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|---|---|---|
| @@ -1,9 +1,9 @@ | ||
| Package: visualizeR | ||
| Depends: | ||
| R(>= 3.1.0), | ||
| sm | ||
| sm, | ||
| transformeR(>= 1.2.0) | ||
| Imports: | ||
| transformeR, | ||
| methods, | ||
| fields, | ||
| RColorBrewer, | ||
|
|
@@ -15,15 +15,21 @@ Imports: | |
| SpecsVerification, | ||
| verification, | ||
| sp, | ||
| lattice | ||
| lattice, | ||
| latticeExtra, | ||
| magrittr, | ||
| padr, | ||
| grDevices, | ||
| data.table | ||
| Suggests: | ||
| loadeR.ECOMS, | ||
| loadeR, | ||
| easyVerification, | ||
| knitr | ||
| Type: Package | ||
| Title: Visualizing and Communicating Uncertainty in Seasonal Climate Prediction | ||
| Version: 1.0.0 | ||
| Date: 2017-10-20 | ||
| Version: 1.1.0 | ||
| Date: 2017-12-20 | ||
| Authors@R: as.person(c( | ||
| "Santander Meteorology Group <http://meteo.unican.es> [ctb]", | ||
| "Maria Dolores Frias <[email protected]> [aut, cre]", | ||
|
|
||
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| @@ -1,7 +1,8 @@ | ||
| visualizeR 1.0.0 | ||
| visualizeR 1.1.0 | ||
| ================= | ||
|
|
||
| * Internal adaptation of reliabilityCategories to be consistent with the other functions. | ||
| * Implemented the ROCSS significance in tercilePlot and tercileBarplot. | ||
| * Added CITATION file to Environmental Modelling & Software. | ||
| * New function `spatialPlot` (essentially a renaming of `transformeR::plotClimatology`, the latter planned to be deprecated in future `transformeR` releases) | ||
| * New plotting functions for seasonal forecast products: | ||
| * `tercileMap` for forecast tercile maps (based on C3S seasonal forecast graphical products, http://climate.copernicus.eu/s/charts/c3s_seasonal/) | ||
| * `skillMap`: A convenient wrapper of `SpatialPlot` and `map.stippling` for plotting skill maps | ||
| * Other minor changes and documentation updates. |
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| # skillMap.R Skill maps for seasonal forecasts | ||
| # | ||
| # Copyright (C) 2017 Santander Meteorology Group (http://www.meteo.unican.es) | ||
| # | ||
| # This program is free software: you can redistribute it and/or modify | ||
| # it under the terms of the GNU General Public License as published by | ||
| # the Free Software Foundation, either version 3 of the License, or | ||
| # (at your option) any later version. | ||
| # | ||
| # This program is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
|
|
||
| #' @title A wrapper of \code{spatialPlot} for the creation of verification maps for seasonal forecast systems | ||
| #' | ||
| #' @description A wrapper of \code{spatialPlot} for the creation of verification maps for seasonal forecast systems. | ||
| #' It provides a convenient interface for \code{\link{map.stippling}} | ||
| #' | ||
| #' | ||
| #' @param easyVeriGrid A climatological grid with a verification output. See details | ||
| #' @param stippling A key-value list of arguments passed to \code{map.stippling}: | ||
| #' \code{threshold} and \code{condition}. Ignored by default, returning a map without stippling. | ||
| #' @param stippling.point.options Default to \code{NULL}. Further graphical arguments passed to points | ||
| #' (e.g. \code{cex}, \code{pch} etc.) | ||
| #' @param backdrop.theme See \code{\link{spatialPlot}} | ||
| #' @param title Title of the plot | ||
| #' @param ... Further graphical options passed to \code{\link{spatialPlot}}. | ||
| #' | ||
| #' @details The function applies the \code{\link{spatialPlot}} function, that in turn uses \code{lattice-methods}. | ||
| #' | ||
| #' \strong{Graphical options} | ||
| #' | ||
| #' Some examples of specific map graphical options are available in the help of function \code{\link[sp]{spplot}}. | ||
| #' In addtion, fine-tuning of the resulting plots can be obtained using the arguments of \pkg{lattice} plots. For | ||
| #' an overview, see the help of function \code{\link[lattice]{xyplot}}. | ||
| #' | ||
| #' @seealso The bridging function \code{\link[transformeR]{easyVeri2grid}} from package \pkg{transformeR} allows for | ||
| #' the conversion of verification outputs from package \pkg{easyVerification} to the \code{climate4R} data structure | ||
| #' used by the function. | ||
| #' | ||
