diff --git a/NAMESPACE b/NAMESPACE index 1153623fd38fe20490d13a0858e13240f1643154..7e313bc5e0cdbdfbd3f2735c6958745477e20276 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,5 +1,6 @@ # Generated by roxygen2: do not edit by hand +export(AdamontAnalog) export(Analogs) export(BEI_PDFBest) export(BEI_Weights) @@ -113,4 +114,4 @@ importFrom(utils,head) importFrom(utils,read.table) importFrom(utils,tail) importFrom(verification,verify) -useDynLib(CSTools, .registration=TRUE) +useDynLib(CSTools) diff --git a/NEWS.md b/NEWS.md index 3b1244c0197d66462829f98b8c6209b787a4309b..23d198894d3d5db5510465662479fd0a6947b591 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,8 @@ **Submission date to CRAN: XX-12-2020** - New features: + + ADAMONT downscaling method: requires CST_AdamontAnalogs and CST_AdamontQQCor functions + + Analogs method using Predictors: requires training_analogs and CST_AnalogsPredictors + PlotPDFsOLE includes parameters to modify legend style + CST_RFSlope handless missing values in the temporal dimension and new 'ncores' parameter allows parallel computation + CST_RFWeights accepts s2dv_cube objects as input and new 'ncores' paramenter allows parallel computation @@ -25,6 +27,7 @@ + Figures resize option from vignettes has been removed + Fix Analogs to work with three diferent criteria + Vignette PlotForecastPDF updated plots + + Decrease package size compresing vignettes figures and removing areave_data sample ### CSTools 3.1.0 **Submission date to CRAN: 02-07-2020** diff --git a/R/CST_AdamontAnalog.R b/R/CST_AdamontAnalog.R index 104913acd04a8bab563a67999963dc3c7f7dd925..1238b3b19b7d1757c6313427674de160c76f1558 100644 --- a/R/CST_AdamontAnalog.R +++ b/R/CST_AdamontAnalog.R @@ -7,12 +7,16 @@ #'@author Paola Marson, \email{paola.marson@meteo.fr} for PROSNOW version #'@author Lauriane Batté, \email{lauriane.batte@meteo.fr} for CSTools adaptation #' -#'@param exp experiment data an object of class \code{s2dv_cube}, can be output -#'from quantile correction using CST_AdamontQQCorr.R +#'@param exp \itemize{ +#'\item\code{CST_AdamontAnalog}{experiment data an object of class \code{s2dv_cube}, can be output +#'from quantile correction using CST_AdamontQQCorr} +#'\item\code{AdamontAnalog}{experiment data array with named dimension}} #'@param wt_exp corresponding weather types (same dimensions as \code{exp$data} #'but lat/lon) -#'@param obs reference data, also of class \code{s2dv_cube}. Note that lat/lon -#'dimensions need to be the same as \code{exp} +#'@param obs \itemize{ +#'\item\code{CST_AdamontAnalog}{reference data, also of class \code{s2dv_cube}.} +#'\item\code{AdamontAnalog}{reference data array with named dimension.}} +#'Note that lat/lon dimensions need to be the same as \code{exp} #'@param wt_obs corresponding weather types (same dimensions as \code{obs$data} #'but lat/lon) #'@param nanalogs integer defining the number of analog values to return @@ -29,8 +33,11 @@ #'searched for #'@param londim name of longitude dimension #'@param latdim name of latitude dimension -#'@return analog_vals an object of class \code{s2dv_cube} containing nanalogs -#'analog values for each value of \code{exp} input data +#'@return analog_vals +#'\itemize{ +#'\item\code{CST_AdamontAnalog}{an object of class \code{s2dv_cube} containing nanalogs +#'analog values for each value of \code{exp} input data} +#'\item\code{AdamontAnalog}{an array containing nanalogs analog values}} #'@import multiApply #'@importFrom s2dverification Subset #'@examples @@ -41,6 +48,15 @@ #'dim(wt_obs) <- c(dataset=1, member=1, sdate=6, ftime=3) # analog_vals <- CST_AdamontAnalog(exp=lonlat_data$exp, obs=lonlat_data$obs, wt_exp=wt_exp, wt_obs=wt_obs, nanalogs=2) #'} +#'\dontrun{ +#'wt_exp <- sample(1:3, 15*6*3, replace=T) +#'dim(wt_exp) <- c(dataset=1, member=15, sdate=6, ftime=3) +#'wt_obs <- sample(1:3, 6*3, replace=T) +#'dim(wt_obs) <- c(dataset=1, member=1, sdate=6, ftime=3) +# analog_vals <- AdamontAnalog(exp=lonlat_data$exp$data, +#' obs=lonlat_data$obs$data, wt_exp=wt_exp, wt_obs=wt_obs, nanalogs=2) +#'} + CST_AdamontAnalog <- function(exp, obs, wt_exp, wt_obs, nanalogs, method = 'pattcorr', thres = NULL, search_obsdims = c('member', 'sdate', 'ftime'), @@ -98,50 +114,10 @@ CST_AdamontAnalog <- function(exp, obs, wt_exp, wt_obs, nanalogs, #'AdamontAnalog finds analogous data in the reference dataset to experiment data #'based on weather types #' -#'@description This function searches for analogs in a reference dataset for -#'experiment data, based on corresponding weather types. The experiment data is -#'typically a hindcast, observations are typically provided by reanalysis data. -#'@author Paola Marson, \email{paola.marson@meteo.fr} for PROSNOW version -#'@author Lauriane Batté, \email{lauriane.batte@meteo.fr} for CSTools adaptation -#' -#'@param exp experiment data, such as \code{$data} array of an object of class -#'\code{s2dv_cube}, can be output from quantile correction using -#'\code{CST_AdamontQQCorr.R} -#'@param wt_exp corresponding weather types (same dimensions as \code{exp} but -#'lat/lon) -#'@param obs reference data, can also be \code{$data} array of class -#'\code{s2dv_cube}. Note that lat/lon dimensions need to be the same as -#'\code{exp} -#'@param wt_obs corresponding weather types (same dimensions as \code{obs} but * -#'lat/lon) -#'@param nanalogs integer defining the number of analog values to return -#'(default: 5) -#'@param method a character string indicating the method used for analog -#'definition -#' Coded are 'pattcorr': pattern correlation -#' 'rain1' (for precip patterns): rain occurrence consistency -#' 'rain01' (for precip patterns): rain occurrence/non -#' occurrence consistency -#'@param thres real number indicating the threshold to define rain occurrence -#'/non occurrence in rain(0)1 -#'@param search_obsdims list of dimensions in \code{obs} along which analogs are -#'searched for -#'@param londim name of longitude dimension -#'@param latdim name of latitude dimension -#'@return analog_vals an object of class \code{s2dv_cube} containing nanalogs -#'analog values for each value of \code{exp} input data #'@import multiApply #'@importFrom s2dverification Subset -#'@examples -#'\dontrun{ -#'wt_exp <- sample(1:3, 15*6*3, replace=T) -#'dim(wt_exp) <- c(dataset=1, member=15, sdate=6, ftime=3) -#'wt_obs <- sample(1:3, 6*3, replace=T) -#'dim(wt_obs) <- c(dataset=1, member=1, sdate=6, ftime=3) -# analog_vals <- AdamontAnalog(exp=lonlat_data$exp$data, -#' obs=lonlat_data$obs$data, wt_exp=wt_exp, wt_obs=wt_obs, nanalogs=2) -#'} - +#'@rdname CST_AdamontAnalog +#'@export AdamontAnalog <- function(exp, obs, wt_exp, wt_obs, nanalogs=5, method = 'pattcorr', thres = NULL, search_obsdims = c('member', 'sdate', 'ftime'), diff --git a/R/sample_data.R b/R/sample_data.R index 3a59ec1b546be9aa6212741fb1069ec76a5e8a0d..666c0143b701e2ecd47d53178ddbe9926d8d02a1 100644 --- a/R/sample_data.R +++ b/R/sample_data.R @@ -63,42 +63,3 @@ NULL #' @author Jost von Hardenberg \email{j.vonhardenberg@isac.cnr.it} #' @keywords data NULL - -#' Sample Of Experimental And Observational Climate Data Averaged Over A Region -#' -#' This sample data set contains area-averaged seasonal forecast and corresponding observational data from the Copernicus Climate Change ECMWF-System 5 forecast system, and from the Copernicus Climate Change ERA-5 reconstruction. Specifically, for the 'tas' (2-meter temperature) variable, for the 15 first forecast ensemble members, monthly averaged, for the 3 first forecast time steps (lead months 1 to 4) of the November start dates of 2000 to 2005, for the Mediterranean region (27N-48N, 12W-40E). -#' -#' It is recommended to use the data set as follows: -#'\preformatted{ -#' require(zeallot) -#' c(exp, obs) %<-% CSTools::areave_data -#'} -#' -#' The `CST_Load` call used to generate the data set in the infrastructure of the Earth Sciences Department of the Barcelona Supercomputing Center is shown next. Note that `CST_Load` internally calls `s2dverification::Load`, which would require a configuration file (not provided here) expressing the distribution of the 'system5c3s' and 'era5' NetCDF files in the file system. -#'\preformatted{ -#' library(CSTools) -#' require(zeallot) -#' -#' startDates <- c('20001101', '20011101', '20021101', -#' '20031101', '20041101', '20051101') -#' -#' areave_data <- -#' CST_Load( -#' var = 'tas', -#' exp = 'system5c3s', -#' obs = 'era5', -#' nmember = 15, -#' sdates = startDates, -#' leadtimemax = 3, -#' latmin = 27, latmax = 48, -#' lonmin = -12, lonmax = 40, -#' output = 'areave', -#' nprocs = 1 -#' ) -#'} -#' -#' @name areave_data -#' @docType data -#' @author Nicolau Manubens \email{nicolau.manubens@bsc.es} -#' @keywords data -NULL diff --git a/data/areave_data.RData b/data/areave_data.RData deleted file mode 100644 index 426d4e165fada19e79a8a6912cc78124b24fd9f1..0000000000000000000000000000000000000000 Binary files a/data/areave_data.RData and /dev/null differ diff --git a/man/AdamontAnalog.Rd b/man/AdamontAnalog.Rd deleted file mode 100644 index 728ed9bccf2ab7eb6c74b37cbc5bef377817bbd8..0000000000000000000000000000000000000000 --- a/man/AdamontAnalog.Rd +++ /dev/null @@ -1,78 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/CST_AdamontAnalog.R -\name{AdamontAnalog} -\alias{AdamontAnalog} -\title{AdamontAnalog finds analogous data in the reference dataset to experiment data -based on weather types} -\usage{ -AdamontAnalog( - exp, - obs, - wt_exp, - wt_obs, - nanalogs = 5, - method = "pattcorr", - thres = NULL, - search_obsdims = c("member", "sdate", "ftime"), - londim = "lon", - latdim = "lat" -) -} -\arguments{ -\item{exp}{experiment data, such as \code{$data} array of an object of class -\code{s2dv_cube}, can be output from quantile correction using -\code{CST_AdamontQQCorr.R}} - -\item{obs}{reference data, can also be \code{$data} array of class -\code{s2dv_cube}. Note that lat/lon dimensions need to be the same as -\code{exp}} - -\item{wt_exp}{corresponding weather types (same dimensions as \code{exp} but -lat/lon)} - -\item{wt_obs}{corresponding weather types (same dimensions as \code{obs} but * -lat/lon)} - -\item{nanalogs}{integer defining the number of analog values to return -(default: 5)} - -\item{method}{a character string indicating the method used for analog -definition - Coded are 'pattcorr': pattern correlation - 'rain1' (for precip patterns): rain occurrence consistency - 'rain01' (for precip patterns): rain occurrence/non - occurrence consistency} - -\item{thres}{real number indicating the threshold to define rain occurrence -/non occurrence in rain(0)1} - -\item{search_obsdims}{list of dimensions in \code{obs} along which analogs are -searched for} - -\item{londim}{name of longitude dimension} - -\item{latdim}{name of latitude dimension} -} -\value{ -analog_vals an object of class \code{s2dv_cube} containing nanalogs -analog values for each value of \code{exp} input data -} -\description{ -This function searches for analogs in a reference dataset for -experiment data, based on corresponding weather types. The experiment data is -typically a hindcast, observations are typically provided by reanalysis data. -} -\examples{ -\dontrun{ -wt_exp <- sample(1:3, 15*6*3, replace=T) -dim(wt_exp) <- c(dataset=1, member=15, sdate=6, ftime=3) -wt_obs <- sample(1:3, 6*3, replace=T) -dim(wt_obs) <- c(dataset=1, member=1, sdate=6, ftime=3) - obs=lonlat_data$obs$data, wt_exp=wt_exp, wt_obs=wt_obs, nanalogs=2) -} -} -\author{ -Paola Marson, \email{paola.marson@meteo.fr} for PROSNOW version - -Lauriane Batté, \email{lauriane.batte@meteo.fr} for CSTools adaptation -} diff --git a/man/CST_AdamontAnalog.Rd b/man/CST_AdamontAnalog.Rd index 7d10ae02e62255e74ee3e17553f5a6da716b8a54..91372564305a9a0a77f6279ca393fd72c2014292 100644 --- a/man/CST_AdamontAnalog.Rd +++ b/man/CST_AdamontAnalog.Rd @@ -2,6 +2,7 @@ % Please edit documentation in R/CST_AdamontAnalog.R \name{CST_AdamontAnalog} \alias{CST_AdamontAnalog} +\alias{AdamontAnalog} \title{CST_AdamontAnalog finds analogous data in the reference dataset to experiment data based on weather types} \usage{ @@ -17,13 +18,30 @@ CST_AdamontAnalog( londim = "lon", latdim = "lat" ) + +AdamontAnalog( + exp, + obs, + wt_exp, + wt_obs, + nanalogs = 5, + method = "pattcorr", + thres = NULL, + search_obsdims = c("member", "sdate", "ftime"), + londim = "lon", + latdim = "lat" +) } \arguments{ -\item{exp}{experiment data an object of class \code{s2dv_cube}, can be output -from quantile correction using CST_AdamontQQCorr.R} +\item{exp}{\itemize{ +\item\code{CST_AdamontAnalog}{experiment data an object of class \code{s2dv_cube}, can be output +from quantile correction using CST_AdamontQQCorr} +\item\code{AdamontAnalog}{experiment data array with named dimension}}} -\item{obs}{reference data, also of class \code{s2dv_cube}. Note that lat/lon -dimensions need to be the same as \code{exp}} +\item{obs}{\itemize{ +\item\code{CST_AdamontAnalog}{reference data, also of class \code{s2dv_cube}.