Newer
Older
Carlos Delgado Torres
committed
#'Compute the Atlantic Multidecadal Variability (AMV) index
#'
#'The Atlantic Multidecadal Variability (AMV), also known as Atlantic
#'Multidecadal Oscillation (AMO), is a mode of natural variability of the sea
#'surface temperatures (SST) over the North Atlantic Ocean on multi-decadal
#'time scales. The AMV index is computed as the difference of weighted-averaged
#'SST anomalies over the North Atlantic region (0ºN-60ºN, 280ºE-360ºE) and the
#'weighted-averaged SST anomalies over 60ºS-60ºN, 0ºE-360ºE (Trenberth &
#'Dennis, 2005; Doblas-Reyes et al., 2013).
Carlos Delgado Torres
committed
#'
Carlos Delgado Torres
committed
#'@param data A numerical array to be used for the index computation with, at least, the
#' dimensions: 1) latitude, longitude, start date and forecast month
#' (in case of decadal predictions), 2) latitude, longitude, year and month
#' (in case of historical simulations or observations). This data has to be
#' provided, at least, over the whole region needed to compute the index.
#'@param data_lats A numeric vector indicating the latitudes of the data.
#'@param data_lons A numeric vector indicating the longitudes of the data.
#'@param type A character string indicating the type of data ('dcpp' for
#' decadal predictions, 'hist' for historical simulations, or 'obs' for
#' observations or reanalyses).
#'@param lat_dim A character string of the name of the latitude dimension. The
#' default value is 'lat'.
#'@param lon_dim A character string of the name of the longitude dimension. The
#' default value is 'lon'.
#'@param mask An array of a mask (with 0's in the grid points that have to be
#' masked) or NULL (i.e., no mask is used). This parameter allows to remove
#' the values over land in case the dataset is a combination of surface air
#' temperature over land and sea surface temperature over the ocean. Also, it
#' can be used to mask those grid points that are missing in the observational
#' dataset for a fair comparison between the forecast system and the reference
#' dataset. The default value is NULL.
#'@param monini An integer indicating the month in which the forecast system is
#' initialized. Only used when parameter 'type' is 'dcpp'. The default value
#' is 11, i.e., initialized in November.
#'@param fmonth_dim A character string indicating the name of the forecast
#' month dimension. Only used if parameter 'type' is 'dcpp'. The default value
#' is 'fmonth'.
#'@param sdate_dim A character string indicating the name of the start date
#' dimension. Only used if parameter 'type' is 'dcpp'. The default value is
#' 'sdate'.
#'@param indices_for_clim A numeric vector of the indices of the years to
#' compute the climatology for calculating the anomalies, or NULL so the
#' climatology is calculated over the whole period. If the data are already
#' anomalies, set it to FALSE. The default value is NULL.\cr
#' In case of parameter 'type' is 'dcpp', 'indices_for_clim' must be relative
#' to the first forecast year, and the climatology is automatically computed
Carlos Delgado Torres
committed
#' over the common calendar period for the different forecast years.
#'@param year_dim A character string indicating the name of the year dimension
#' The default value is 'year'. Only used if parameter 'type' is 'hist' or
#' 'obs'.
#'@param month_dim A character string indicating the name of the month
#' dimension. The default value is 'month'. Only used if parameter 'type' is
#' 'hist' or 'obs'.
#'@param member_dim A character string indicating the name of the member
#' dimension. The default value is 'member'. Only used if parameter 'type' is
#' 'dcpp' or 'hist'.
Carlos Delgado Torres
committed
#'@param na.rm A logical value indicanting whether to remove NA values. The default
#' value is TRUE.
#'@param ncores An integer indicating the number of cores to use for parallel
#' computation. The default value is NULL.
