From f7dab663dd139d2c0c96169015390a370321616f Mon Sep 17 00:00:00 2001 From: Eva Rifa Date: Fri, 17 Nov 2023 18:01:08 +0100 Subject: [PATCH 1/6] Develop v 1.1.0 --- DESCRIPTION | 2 +- NEWS.md | 31 +++++-- inst/doc/paper-figure-PlotForecastPDF.R | 104 ------------------------ 3 files changed, 27 insertions(+), 110 deletions(-) delete mode 100644 inst/doc/paper-figure-PlotForecastPDF.R diff --git a/DESCRIPTION b/DESCRIPTION index b716d5d..a54bf19 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: CSIndicators Title: Climate Services' Indicators Based on Sub-Seasonal to Decadal Predictions -Version: 1.0.1 +Version: 1.1.0 Authors@R: c( person("Eva", "Rifà", , "eva.rifarovira@bsc.es", role = c("cre")), person("Nuria", "Perez-Zanon", , "nuria.perez@bsc.es", role = c("aut"), comment = c(ORCID = "0000-0001-8568-3071")), diff --git a/NEWS.md b/NEWS.md index 44285d2..3f6308b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,19 +1,40 @@ +# CSIndicators 1.1.0 (Release date: 2023-11-20) + +### Fixes +- Improve CST_PeriodMean() and CST_PeriodAccumulation() in order that Dates from the s2dv_cube reflect time aggregation. +- Correct output coordinates consistency (coords element) in CST functions +- Include again ClimProjDiags and s2dv dependency due to a dependency issue with an external package. +- Change default value of time_dim to be 'time' in all the function. +- Improve documentation of function MergeRefToExp mentioned the method used. + +### New features +- Include new publication in documentation. +- Change to testthat edition 3. +- Add 'memb_dim' parameter to MergeRefToExp. +- Add reference and improve documentation in MergeRefToExp. +- Substitute CST_Load by CST_Start in vignettes. +- New functions to compute SPEI: PeriodPET, PeriodAccumulation with rolling accumulation and PeriodStandardization. +- New functions to compute bioclimatic indicators: PeriodMax, PeriodMin and PeriodVariance. + # CSIndicators 1.0.1 (Release date: 2023-05-18) -**Fixes** + +### Fixes - Add EnergyIndicators vignette figures - Remove ClimProjDiags dependency - Remove s2dv dependency -# CSIndicators 1.0.0 (Release date: 2023-04-05) -**Fixes** +# CSIndicators 1.0.0 (Release date: 2023-04-05) + +### Fixes - Correct vignettes figures links. -**New features** +### New features - Exceeding Threshold functions to allow between thresholds or equal threshold options. - New s2dv_cube object development for all the functions, unit tests, examples and vignettes. # CSIndicators 0.0.2 (Release date: 2022-10-21) -**Fixes** + +### Fixes - Correct figures of EnergyIndicators vignette. - Sanity check correction in functions CST_PeriodAccumulation, CST_AbsToProbs, CST_AccumulationExceedingThreshold, CST_MergeRefToExp, CST_PeriodMean, CST_QThreshold, CST_SelectPeriodOnData, CST_Threshold, TotalSpellTimeExceedingThreshold, CST_TotalTimeExceedingThreshold, CST_WindCapacityFactor and CST_WindPowerDensity. - Revise examples using s2dv::InsertDim in MergeRefToExp(). diff --git a/inst/doc/paper-figure-PlotForecastPDF.R b/inst/doc/paper-figure-PlotForecastPDF.R deleted file mode 100644 index bebc497..0000000 --- a/inst/doc/paper-figure-PlotForecastPDF.R +++ /dev/null @@ -1,104 +0,0 @@ -rm(list=ls()) - -### Creation date: January 2023 -# Author: N. Pérez-Zanón -# For CSIndicators package manuscript -# ---------------------------------------- -# Figure 1. sprR probability distribution of the forecast initialised on the 1st -# of April 2022 for the western Iberian