Viz cleanup

CHANGELOG.md

@@ -21,7 +21,9 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 
 ### Changed
 - Rebuilt documentation using Roxygen 7. Readers get nicer formatting of usage sections, writers get more flexible behavior when inheriting parameters and less hassle when maintaining namespaces (#2524).
-- PEcAn.priors: renamed functions that looked like S3 methods but were not: `plot.posterior.density`->`plot_posterior.density`, `plot.prior.density`->`plot_prior.density`, `plot.trait`->`plot_trait` (#2439).
+- Renamed functions that looked like S3 methods but were not:
+    * PEcAn.priors: `plot.posterior.density`->`plot_posterior.density`, `plot.prior.density`->`plot_prior.density`, `plot.trait`->`plot_trait` (#2439).
+    * PEcAn.visualization: `plot.netcdf`->`plot_netcdf` (#2526).
 - Stricter package checking: `make check` and CI builds will now fail if `R CMD check` returns any ERRORs or any "newly-added" WARNINGs or NOTEs. "Newly-added" is determined by strict string comparison against a check result saved 2019-09-03; messages that exist in the reference result do not break the build but will be fixed as time allows in future refactorings (#2404).
 - No longer writing an arbitrary num for each PFT, this was breaking ED runs potentially.
 - The pecan/data container has no longer hardcoded path for postgres

base/visualization/DESCRIPTION

@@ -22,12 +22,9 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     efficacy of scientific investigation.
     This module is used to create more complex visualizations from the data
     generated by PEcAn code, specifically the models.
-Depends:
-    ggplot2,
-    raster,
-    sp
 Imports:
     data.table,
+    ggplot2,
     maps,
     ncdf4 (>= 1.15),
     PEcAn.DB,
@@ -40,6 +37,8 @@ Imports:
 Suggests:
     grid,
     png,
+    raster,
+    sp,
     testthat (>= 1.0.2)
 License: BSD_3_clause + file LICENSE
 Copyright: Authors

base/visualization/NAMESPACE

@@ -4,5 +4,5 @@ export(add_icon)
 export(ciEnvelope)
 export(create_status_page)
 export(map.output)
-export(plot.netcdf)
+export(plot_netcdf)
 export(vwReg)

base/visualization/R/ciEnvelope.R

@@ -3,7 +3,9 @@
 #' @param x Vector defining CI center
 #' @param ylo Vector defining bottom of CI envelope
 #' @param yhi Vector defining top of CI envelope
-#' @export 
+#' @param ... further arguments passed on to `graphics::polygon`
+#'
+#' @export
 #' @author Michael Dietze, David LeBauer
 ciEnvelope <- function(x, ylo, yhi, ...) {
   m   <- rbind(x, ylo, yhi)
@@ -30,6 +32,7 @@ ciEnvelope <- function(x, ylo, yhi, ...) {
     x <- sub.m[[i]]["x", ]
     ylo <- sub.m[[i]]["ylo", ]
     yhi <- sub.m[[i]]["yhi", ]
-    polygon(cbind(c(x, rev(x), x[1]), c(ylo, rev(yhi), ylo[1])), border = NA, ...)
+    graphics::polygon(
+      cbind(c(x, rev(x), x[1]), c(ylo, rev(yhi), ylo[1])), border = NA, ...)
   }
 } # ciEnvelope

base/visualization/R/create_status_page.R

@@ -95,7 +95,7 @@ create_status_page <- function(config_file, file_prefix='status', delta=3600) {
     lastdump <- 0 # never dumped
     if(RCurl::url.exists(version_url)) {
       temporaryFile <- tempfile()
-      download.file(version_url, destfile = temporaryFile, quiet = TRUE)
+      utils::download.file(version_url, destfile = temporaryFile, quiet = TRUE)
       version <- scan(temporaryFile,what = "character", sep = "\t", quiet = TRUE)
       unlink(temporaryFile)
 