Carlos Delgado Torres
committed
#'
Carlos Delgado Torres
committed
#'@return A numerical array with the AMV index with the same dimensions as data except
#' the lat_dim, lon_dim and fmonth_dim (month_dim) in case of decadal predictions
#' (historical simulations or observations)
Carlos Delgado Torres
committed
#'
#'@examples
#' ## Observations or reanalyses
#' obs <- array(1:100, dim = c(year = 5, lat = 19, lon = 37, month = 12))
#' lat <- seq(-90, 90, 10)
#' lon <- seq(0, 360, 10)
#' index_obs <- AMV(data = obs, data_lats = lat, data_lons = lon, type = 'obs')
Carlos Delgado Torres
committed
#'
#' ## Historical simulations
#' hist <- array(1:100, dim = c(year = 5, lat = 19, lon = 37, month = 12, member = 5))
#' lat <- seq(-90, 90, 10)
#' lon <- seq(0, 360, 10)
#' index_hist <- AMV(data = hist, data_lats = lat, data_lons = lon, type = 'hist')
Carlos Delgado Torres
committed
#'
#' ## Decadal predictions
#' dcpp <- array(1:100, dim = c(sdate = 5, lat = 19, lon = 37, fmonth = 24, member = 5))
#' lat <- seq(-90, 90, 10)
#' lon <- seq(0, 360, 10)
#' index_dcpp <- AMV(data = dcpp, data_lats = lat, data_lons = lon, type = 'dcpp', monini = 1)
#'
#'@importFrom ClimProjDiags WeightedMean
Carlos Delgado Torres
committed
#'@import multiApply
#'@export
AMV <- function(data, data_lats, data_lons, type, lat_dim = 'lat', lon_dim = 'lon',
mask = NULL, monini = 11, fmonth_dim = 'fmonth', sdate_dim = 'sdate',
indices_for_clim = NULL, year_dim = 'year', month_dim = 'month',
Carlos Delgado Torres
committed
na.rm = TRUE, ncores = NULL) {
Carlos Delgado Torres
committed
## Input Checks
# data
if (is.null(data)) {
stop("Parameter 'data' cannot be NULL.")
Carlos Delgado Torres
committed
}
if (!is.numeric(data)) {
stop("Parameter 'data' must be a numeric array.")
Carlos Delgado Torres
committed
}
if (!(class(data_lats) == 'numeric' | class(data_lats) == 'integer')) {
stop("Parameter 'data_lats' must be a numeric vector.")
Carlos Delgado Torres
committed
}
if (!(class(data_lons) == 'numeric' | class(data_lons) == 'integer')) {
stop("Parameter 'data_lons' must be a numeric vector.")
Carlos Delgado Torres
committed
}
# type
if (!type %in% c('dcpp', 'hist', 'obs')) {
stop("Parameter 'type' must be 'dcpp', 'hist', or 'obs'.")
Carlos Delgado Torres
committed
}
# lat_dim
if (!(is.character(lat_dim) & length(lat_dim) == 1)) {
stop("Parameter 'lat_dim' must be a character string.")
Carlos Delgado Torres
committed
}
if (!lat_dim %in% names(dim(data))) {
stop("Parameter 'lat_dim' is not found in 'data' dimension.")
Carlos Delgado Torres
committed
}
# lon_dim
if (!(is.character(lon_dim) & length(lon_dim) == 1)) {
stop("Parameter 'lon_dim' must be a character string.")
Carlos Delgado Torres
committed
}
if (!lon_dim %in% names(dim(data))) {
stop("Parameter 'lon_dim' is not found in 'data' dimension.")
Carlos Delgado Torres
committed
}
# data_lats and data_lons part2
if (dim(data)[lat_dim] != length(data_lats)){
stop(paste0("The latitude dimension of parameter 'data' must be the same",
" length of parameter 'data_lats'."))
Carlos Delgado Torres
committed
}
if (dim(data)[lon_dim] != length(data_lons)){
stop(paste0("The longitude dimension of parameter 'data' must be the same",
" length of parameter 'data_lons'."))
Carlos Delgado Torres
committed
}
# ncores
if (!is.null(ncores)) {
if (!is.numeric(ncores) | ncores %% 1 != 0 | ncores <= 0 |
length(ncores) > 1) {
stop("Parameter 'ncores' must be a positive integer.")
}
}
# mask
if (!is.null(mask)) {
if (is.array(mask) & identical(names(dim(mask)), c(lat_dim,lon_dim)) &
identical(as.integer(dim(mask)), c(length(data_lats), length(data_lons)))) {
Carlos Delgado Torres
committed
## To mask those grid point that are missing in the observations
mask <- s2dv::Reorder(data = mask, order = c(lat_dim, lon_dim))
Carlos Delgado Torres
committed
fun_mask <- function(data, mask){
data[mask == 0] <- NA
return(data)
}
data <- multiApply::Apply(data = data, target_dims = c(lat_dim, lon_dim),
fun = fun_mask, mask = mask, ncores = ncores)$output1
Carlos Delgado Torres
committed
} else {
stop(paste0("Parameter 'mask' must be NULL (no mask) or a numerical array ",
"with c(lat_dim, lon_dim) dimensions and 0 in those grid ",
"points that have to be masked."))