peninsula. The daily values of the -# hindcast and forecast have been corrected before calculating the sprR and the -# spatial aggregation. The adjusted hindcast has been used to calculate the -# fRPSS and the terciles and extremes thresholds. -# ---------------------------------------- - -library(CSIndicators) -library(CSTools) -library(zeallot) -library(s2dv) - -S5path <- list(name = 'SEAS5', - path = '/esarchive/exp/ecmwf/system5c3s/$STORE_FREQ$_mean/$VAR_NAME$_s0-24h/$VAR_NAME$_$START_DATE$.nc') - -ERA5path <- list(name = 'ERA5', - path = '/esarchive/recon/ecmwf/era5/$STORE_FREQ$_mean/$VAR_NAME$_f1h-r1440x721cds/$VAR_NAME$_$YEAR$$MONTH$.nc') - -sdates <- paste0(1993:2016, '04', '01') - -c(hcst, hcst_ref) %<-% CST_Load(var = 'prlr', - exp = list(S5path), - obs = list(ERA5path), - sdates = sdates, - lonmin = -10, lonmax = 0, - latmin = 35, latmax = 40, - storefreq = 'daily', - leadtimemin = 1, leadtimemax = 214, - nmember = 25, output = "lonlat") -hcst$data <- hcst$data * 3600 * 24 * 1000 -hcst$attrs$Variable$metadata$prlr$units <- 'mm' -hcst_ref$data <- hcst_ref$data * 3600 * 24 * 1000 -hcst_ref$attrs$Variable$metadata$prlr$units <- 'mm' - - -c(fcst, obs) %<-% CST_Load(var = 'prlr', - exp = list(S5path), - obs = list(ERA5path), - sdates = '20220401', - lonmin = -10, lonmax = 0, - latmin = 35, latmax = 40, - storefreq = 'daily', - leadtimemin = 1, leadtimemax = 214, - nmember = 50, output = "lonlat") -fcst$data <- fcst$data * 1000 * 3600 * 24 -fcst$attrs$Variable$metadata$prlr$units <- 'mm' -obs$data <- obs$data * 1000 * 3600 * 24 -obs$attrs$Variable$metadata$prlr$units <- 'mm' - - -fcst_QM <- CST_QuantileMapping(exp = hcst, - obs = hcst_ref, - exp_cor = fcst, wet = TRUE, - ncores = 6) -hcst_QM <- CST_QuantileMapping(exp = hcst, - obs = hcst_ref, wet = TRUE, - ncores = 6) - -sprR_fcst <- CST_PeriodAccumulation(fcst_QM, - start = list(21,4), - end = list(21,6), na.rm = FALSE, - time_dim = 'ftime', ncores = 6) -sprR_hcst_ref <- CST_PeriodAccumulation(hcst_ref, - start = list(21,4), - end = list(21,6), - time_dim = 'ftime', ncores = 6) -sprR_obs <- CST_PeriodAccumulation(obs, - start = list(21,4), - end = list(21,6), - time_dim = 'ftime', ncores = 6) -sprR_hcst <- CST_PeriodAccumulation(hcst_QM, - start = list(21,4), - end = list(21,6), - time_dim = 'ftime', ncores = 6) - -sprR_fcst$data <- MeanDims(sprR_fcst$data, c('lat', 'lon')) -sprR_hcst_ref$data <- MeanDims(sprR_hcst_ref$data, c('lat', 'lon')) -sprR_obs$data <- MeanDims(sprR_obs$data, c('lat', 'lon')) -sprR_hcst$data <- MeanDims(sprR_hcst$data, c('lat', 'lon')) - - -metric <- RPSS(sprR_hcst$data, obs = sprR_hcst_ref$data) - -terciles <- quantile(sprR_hcst$data, c(0.33, 0.66)) -extremes <- quantile(sprR_hcst$data, c(0.10, 0.90)) - -dim(sprR_fcst$data) <- c(member = 50, sdate = 1) -PlotForecastPDF(sprR_fcst$data, - tercile.limits = as.vector(terciles), - extreme.limits = extremes, - var.name = "sprR (mm)", - title = "Seasonal forecasts at West Iberian Peninsula", - fcst.names = paste("Start date: 2022-04-01\n fRPSS:", - round(metric$rpss, 3)), - obs = as.vector(sprR_obs$data), - plotfile = "sprR_PlotForecast_csindicators_2022.png") - - -- GitLab From 34597453da18f5a1dfdc8e84afb4ba714a24ff7f Mon Sep 17 00:00:00 2001 From: EVA RIFA ROVIRA Date: Mon, 20 Nov 2023 10:44:35 +0100 Subject: [PATCH 2/6] Change NEWS order --- NEWS.