@@ -113,8 +113,8 @@ create_status_page <- function(config_file, file_prefix='status', delta=3600) {
         # check if the schema has been updated, if so log the event
         if ((hostname %in% nodes) && (nodes[[hostname]]['schema'] != schema)) {
           msg <- paste(Sys.time(), "SCHEMA UPDATE DETECTED ON NODE", x$sync_host_id, hostname,
-                       "FROM", nodeinfo[[hostname]]['schema'], "TO", schema)
-          write(msg, file=paste0(file_prefix, ".log"), append=TRUE)
+                       "FROM", nodes[[hostname]]['schema'], "TO", schema)
+          write(msg, file = paste0(file_prefix, ".log"), append = TRUE)
         }
       }
     }
@@ -124,7 +124,7 @@ create_status_page <- function(config_file, file_prefix='status', delta=3600) {
     sync <- list()
     if (RCurl::url.exists(log_url)) {
       temporaryFile <- tempfile()
-      download.file(log_url, destfile = temporaryFile, quiet = TRUE)
+      utils::download.file(log_url, destfile = temporaryFile, quiet = TRUE)
       log <- scan(temporaryFile,what = "character", sep = "\n", quiet = TRUE)
       unlink(temporaryFile)
 
@@ -176,30 +176,38 @@ create_status_page <- function(config_file, file_prefix='status', delta=3600) {
   save(geoinfo, schema_versions, nodes, file=paste0(file_prefix, ".RData"))
 
   ## create image
-  png(filename=paste0(file_prefix, ".png"), width=1200)
-  xlim <- extendrange(sapply(nodes, function(x) { x$lon }), f=1)
-  ylim <- extendrange(sapply(nodes, function(x) { x$lat }), f=1)
-  maps::map("world", xlim=xlim, ylim=ylim)
-  maps::map("state",add=TRUE)
+  grDevices::png(filename = paste0(file_prefix, ".png"), width = 1200)
+  xlim <- grDevices::extendrange(sapply(nodes, function(x) { x$lon }), f = 1)
+  ylim <- grDevices::extendrange(sapply(nodes, function(x) { x$lat }), f = 1)
+  maps::map("world", xlim = xlim, ylim = ylim)
+  maps::map("state", add = TRUE)
 
   # show all edges
   edgecolors <- c("green","red", "yellow")
   x <- lapply(nodes, function(x) {
     lapply(x$sync, function(y) {
-      segments((x$lon+nodes[[y$id]]$lon)/2, ( x$lat+nodes[[y$id]]$lat)/2, x$lon, x$lat, col=edgecolors[y$status+1], lwd=2)
+      graphics::segments(
+        (x$lon + nodes[[y$id]]$lon) / 2,
+        (x$lat + nodes[[y$id]]$lat) / 2,
+        x$lon,
+        x$lat,
+        col = edgecolors[y$status + 1], lwd = 2)
     })
   })
 
   # show all pecan sites
-  nodecolors <- c("green","yellow", "red")
+  nodecolors <- c("green", "yellow", "red")
   x <- lapply(nodes, function(x) {
-    points(x$lon, x$lat, col=nodecolors[x$state+1], pch=19, cex=3)
-    text(x$lon, x$lat, labels=x$sync_host_id)
+    graphics::points(
+      x$lon, x$lat,
+      col = nodecolors[x$state + 1],
+      pch = 19, cex = 3)
+    graphics::text(x$lon, x$lat, labels = x$sync_host_id)
   })
 
   # graph done
-  text(xlim[1], ylim[1], labels = Sys.time(), pos=4)
-  dev.off()
+  graphics::text(xlim[1], ylim[1], labels = Sys.time(), pos = 4)
+  grDevices::dev.off()
 