} +\item\code{AdamontAnalog}{reference data array with named dimension.}} +Note that lat/lon dimensions need to be the same as \code{exp}} \item{wt_exp}{corresponding weather types (same dimensions as \code{exp$data} but lat/lon)} @@ -52,8 +70,11 @@ searched for} \item{latdim}{name of latitude dimension} } \value{ -analog_vals an object of class \code{s2dv_cube} containing nanalogs -analog values for each value of \code{exp} input data +analog_vals +\itemize{ +\item\code{CST_AdamontAnalog}{an object of class \code{s2dv_cube} containing nanalogs +analog values for each value of \code{exp} input data} +\item\code{AdamontAnalog}{an array containing nanalogs analog values}} } \description{ This function searches for analogs in a reference dataset for @@ -67,6 +88,13 @@ dim(wt_exp) <- c(dataset=1, member=15, sdate=6, ftime=3) wt_obs <- sample(1:3, 6*3, replace=T) dim(wt_obs) <- c(dataset=1, member=1, sdate=6, ftime=3) } +\dontrun{ +wt_exp <- sample(1:3, 15*6*3, replace=T) +dim(wt_exp) <- c(dataset=1, member=15, sdate=6, ftime=3) +wt_obs <- sample(1:3, 6*3, replace=T) +dim(wt_obs) <- c(dataset=1, member=1, sdate=6, ftime=3) + obs=lonlat_data$obs$data, wt_exp=wt_exp, wt_obs=wt_obs, nanalogs=2) +} } \author{ Paola Marson, \email{paola.marson@meteo.fr} for PROSNOW version diff --git a/man/areave_data.Rd b/man/areave_data.Rd deleted file mode 100644 index a772220a9e3a7a19a02186938bd9b4f2e72fbc5c..0000000000000000000000000000000000000000 --- a/man/areave_data.Rd +++ /dev/null @@ -1,43 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/sample_data.R -\docType{data} -\name{areave_data} -\alias{areave_data} -\title{Sample Of Experimental And Observational Climate Data Averaged Over A Region} -\description{ -This sample data set contains area-averaged seasonal forecast and corresponding observational data from the Copernicus Climate Change ECMWF-System 5 forecast system, and from the Copernicus Climate Change ERA-5 reconstruction. Specifically, for the 'tas' (2-meter temperature) variable, for the 15 first forecast ensemble members, monthly averaged, for the 3 first forecast time steps (lead months 1 to 4) of the November start dates of 2000 to 2005, for the Mediterranean region (27N-48N, 12W-40E). -} -\details{ -It is recommended to use the data set as follows: -\preformatted{ -require(zeallot) -c(exp, obs) %<-% CSTools::areave_data -} - -The `CST_Load` call used to generate the data set in the infrastructure of the Earth Sciences Department of the Barcelona Supercomputing Center is shown next. Note that `CST_Load` internally calls `s2dverification::Load`, which would require a configuration file (not provided here) expressing the distribution of the 'system5c3s' and 'era5' NetCDF files in the file system. -\preformatted{ -library(CSTools) -require(zeallot) - -startDates <- c('20001101', '20011101', '20021101', - '20031101', '20041101', '20051101') - -areave_data <- - CST_Load( - var = 'tas', - exp = 'system5c3s', - obs = 'era5', - nmember = 15, - sdates = startDates, - leadtimemax = 3, - latmin = 27, latmax = 48, - lonmin = -12, lonmax = 40, - output = 'areave', - nprocs = 1 - ) -} -} -\author{ -Nicolau Manubens \email{nicolau.manubens@bsc.es} -} -\keyword{data} diff --git a/vignettes/Analogs_vignette.md b/vignettes/Analogs_vignette.Rmd similarity index 100% rename from vignettes/Analogs_vignette.md rename to vignettes/Analogs_vignette.Rmd diff --git a/vignettes/Figures/Analogs1.png b/vignettes/Figures/Analogs1.png index 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