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/NEWS.md b/NEWS.md index 3f6308b..c3047f9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -8,13 +8,13 @@ - Improve documentation of function MergeRefToExp mentioned the method used. ### New features -- Include new publication in documentation. -- Change to testthat edition 3. +- New functions to compute SPEI: PeriodPET, PeriodAccumulation with rolling accumulation and PeriodStandardization. +- New functions to compute bioclimatic indicators: PeriodMax, PeriodMin and PeriodVariance. - Add 'memb_dim' parameter to MergeRefToExp. - Add reference and improve documentation in MergeRefToExp. - Substitute CST_Load by CST_Start in vignettes. -- New functions to compute SPEI: PeriodPET, PeriodAccumulation with rolling accumulation and PeriodStandardization. -- New functions to compute bioclimatic indicators: PeriodMax, PeriodMin and PeriodVariance. +- Include new publication in documentation. +- Change to testthat edition 3. # CSIndicators 1.0.1 (Release date: 2023-05-18) -- GitLab From 76a90a4e223948988c82ccc662d6468f90868566 Mon Sep 17 00:00:00 2001 From: Eva Rifa Date: Mon, 20 Nov 2023 10:49:10 +0100 Subject: [PATCH 3/6] Add doc that was deleted --- inst/doc/paper-figure-PlotForecastPDF.R | 104 ++++++++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 inst/doc/paper-figure-PlotForecastPDF.R diff --git a/inst/doc/paper-figure-PlotForecastPDF.R b/inst/doc/paper-figure-PlotForecastPDF.R new file mode 100644 index 0000000..bebc497 --- /dev/null +++ b/inst/doc/paper-figure-PlotForecastPDF.R @@ -0,0 +1,104 @@ +rm(list=ls()) + +### Creation date: January 2023 +# Author: N. Pérez-Zanón +# For CSIndicators package manuscript +# ---------------------------------------- +# Figure 1. sprR probability distribution of the forecast initialised on the 1st +# of April 2022 for the western Iberian peninsula. The daily values of the +# hindcast and forecast have been corrected before calculating the sprR and the +# spatial aggregation. The adjusted hindcast has been used to calculate the +# fRPSS and the terciles and extremes thresholds. +# ---------------------------------------- + +library(CSIndicators) +library(CSTools) +library(zeallot) +library(s2dv) + +S5path <- list(name = 'SEAS5', + path = '/esarchive/exp/ecmwf/system5c3s/$STORE_FREQ$_mean/$VAR_NAME$_s0-24h/$VAR_NAME$_$START_DATE$.nc') + +ERA5path <- list(name = 'ERA5', + path = '/esarchive/recon/ecmwf/era5/$STORE_FREQ$_mean/$VAR_NAME$_f1h-r1440x721cds/$VAR_NAME$_$YEAR$$MONTH$.nc') + +sdates <- paste0(1993:2016, '04', '01') + +c(hcst, hcst_ref) %<-% CST_Load(var = 'prlr', + exp = list(S5path), + obs = list(ERA5path), + sdates = sdates, + lonmin = -10, lonmax = 0, + latmin = 35, latmax = 40, + storefreq = 'daily', + leadtimemin = 1, leadtimemax = 214, + nmember = 25, output = "lonlat") +hcst$data <- hcst$data * 3600 * 24 * 1000 +hcst$attrs$Variable$metadata$prlr$units <- 'mm' +hcst_ref$data <- hcst_ref$data * 3600 * 24 * 1000 +hcst_ref$attrs$Variable$metadata$prlr$units <- 'mm' + + +c(fcst, obs) %<-% CST_Load(var = 'prlr', + exp = list(S5path), + obs = list(ERA5path), + sdates = '20220401', + lonmin = -10, lonmax = 0, + latmin = 35, latmax = 40, + storefreq = 'daily', + leadtimemin = 1, leadtimemax = 214, + nmember = 50, output = "lonlat") +fcst$data <- fcst$data * 1000 * 3600 * 24 +fcst$attrs$Variable$metadata$prlr$units <- 'mm' +obs$data <- obs$data * 1000 * 3600 * 24 +obs$attrs$Variable$metadata$prlr$units <- 'mm' + + +fcst_QM <- CST_QuantileMapping(exp = hcst, + obs = hcst_ref, + exp_cor = fcst, wet = TRUE, + ncores = 6) +hcst_QM <- CST_QuantileMapping(exp = hcst, + obs = hcst_ref, wet = TRUE, + ncores = 6) + +sprR_fcst <- CST_PeriodAccumulation(fcst_QM, + start = list(21,4), + end = list(21,6), na.rm = FALSE, + time_dim = 'ftime', ncores = 6) +sprR_hcst_ref <- CST_PeriodAccumulation(hcst_ref, + start = list(21,4), + end = list(21,6), + time_dim = 'ftime', ncores = 6) +sprR_obs <- CST_PeriodAccumulation(obs, + start = list(21,4), + end = list(21,6), + time_dim = 'ftime', ncores = 6) +sprR_hcst <- CST_PeriodAccumulation(hcst_QM, + start = list(21,4), + end = list(21,6), + time_dim = 'ftime', ncores = 6) + +sprR_fcst$data <- MeanDims(sprR_fcst$data, c('lat', 'lon')) +sprR_hcst_ref$data <- MeanDims(sprR_hcst_ref$data, c('lat', 'lon')) +sprR_obs$data <- MeanDims(sprR_obs$data, c('lat', 'lon')) +sprR_hcst$data <- MeanDims(sprR_hcst$data, c('lat', 'lon')) + + +metric <- RPSS(sprR_hcst$data, obs = sprR_hcst_ref$data) + +terciles <- quantile(sprR_hcst$data, c(0.33, 0.66)) +extremes <- quantile(sprR_hcst$data, c(0.10, 0.90)) + +dim(sprR_fcst$data) <- c(member = 50, sdate = 1) +PlotForecastPDF(sprR_fcst$data, + tercile.limits = as.vector(terciles), + extreme.limits = extremes, + var.name = "sprR (mm)", + title = "Seasonal forecasts at West Iberian Peninsula", + fcst.names = paste("Start date: 2022-04-01\n fRPSS:", + round(metric$rpss, 3)), + obs = as.vector(sprR_obs$data), + plotfile = "sprR_PlotForecast_csindicators_2022.png") + + -- GitLab From 10797be794d098ebf87e491a468bf824428b538b Mon Sep 17 00:00:00 2001 From: Eva Rifa Date: Mon, 20 Nov 2023 10:51:47 +0100 Subject: [PATCH 4/6] Add line in Rbuildignore for issue template --- .Rbuildignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.Rbuildignore b/.Rbuildignore index c0e2736..83f840f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,5 +1,6 @@ .*\.git$ .*\.gitignore$ +.*\.gitlab$ .*\.tar.gz$ .*\.pdf$ ./.nc$ -- GitLab From c409518f6aa48f702ffd589f335410b017b923a8 Mon Sep 17 00:00:00 2001 From: Eva Rifa Date: Mon, 20 Nov 2023 11:32:03 +0100 Subject: [PATCH 5/6] Correct item lists in documentation --- R/AccumulationExceedingThreshold.R | 8 ++-- R/MergeRefToExp.R | 4 +- R/PeriodAccumulation.R | 16 ++++---- R/PeriodMax.R | 26 ++++++------- R/PeriodMean.R | 16 ++++---- R/PeriodMin.R | 26 ++++++------- R/PeriodVariance.R | 42 ++++++++++----------- R/TotalSpellTimeExceedingThreshold.R | 12 +++--- R/TotalTimeExceedingThreshold.R | 36 +++++++++--------- man/AccumulationExceedingThreshold.Rd | 4 +- man/CST_AccumulationExceedingThreshold.Rd | 4 +- man/CST_MergeRefToExp.Rd | 2 +- man/CST_PeriodAccumulation.Rd | 8 ++-- man/CST_PeriodMax.Rd | 13 +++---- man/CST_PeriodMean.Rd | 8 ++-- man/CST_PeriodMin.Rd | 13 +++---- man/CST_PeriodVariance.Rd | 21 +++++------ man/CST_TotalSpellTimeExceedingThreshold.Rd | 6 +-- man/CST_TotalTimeExceedingThreshold.Rd | 18 ++++----- man/MergeRefToExp.Rd | 2 +- man/PeriodAccumulation.Rd | 8 ++-- man/PeriodMax.Rd | 13 +++---- man/PeriodMean.Rd | 8 ++-- man/PeriodMin.Rd | 13 +++---- man/PeriodVariance.Rd | 21 +++++------ man/TotalSpellTimeExceedingThreshold.Rd | 6 +-- man/TotalTimeExceedingThreshold.Rd | 18 ++++----- 27 files changed, 180 insertions(+), 192 deletions(-) diff --git a/R/AccumulationExceedingThreshold.R b/R/AccumulationExceedingThreshold.R index feee031..b8ae9ae 100644 --- a/R/AccumulationExceedingThreshold.R +++ b/R/AccumulationExceedingThreshold.R @@ -8,8 +8,8 @@ #'following agriculture indices for heat stress can be obtained by using this #'function: #'\itemize{ -#' \item\code{GDD}{Summation of daily differences between daily average -#' temperatures and 10°C between April 1st and October 31st} +#' \item{'GDD', Summation of daily differences between daily average +#' temperatures and 10°C between April 1st and October 31st.