   ## create html file
   htmltable <- '<html>'

base/visualization/R/map.output.R

@@ -7,16 +7,24 @@
 #' @author David LeBauer
 map.output <- function(table, variable) {
   if (any(table$lat < 0) | any(table$lon > 0)) {
-    world <- data.table::data.table(map_data("world"))
+    world <- data.table::data.table(ggplot2::map_data("world"))
   } else {
-    world <- data.table::data.table(map_data("usa"))
+    world <- data.table::data.table(ggplot2::map_data("usa"))
   }
-  map <- ggplot() + 
-    geom_polygon(data = world, aes(x = long, y = lat, group = group), fill = "white", color = "darkgrey") + 
-    geom_point(data = table, aes(x = lon, y = lat, color = table[, variable]), size = 5) + 
-    scale_color_gradientn(colours = c("red", "orange", "yellow", "green", "blue", "violet")) +
-    theme_bw() + 
-    xlim(range(pretty(table$lon))) + 
-    ylim(range(pretty(table$lat)))
+  map <- ggplot2::ggplot() +
+    ggplot2::geom_polygon(
+      data = world,
+      ggplot2::aes(x = long, y = lat, group = group),
+      fill = "white",
+      color = "darkgrey") +
+    ggplot2::geom_point(
+      data = table,
+      ggplot2::aes(x = lon, y = lat, color = table[, variable]),
+      size = 5) +
+    ggplot2::scale_color_gradientn(
+      colours = c("red", "orange", "yellow", "green", "blue", "violet")) +
+    ggplot2::theme_bw() +
+    ggplot2::xlim(range(pretty(table$lon))) +
+    ggplot2::ylim(range(pretty(table$lat)))
   return(map)
 }  # map.output

base/visualization/R/plot.netcdf.R → base/visualization/R/plot_netcdf.R

@@ -33,7 +33,7 @@ data.fetch <- function(var, nc, fun = mean) {
 
   # aggregate the data
   data <- ncdf4::ncvar_get(nc, var)
-  val  <- aggregate(data[indices], by = aggrlist, FUN = fun)$x
+  val  <- stats::aggregate(data[indices], by = aggrlist, FUN = fun)$x
 
   # get the label
   title <- nc$var[[var]]$longname
@@ -59,11 +59,10 @@ data.fetch <- function(var, nc, fun = mean) {
 
 ##' Load the tower dataset and create a plot.
 ##'
-##' \code{plot.hdf5} loads the tower data from an HDF5 file generated by
+##' Loads the tower data from an HDF5 file generated by
 ##' ED and will plot the values against one another. The default is for
 ##' the given variable to be plotted against time.
 ##'
-##' @name plot.hdf5
 ##' @param datafile the specific datafile to use.
 ##' @param yvar the variable to plot along the y-axis.
 ##' @param xvar the variable to plot along the x-axis, by default time is
@@ -72,11 +71,13 @@ data.fetch <- function(var, nc, fun = mean) {
 ##' @param height the height of the image generated, default is 600 pixels.
 ##' @param filename is the name of the file name that is geneated, this
 ##'        can be null to use existing device, otherwise it will try and
-# @' create an image based on filename, or display if x11.
+##'        create an image based on filename, or display if x11.
 ##' @param year the year this data is for (only used in the title).
+##'
+##' @aliases plot.netcdf
 ##' @export
 ##' @author Rob Kooper
-plot.netcdf <- function(datafile, yvar, xvar = "time", width = 800, height = 600, 
+plot_netcdf <- function(datafile, yvar, xvar = "time", width = 800, height = 600,
                         filename = NULL, year = NULL) {
   # open netcdf file
   nc <- ncdf4::nc_open(datafile)
@@ -90,33 +91,33 @@ plot.netcdf <- function(datafile, yvar, xvar = "time", width = 800, height = 600
   # setup output
   if (!is.null(filename)) {
     if (tolower(filename) == "x11") {
-      x11(width = width / 96, height = height / 96)
+      grDevices::x11(width = width / 96, height = height / 96)
     } else if (tolower(stringr::str_sub(filename, -4)) == ".png") {
-      png(filename = filename, width = width, height = height)
+      grDevices::png(filename = filename, width = width, height = height)
     } else if (tolower(stringr::str_sub(filename, -4)) == ".pdf") {
-      pdf(filename = filename, width = width, height = height)
+      grDevices::pdf(file = filename, width = width, height = height)
     } else if (tolower(stringr::str_sub(filename, -4)) == ".jpg") {
-      jpg(filename = filename, width = width, height = height)
+      grDevices::jpeg(filename = filename, width = width, height = height)
     } else if (tolower(stringr::str_sub(filename, -5)) == ".tiff") {
-      tiff(filename = filename, width = width, height = height)
+      grDevices::tiff(filename = filename, width = width, height = height)
     }
   }
 