}
}
# monini
if (type == 'dcpp') {
if (!is.numeric(monini) | monini %% 1 != 0 | monini < 1 |
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
stop("Parameter 'monini' must be an integer from 1 to 12.")
}
}
# fmonth_dim
if (type == 'dcpp') {
if (!(is.character(fmonth_dim) & length(fmonth_dim) == 1)) {
stop("Parameter 'fmonth_dim' must be a character string.")
}
if (!fmonth_dim %in% names(dim(data))) {
stop("Parameter 'fmonth_dim' is not found in 'data' dimension.")
}
}
# sdate_dim
if (type == 'dcpp') {
if (!(is.character(sdate_dim) & length(sdate_dim) == 1)) {
stop("Parameter 'sdate_dim' must be a character string.")
}
if (!sdate_dim %in% names(dim(data))) {
stop("Parameter 'sdate_dim' is not found in 'data' dimension.")
}
}
# indices_for_clim
if (!is.null(indices_for_clim)) {
if (!class(indices_for_clim) %in% c('numeric', 'integer')
& !(is.logical(indices_for_clim) & !any(indices_for_clim))) {
stop(paste0("The parameter 'indices_for_clim' must be a numeric vector ",
"or NULL to compute the anomalies based on the whole period, ",
"or FALSE if data are already anomalies"))
}
}
# year_dim
if (type == 'hist' | type == 'obs') {
if (!(is.character(year_dim) & length(year_dim) == 1)) {
stop("Parameter 'year_dim' must be a character string.")
}
if (!year_dim %in% names(dim(data))) {
stop("Parameter 'year_dim' is not found in 'data' dimension.")
}
}
# month_dim
if (type == 'hist' | type == 'obs') {
if (!(is.character(month_dim) & length(month_dim) == 1)) {
stop("Parameter 'month_dim' must be a character string.")
}
if (!month_dim %in% names(dim(data))) {
stop("Parameter 'month_dim' is not found in 'data' dimension.")
}
}
Carlos Delgado Torres
committed
# na.rm
if (!na.rm %in% c(TRUE,FALSE)) {
stop("Parameter 'na.rm' must be TRUE or FALSE")
Carlos Delgado Torres
committed
}
Carlos Delgado Torres
committed
Carlos Delgado Torres
committed
## Regions for AMV (Doblas-Reyes et al., 2013)
lat_min_1 <- 0; lat_max_1 <- 60
lon_min_1 <- 280; lon_max_1 <- 359.9
Carlos Delgado Torres
committed
lon_min_2 <- 0; lon_max_2 <- 359.9
regions <- NULL
regions$reg1 <- c(lon_min_1, lon_max_1, lat_min_1, lat_max_1)
regions$reg2 <- c(lon_min_2, lon_max_2, lat_min_2, lat_max_2)
mean_1 <- ClimProjDiags::WeightedMean(data = data, lon = data_lons, lat = data_lats,
region = regions$reg1,
londim = which(names(dim(data)) == lon_dim),
latdim = which(names(dim(data)) == lat_dim))
mean_2 <- ClimProjDiags::WeightedMean(data = data, lon = data_lons, lat = data_lats,
region = regions$reg2,
londim = which(names(dim(data)) == lon_dim),
latdim = which(names(dim(data)) == lat_dim))
data <- ClimProjDiags::CombineIndices(indices = list(mean_1,mean_2), weights = NULL,
operation = 'subtract') # (mean_1 - mean_2)
Carlos Delgado Torres
committed
Carlos Delgado Torres
committed
if (type == 'dcpp'){
target_dims <- c(sdate_dim, fmonth_dim)
} else if (type %in% c('hist','obs')){
target_dims <- c(year_dim, month_dim)
}
source('/esarchive/scratch/cdelgado/gitlab/s2dv/R/Utils.R')
INDEX <- multiApply::Apply(data = data, target_dims = target_dims, fun = .Indices,
type = type, monini = monini, indices_for_clim = indices_for_clim,
fmonth_dim = fmonth_dim, sdate_dim = sdate_dim,
year_dim = year_dim, month_dim = month_dim,
na.rm = na.rm, ncores = ncores)$output1
Carlos Delgado Torres
committed
return(INDEX)