} #'} #' #'@param data An 's2dv_cube' object as provided function \code{CST_Start} or @@ -151,8 +151,8 @@ CST_AccumulationExceedingThreshold <- function(data, threshold, op = '>', diff = #'following agriculture indices for heat stress can be obtained by using this #'function: #'\itemize{ -#' \item\code{GDD}{Summation of daily differences between daily average -#' temperatures and 10°C between April 1st and October 31st} +#' \item{'GDD', Summation of daily differences between daily average +#' temperatures and 10°C between April 1st and October 31st.} #'} #' #'@param data A multidimensional array with named dimensions. diff --git a/R/MergeRefToExp.R b/R/MergeRefToExp.R index 56c3c3d..6d9fd6e 100644 --- a/R/MergeRefToExp.R +++ b/R/MergeRefToExp.R @@ -68,7 +68,7 @@ #'M. Teixeira, S. Silva, N. Fontes, A. Graça, A. Dell'Aquila, S. Calmanti and #'N. González-Reviriego (2023). Advanced seasonal predictions for vine #'management based on bioclimatic indicators tailored to the wine sector. -#'Climate Services, 30, 100343, \doi{doi.org/10.1016/j.cliser.2023.100343}. +#'Climate Services, 30, 100343, \doi{10.1016/j.cliser.2023.100343}. #' #'@examples #'data_dates <- c(seq(as.Date("01-07-1993", "%d-%m-%Y", tz = 'UTC'), @@ -295,7 +295,7 @@ CST_MergeRefToExp <- function(data1, data2, start1 = NULL, end1 = NULL, #'M. Teixeira, S. Silva, N. Fontes, A. Graça, A. Dell'Aquila, S. Calmanti and #'N. González-Reviriego (2023). Advanced seasonal predictions for vine #'management based on bioclimatic indicators tailored to the wine sector. -#'Climate Services, 30, 100343, \doi{doi.org/10.1016/j.cliser.2023.100343}. +#'Climate Services, 30, 100343, \doi{10.1016/j.cliser.2023.100343}. #' #'@examples #'data_dates <- c(seq(as.Date("01-07-1993", "%d-%m-%Y", tz = 'UTC'), diff --git a/R/PeriodAccumulation.R b/R/PeriodAccumulation.R index 60245b6..8986e3f 100644 --- a/R/PeriodAccumulation.R +++ b/R/PeriodAccumulation.R @@ -4,10 +4,10 @@ #'period. Providing precipitation data, two agriculture indices can be obtained #'by using this function: #'\itemize{ -#' \item\code{SprR}{Spring Total Precipitation: The total precipitation from -#' April 21th to June 21st} -#' \item\code{HarR}{Harvest Total Precipitation: The total precipitation from -#' August 21st to October 21st} +#' \item{'SprR', Spring Total Precipitation: The total precipitation from +#' April 21th to June 21st.} +#' \item{'HarR', Harvest Total Precipitation: The total precipitation from +#' August 21st to October 21st.} #'} #' #'There are two possible ways of performing the accumulation. The default one @@ -151,10 +151,10 @@ CST_PeriodAccumulation <- function(data, start = NULL, end = NULL, #'period. Providing precipitation data, two agriculture indices can be obtained #'by using this function: #'\itemize{ -#' \item\code{SprR}{Spring Total Precipitation: The total precipitation from -#' April 21th to June 21st} -#' \item\code{HarR}{Harvest Total Precipitation: The total precipitation from -#' August 21st to October 21st} +#' \item{'SprR', Spring Total Precipitation: The total precipitation from +#' April 21th to June 21st.} +#' \item{'HarR', Harvest Total Precipitation: The total precipitation from +#' August 21st to October 21st.