   # setup plot (needs to be done before removing of NA since that removes attr as well).
-  plot.new()
-  title(xlab = attr(xval_mean, "lbl"))
-  title(ylab = attr(yval_mean, "lbl"))
+  graphics::plot.new()
+  graphics::title(xlab = attr(xval_mean, "lbl"))
+  graphics::title(ylab = attr(yval_mean, "lbl"))
   if (xvar == "time") {
     if (is.null(year)) {
-      title(main = nc$var[[yvar]]$longname)
+      graphics::title(main = nc$var[[yvar]]$longname)
     } else {
-      title(main = paste(nc$var[[yvar]]$longname, "for", year))
+      graphics::title(main = paste(nc$var[[yvar]]$longname, "for", year))
     }
   } else {
     if (is.null(year)) {
-      title(main = paste(xvar, "VS", yvar))
+      graphics::title(main = paste(xvar, "VS", yvar))
     } else {
-      title(main = paste(xvar, "VS", yvar, "for", year))
+      graphics::title(main = paste(xvar, "VS", yvar, "for", year))
     }
   }
   # done with netcdf file
@@ -139,29 +140,35 @@ plot.netcdf <- function(datafile, yvar, xvar = "time", width = 800, height = 600
   o <- order(xval_mean, yval_mean)
 
   # plot actual data
-  plot.window(xlim = c(min(xval_mean), max(xval_mean)),
+  graphics::plot.window(xlim = c(min(xval_mean), max(xval_mean)),
               ylim = c(min(yvals), max(yvals)))
-  polygon(c(xval_mean[o], rev(xval_mean[o])), 
-          c(yval_max[o], rev(yval_min[o])), 
-          col = "gray", 
-          border = "black")
-  lines(x = xval_mean[o], y = yval_mean[o], col = "red")
-  points(x = xval_mean[o], y = yval_mean[o], col = "black", pch = ".", cex = 5)
-
+  graphics::polygon(
+    c(xval_mean[o], rev(xval_mean[o])),
+    c(yval_max[o], rev(yval_min[o])),
+    col = "gray",
+    border = "black")
+  graphics::lines(x = xval_mean[o], y = yval_mean[o], col = "red")
+  graphics::points(
+    x = xval_mean[o],
+    y = yval_mean[o],
+    col = "black",
+    pch = ".",
+    cex = 5)
+
   # legend
-  legend("bottomright", col = c(1, "gray"), lwd = c(3, 6), 
-         legend = c("mean", "min/max"), 
+  graphics::legend("bottomright", col = c(1, "gray"), lwd = c(3, 6),
+         legend = c("mean", "min/max"),
          cex = 1.5)
-  
+
   # draw axis and box
-  axis(1)
-  axis(2)
-  box()
-  
+  graphics::axis(1)
+  graphics::axis(2)
+  graphics::box()
+
   ## add PEcAn icon
   add_icon()
-  
+
   if (!is.null(filename) && (tolower(filename) != "x11")) {
-    dev.off()
+    grDevices::dev.off()
   }
-}  # plot.netcdf
+}  # plot_netcdf