| #' Many different aspects of the plot can be controlled passing the relevant arguments to | ||
| #' \code{\link[sp]{spplot}}. | ||
| #' | ||
| #' @return A lattice plot of class \dQuote{trellis}. | ||
| #' | ||
| #' @author J. Bedia | ||
| #' @export | ||
| #' @examples \dontrun{ | ||
| #' | ||
| #' # The package 'easyVerification' will be used to calculate the RPSS: | ||
| #' | ||
| #' require(easyVerification) | ||
| #' require(transformeR) | ||
| #' # First of all, a data subset is done, considering a spatial domain centered on the North Atlantic: | ||
| #' tas.cfs2 <- subsetGrid(tas.cfs, lonLim = c(-100, 40), latLim = c(-5, 75)) | ||
| #' # The same is done with the reanalysis dataset: | ||
| #' tas.ncep2 <- subsetGrid(tas.ncep, lonLim = c(-100, 40), latLim = c(-5, 75)) | ||
| #' # In the next step, the reanalysis data are interpolated to the hindcast grid: | ||
| #' tas.ncep2.int <- interpGrid(tas.ncep2, new.coordinates = getGrid(tas.cfs2), method = "nearest") | ||
| #' # We compute the Ranked Probabiloity SKill Score using veriApply, and a cross-validation strategy: | ||
| #' ev <- easyVerification::veriApply(verifun = "EnsRpss", | ||
| #' fcst = tas.cfs2$Data, | ||
| #' obs = tas.ncep2.int$Data, | ||
| #' prob = 1:2/3, | ||
| #' tdim = 2, | ||
| #' ensdim = 1, | ||
| #' parallel = TRUE, | ||
| #' ncpus = 3, | ||
| #' strategy = "crossval") | ||
| #' # The bridging function 'easyVeri2grid' converts the object returned by 'veriApply' | ||
| #' # to a 'climate4R' climatological grid: | ||
| #' | ||
| #' easyVeriGrid <- easyVeri2grid(ev$skillscore, | ||
| #' obs.grid = tas.ncep2.int, | ||
| #' verifun = "EnsRpss") | ||
| #' | ||
| #' # A basic RPSS map, using the spatialPlot defaults: | ||
| #' skillMap(easyVeriGrid = easyVeriGrid, backdrop.theme = "coastline") | ||
| #' | ||
| #' # Stippling. Mark significant RPSS values at the 95% ci | ||
| #' thresh <- ev$skillscore.sd*qnorm(0.95) | ||
| #' | ||
| #' skillMap(easyVeriGrid = easyVeriGrid, | ||
| #' stippling = list(threshold = th, condition = "GT"), # GT = greater than | ||
| #' stippling.point.options = list(pch = 19, cex = .2, col = "black"), | ||
| #' backdrop.theme = "coastline") | ||
| #' | ||
| #' # Further customization: For instance a more elaborated title, colorblind-friendly palette etc.: | ||
| #' | ||
| #' cb.colors <- colorRampPalette(rev(RColorBrewer::brewer.pal(11, "Spectral"))) | ||
| #' skillMap(easyVeriGrid = easyVeriGrid, | ||
| #' stippling = list(threshold = th, condition = "GT"), | ||
| #' stippling.point.options = list(pch = 19, cex = .2, col = "black"), | ||
| #' backdrop.theme = "coastline", | ||
| #' at = seq(-0.7, 0.7, .05), | ||
| #' set.max = 0.7, set.min = -0.7, | ||
| #' scales = list(draw = TRUE, alternating = 3), | ||
| #' colorkey = list(space = "bottom"), | ||
| #' col.regions = cb.colors(51), | ||
| #' title = paste("Ranked Probability Skill Score", | ||
| #' "Forecasting System: CFSv2 - 24 members", | ||
| #' "November Initializations", | ||
| #' "Observing System: NCEP/NCAR Reanalysis 1", | ||
| #' "t2m DJF 1983-2010", sep = "\n") | ||
| #' ) | ||
| #' } | ||
|
|
||
| skillMap <- function(easyVeriGrid, | ||
| stippling = list(threshold = NULL, condition = NULL), | ||
| stippling.point.options = NULL, | ||
| backdrop.theme = NULL, | ||
| title = NULL, | ||
| ...) { | ||
| arg.list <- list(...) | ||
| arg.list[["grid"]] <- easyVeriGrid | ||
| if (!is.null(stippling$threshold)) { | ||
| stippling[["clim"]] <- easyVeriGrid | ||
| if (!is.null(stippling.point.options)) { | ||
| stippling <- c(stippling, stippling.point.options) | ||
| } | ||
| stip.list <- list(do.call("map.stippling", stippling)) | ||
| if ("sp.layout" %in% names(arg.list)) { | ||
| arg.list[["sp.layout"]] <- c(arg.list[["sp.layout"]], stip.list) | ||
| } else { | ||
| arg.list[["sp.layout"]] <- stip.list | ||
| } | ||
| } | ||
| if (!is.null(backdrop.theme)) { | ||
| arg.list[["backdrop.theme"]] <- backdrop.theme | ||
| } | ||
| if (!is.null(title)) { | ||
| arg.list[["main"]] <- list(label = title, | ||
| cex = .9, | ||
| col = "blue", | ||
| font = 1, | ||
| just = "left", x = 0.05) | ||
| } | ||
| map <- do.call("spatialPlot", arg.list) | ||
| print(map) | ||
| } |
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