} #'} #' #'There are two possible ways of performing the accumulation. The default one diff --git a/R/PeriodMax.R b/R/PeriodMax.R index 8c56156..3ae23ec 100644 --- a/R/PeriodMax.R +++ b/R/PeriodMax.R @@ -3,13 +3,12 @@ #'Period Max computes the maximum (max) of a given variable in a period. #'Two bioclimatic indicators can be obtained by using this function: #'\itemize{ -#' \item\code{BIO5}{(Providing temperature data) Max Temperature of Warmest -#' Month. The maximum monthly temperature occurrence over a -#' given year (time-series) or averaged span of years -#' (normal).} -#' \item\code{BIO13}{(Providing precipitation data) Precipitation of Wettest -#' Month. This index identifies the total precipitation -#' that prevails during the wettest month.} +#' \item{'BIO5', (Providing temperature data) Max Temperature of Warmest +#' Month. The maximum monthly temperature occurrence over a +#' given year (time-series) or averaged span of years (normal).} +#' \item{'BIO13', (Providing precipitation data) Precipitation of Wettest +#' Month. This index identifies the total precipitation +#' that prevails during the wettest month.} #'} #' #'@param data An 's2dv_cube' object as provided function \code{CST_Start} or @@ -117,13 +116,12 @@ CST_PeriodMax <- function(data, start = NULL, end = NULL, #'Period max computes the average (max) of a given variable in a period. #'Two bioclimatic indicators can be obtained by using this function: #'\itemize{ -#' \item\code{BIO5}{(Providing temperature data) Max Temperature of Warmest -#' Month. The maximum monthly temperature occurrence over a -#' given year (time-series) or averaged span of years -#' (normal).} -#' \item\code{BIO13}{(Providing precipitation data) Precipitation of Wettest -#' Month. This index identifies the total precipitation -#' that prevails during the wettest month.} +#' \item{'BIO5', (Providing temperature data) Max Temperature of Warmest +#' Month. The maximum monthly temperature occurrence over a +#' given year (time-series) or averaged span of years (normal).} +#' \item{'BIO13', (Providing precipitation data) Precipitation of Wettest +#' Month. This index identifies the total precipitation +#' that prevails during the wettest month.} #'} #' #'@param data A multidimensional array with named dimensions. diff --git a/R/PeriodMean.R b/R/PeriodMean.R index 9106927..f58bbeb 100644 --- a/R/PeriodMean.R +++ b/R/PeriodMean.R @@ -4,10 +4,10 @@ #'Providing temperature data, two agriculture indices can be obtained by using #'this function: #'\itemize{ -#' \item\code{GST}{Growing Season average Temperature: The average temperature -#' from April 1st to Octobe 31st} -#' \item\code{SprTX}{Spring Average Maximum Temperature: The average daily -#' maximum temperature from April 1st to May 31st} +#' \item{'GST', Growing Season average Temperature: The average temperature +#' from April 1st to Octobe 31st.} +#' \item{'SprTX', Spring Average Maximum Temperature: The average daily +#' maximum temperature from April 1st to May 31st.} #'} #' #'@param data An 's2dv_cube' object as provided function \code{CST_Start} or @@ -117,10 +117,10 @@ CST_PeriodMean <- function(data, start = NULL, end = NULL, #'Providing temperature data, two agriculture indices can be obtained by using #'this function: #'\itemize{ -#' \item\code{GST}{Growing Season average Temperature: The average -#' temperature from April 1st to Octobe 31st} -#' \item\code{SprTX}{Spring Average Maximum Temperature: The average daily -#' maximum temperature from April 1st to May 31st} +#' \item{'GST', Growing Season average Temperature: The average temperature +#' from April 1st to Octobe 31st.