forcings$temp_daily_ave,mean,na.rm=TRUE)
+#' # apply mean (with colMeans) as FUN to daily average temperature
+#' rvn_apply_wyearly(rvn_forcing_data$forcings$temp_daily_ave,colMeans,na.rm=TRUE)
 #'
 #' # apply mean as FUN to all forcings
-#' rvn_apply_wyearly(rvn_forcing_data$forcings,mean,na.rm=TRUE)
+#' rvn_apply_wyearly(rvn_forcing_data$forcings,colMeans,na.rm=TRUE)
 #'
 #' # apply maximum via RavenR::cmax as FUN to all forcings (takes the max in each column)
 #' ## note that the base::max will not work properly here

R/rvn_budyko_plot.R

@@ -114,7 +114,7 @@ rvn_budyko_plot <- function(x=NULL, x_indices=NULL, limiting_labels=FALSE, budyk
 
   if (!is.null(x)) {
     # convert x into x_indices
-    temp <- rvn_apply_wyearly(x, FUN=mean,na.rm=TRUE,mm=mm,dd=dd)
+    temp <- rvn_apply_wyearly(x, FUN=colMeans,na.rm=TRUE,mm=mm,dd=dd)
 
     if (year(temp[nrow(temp)]) == year(temp[(nrow(temp)-1)])) {
       temp <- temp[1:(nrow(temp)-1),]

R/rvn_hyd_extract.R

@@ -17,7 +17,7 @@
 #' form "subXX", for example "sub24".
 #'
 #' The hyd object is the full hydrograph object (hyd and units in one data
-#' frame) created by the hyd.read function. Both the hyd and units are
+#' frame) created by the rvn_hyd_read function. Both the hyd and units are
 #' required, since the units are placed onto the plots if one is created. This
 #' is useful to at least see the units of the plotted variable, even if the
 #' plot is later modified.
@@ -28,7 +28,7 @@
 #' no period is supplied, the entire time series will be used.
 #'
 #' @param subs column name for plotting/extracting
-#' @param hyd full hydrograph data frame (including units) produced by hyd.read
+#' @param hyd full hydrograph data frame (including units) produced by rvn_hyd_read
 #' @param prd time period for plotting, as string. See details
 #' @param rename_cols boolean for whether to rename columns to generic terms (sim, obs, etc.) or leave
 #' column names as they appear in hyd
@@ -72,7 +72,7 @@ rvn_hyd_extract <- function(subs=NA, hyd=NA, prd=NULL, rename_cols=TRUE) {
     stop("subs is required for this function.")
   }
   if (missing(hyd)) {
-    stop("hyd is required for this function; please supply the full output file from hyd.read.")
+    stop("hyd is required for this function; please supply the full output file from rvn_hyd_read.")
   }
 
   mysub <- ind <- NULL

R/rvn_hyd_plot.R

@@ -125,7 +125,8 @@ rvn_hyd_plot <- function(sim=NULL,obs=NULL,inflow=NULL,precip=NULL,prd=NULL,
     ylab(expression("Flow ("*m^3*"/s)"))+
     rvn_theme_RavenR()+
     theme(legend.position = "bottom") +
-    scale_colour_brewer(type = "qual", palette = 3)
+    # scale_colour_brewer(type = "qual", palette = 3)+
+    scale_colour_manual(name='Legend',values=c("Obs"='black',"Sim"='darkorange',"Inflow"="purple"))
 
   #Shade Winter Months
   if (winter_shading){

R/rvn_met_recordplot.R

@@ -10,6 +10,11 @@
 #' from the \pkg{weathercan} package and extracts the start and end dates of the record
 #' from each station for plotting.
 #'
+#' Outputs from \code{stations_search()} indicate when data collection at a station generally
+#' began but do not contain information for specific climate variables and thus should
+#' only be used for a "first look". Plots created with station metadata do not refer to
+#' specific climate variables.
+#'
 #' Station records are plotted chronologically on a timeline, and can be colored
 #' according to either the station's elevation (default, works for both types of inputs)
 #' or the station's distance from a point of interest (works only when supplying
@@ -22,7 +27,7 @@
 #' the effect of lapse rates on climate forcings driving a model response.
 #'
 #' @param metadata tibble of the station meta-data from \code{weathercan::stations_search()}
-#' @param stndata tibble of the station data from \code{weathercan::weather_dl()}
+#' @param stndata tibble of the station data from \code{weathercan::weather_dl()}. Used in conjunction with \code{variables} argument.
 #' @param variables if using \code{weathercan::weather_dl()}, column names for variables of interest (currently only accepts 1 per call)
 #' @param colorby column name by which to color station records. Set to 'elev' (elevation) by default. Can be set to
 #' "dist" (distance from coordinates of interest) if supplying \code{weathercan::stations_search} results.
@@ -66,9 +71,18 @@ rvn_met_recordplot <- function(metadata=NULL,stndata=NULL,variables=NULL,colorby
 
   start <- station_name <- nstations <- NA
 
+  # ensure there is a list of stations to read
   if(!is.null(metadata) & !is.null(stndata)){
     stop('Please supply either one of the outputs from weathercan::weather_dl() OR weathercan::stations_search(), not both')}
 
+  # prevent user from searching climate variable records from stations_search( ) results
+  if(!is.null(metadata) & !is.null(variables)){
+    stop(paste("Metadata argument returns overall station record periods (which may not reflect the record period for a specific climate variable observed at that station).",
+               "If looking for records pertaining to a specific climate variable, please use the 'stndata' and 'variables' arguments together.",sep='\n'
+    ))
+  }
+
+  # restrict user to only plotting a subset of climate variables (not all at once)
   if(!is.null(stndata) & is.null(variables)){
     stop('Please specify which variable you would like to view record lengths for')
   }
@@ -92,8 +106,8 @@ rvn_met_recordplot <- function(metadata=NULL,stndata=NULL,variables=NULL,colorby
     metadata$station_name=factor(metadata$station_name,levels=metadata$station_name[order(-metadata$start)])
 