} +#' \item{'SprTX', Spring Average Maximum Temperature: The average daily +#' maximum temperature from April 1st to May 31st.} #'} #' #'@param data A multidimensional array with named dimensions. diff --git a/R/PeriodMin.R b/R/PeriodMin.R index 74547cc..99ce801 100644 --- a/R/PeriodMin.R +++ b/R/PeriodMin.R @@ -3,13 +3,12 @@ #'Period Min computes the average (min) of a given variable in a period. #'Two bioclimatic indicators can be obtained by using this function: #'\itemize{ -#' \item\code{BIO6}{(Providing temperature data) Min Temperature of Coldest -#' Month. The minimum monthly temperature occurrence over a -#' given year (time-series) or averaged span of years -#' (normal).} -#' \item\code{BIO14}{(Providing precipitation data) Precipitation of Driest -#' Month. This index identifies the total precipitation -#' that prevails during the driest month.} +#' \item{'BIO6', (Providing temperature data) Min Temperature of Coldest +#' Month. The minimum monthly temperature occurrence over a +#' given year (time-series) or averaged span of years (normal).} +#' \item{'BIO14', (Providing precipitation data) Precipitation of Driest +#' Month. This index identifies the total precipitation +#' that prevails during the driest month.} #'} #' #'@param data An 's2dv_cube' object as provided function \code{CST_Start} or @@ -117,13 +116,12 @@ CST_PeriodMin <- function(data, start = NULL, end = NULL, #'Period Min computes the average (min) of a given variable in a period. #'Two bioclimatic indicators can be obtained by using this function: #'\itemize{ -#' \item\code{BIO6}{(Providing temperature data) Min Temperature of Coldest -#' Month. The minimum monthly temperature occurrence over a -#' given year (time-series) or averaged span of years -#' (normal).} -#' \item\code{BIO14}{(Providing precipitation data) Precipitation of Driest -#' Month. This index identifies the total precipitation -#' that prevails during the driest month.} +#' \item{'BIO6', (Providing temperature data) Min Temperature of Coldest +#' Month. The minimum monthly temperature occurrence over a +#' given year (time-series) or averaged span of years (normal).} +#' \item{'BIO14', (Providing precipitation data) Precipitation of Driest +#' Month. This index identifies the total precipitation +#' that prevails during the driest month.} #'} #' #'@param data A multidimensional array with named dimensions. diff --git a/R/PeriodVariance.R b/R/PeriodVariance.R index f95b8e4..4e1e93e 100644 --- a/R/PeriodVariance.R +++ b/R/PeriodVariance.R @@ -3,17 +3,16 @@ #'Period Variance computes the average (var) of a given variable in a period. #'Two bioclimatic indicators can be obtained by using this function: #'\itemize{ -#' \item\code{BIO4}{(Providing temperature data) Temperature Seasonality -#' (Standard Deviation). The amount of temperature variation -#' over a given year (or averaged years) based on the standard -#' deviation (variation) of monthly temperature averages. } -#' \item\code{BIO15}{(Providing precipitation data) Precipitation Seasonality -#' (CV). This is a measure of the variation in -#' monthly precipitation totals over the course of the year. -#' This index is the ratio of the standard deviation of the -#' monthly total precipitation to the mean monthly total -#' precipitation (also known as the coefficient of variation) -#' and is expressed as a percentage} +#' \item{'BIO4', (Providing temperature data) Temperature Seasonality +#' (Standard Deviation). The amount of temperature variation +#' over a given year (or averaged years) based on the standard +#' deviation (variation) of monthly temperature averages.