     # plot records to show overlap
-    xmax = max(metadata$end)
-    xmin = min(metadata$start)
+    xmax = max(na.omit(metadata$end))
+    xmin = min(na.omit(metadata$start))
 
     if(is.null(variables)){variables = 'overall station records'} # plot title
 
@@ -123,13 +137,13 @@ rvn_met_recordplot <- function(metadata=NULL,stndata=NULL,variables=NULL,colorby
       scale_x_continuous(limits=c(xmin,xmax),breaks=seq(xmin,xmax,1))+
       theme_bw()+
       theme(plot.title=element_text(hjust=0.5),plot.subtitle=element_text(hjust = 0.5),
-            legend.position = 'bottom',axis.title.y=element_blank())
+            legend.position = 'bottom',axis.title.y=element_blank(),axis.text.x=element_text(angle=90))
   }
 
   # Count number of station records available for each year
-  year = min(metadata$start):max(metadata$end)
+  year = min(na.omit(metadata$start)):max(na.omit(metadata$end))
   recordsum = do.call('rbind',lapply(year,function(y){
-    n = sum(metadata$start <= y & metadata$end >= y)
+    n = sum(metadata$start <= y & metadata$end >= y,na.rm=T)
     return(data.frame(year=y,nstations=n))
   }))
 
@@ -141,7 +155,7 @@ rvn_met_recordplot <- function(metadata=NULL,stndata=NULL,variables=NULL,colorby
     ylab('stations')+
     scale_x_continuous(breaks=seq(xmin,xmax,1))+
     theme_bw()+
-    theme(plot.title=element_text(hjust = 0.5))
+    theme(plot.title=element_text(hjust = 0.5),axis.text.x=element_text(angle=90))
 
   out <- plot_grid(overlapPlot,stncount,nrow=2 )
   return(out)

R/rvn_monthly_vbias.R

@@ -55,7 +55,7 @@
 #' @importFrom ggplot2 ggplot geom_bar aes scale_y_continuous scale_x_continuous geom_hline geom_text
 #' @importFrom xts apply.monthly
 #' @importFrom lubridate month
-rvn_monthly_vbias <- function (sim, obs, add_line = TRUE, normalize = TRUE, add_labels = TRUE,
+rvn_monthly_vbias <- function(sim, obs, add_line = TRUE, normalize = TRUE, add_labels = TRUE,
                                incomplete_month = FALSE)
 {
 

R/rvn_rvh_blankSBdf.R

@@ -37,7 +37,7 @@ rvn_rvh_blankSBdf <- function(nSubBasins = 1) {
   df <- data.frame('SBID'          = 1:nSubBasins,
                    'Name'          = subnames,
                    'Downstream_ID' = downstreamid,
-                   'Profile'       = "DEFAULT",
+                   'Profile'       = "NONE",
                    'ReachLength'   = 0.0,
                    'Gauged'        = 0)
   return(df)

R/rvn_rvh_write_subbasingroup.R

@@ -42,31 +42,28 @@
 #' @export rvn_rvh_write_subbasingroup
 rvn_rvh_write_subbasingroup <- function(rvh=NULL, sbgroup_name=NULL, outfile=NULL, subs_per_line=30, overwrite=TRUE)
 {
-
   # input checking
   if (is.null(rvh) | is.null(rvh$SBtable)) {
-    stop("rvn_rvh_summarize: valid rvh object is required")
-  }
-
-  if (is.null(sbgroup_name)) {
-    sbgroup_name <- "subgroup_RavenR_generated"
-  }
-
-  if (is.null(outfile)) {
-    outfile <- "subbasingroup_RavenR.rvh"
-  }
-
-  fc <- file(outfile, open = "wt")
-  writeLines(sprintf(":SubBasinGroup  %s",sbgroup_name), fc)
-  for (i in seq(from=1,to=min(nrow(rvh$SBtable),subs_per_line), by=subs_per_line))  {
-    temp <- rvh$SBtable$SBID[i:(min(i+subs_per_line-1,nrow(rvh$SBtable)))] %>%
-      paste0(collapse=", ")
-    sprintf("  %s",temp) %>%
-      writeLines(fc)
-  }
-  writeLines(":EndSubBasinGroup", fc)
-  close(fc)
-
-  message(sprintf("Successfully wrote SubBasinGroup '%s' to file %s",sbgroup_name,outfile))
-  return(TRUE)
+        stop("rvn_rvh_write_subbasingroup: valid rvh object is required")
+    }
+    if (is.null(sbgroup_name)) {
+        sbgroup_name <- "subgroup_RavenR_generated"
+    }
+    if (is.null(outfile)) {
+        outfile <- "subbasingroup_RavenR.rvh"
+    }
+    fc <- file(outfile, open = "wt")
+    writeLines(sprintf(":SubBasinGroup  %s", sbgroup_name),
+        fc)
+    iseq <- seq(from = 1, to = nrow(rvh$SBtable),
+        by = (subs_per_line-1))
+    for (i in 1:(length(iseq)-1) ) {
+        temp <- rvh$SBtable$SBID[iseq[i]:iseq[i+1]] %>% paste0(collapse = ", ")
+        sprintf("  %s", temp) %>% writeLines(fc)
+    }
+    writeLines(":EndSubBasinGroup", fc)
+    close(fc)
+    message(sprintf("Successfully wrote SubBasinGroup '%s' to file %s on %i lines",
+        sbgroup_name, outfile, length(iseq)+1))
+    return(TRUE)
 }