} +#' \item{'BIO15', (Providing precipitation data) Precipitation Seasonality +#' (CV). This is a measure of the variation in monthly precipitation +#' totals over the course of the year. This index is the ratio of the +#' standard deviation of the monthly total precipitation to the mean +#' monthly total precipitation (also known as the coefficient of +#' variation) and is expressed as a percentage.} #'} #' #'@param data An 's2dv_cube' object as provided function \code{CST_Start} or @@ -121,17 +120,16 @@ CST_PeriodVariance <- function(data, start = NULL, end = NULL, #'Period Variance computes the average (var) of a given variable in a period. #'Two bioclimatic indicators can be obtained by using this function: #'\itemize{ -#' \item\code{BIO4}{(Providing temperature data) Temperature Seasonality -#' (Standard Deviation). The amount of temperature variation -#' over a given year (or averaged years) based on the standard -#' deviation (variation) of monthly temperature averages. } -#' \item\code{BIO15}{(Providing precipitation data) Precipitation Seasonality -#' (CV). This is a measure of the variation in -#' monthly precipitation totals over the course of the year. -#' This index is the ratio of the standard deviation of the -#' monthly total precipitation to the mean monthly total -#' precipitation (also known as the coefficient of variation) -#' and is expressed as a percentage} +#' \item{'BIO4', (Providing temperature data) Temperature Seasonality +#' (Standard Deviation). The amount of temperature variation +#' over a given year (or averaged years) based on the standard +#' deviation (variation) of monthly temperature averages.} +#' \item{'BIO15', (Providing precipitation data) Precipitation Seasonality +#' (CV). This is a measure of the variation in monthly precipitation +#' totals over the course of the year. This index is the ratio of the +#' standard deviation of the monthly total precipitation to the mean +#' monthly total precipitation (also known as the coefficient of +#' variation) and is expressed as a percentage.} #'} #' #'@param data A multidimensional array with named dimensions. diff --git a/R/TotalSpellTimeExceedingThreshold.R b/R/TotalSpellTimeExceedingThreshold.R index cd2676e..1450703 100644 --- a/R/TotalSpellTimeExceedingThreshold.R +++ b/R/TotalSpellTimeExceedingThreshold.R @@ -6,9 +6,9 @@ #'This function allows to compute indicators widely used in Climate Services, #'such as: #'\itemize{ -#' \code{WSDI}{Warm Spell Duration Index that count the total number of days -#' with at least 6 consecutive days when the daily temperature -#' maximum exceeds its 90th percentile.} +#' \item{'WSDI', Warm Spell Duration Index that count the total number of days +#' with at least 6 consecutive days when the daily temperature +#' maximum exceeds its 90th percentile.} #'} #'This function requires the data and the threshold to be in the same units. The #'90th percentile can be translate into absolute values given a reference dataset @@ -151,9 +151,9 @@ CST_TotalSpellTimeExceedingThreshold <- function(data, threshold, spell, op = '> #'This function allows to compute indicators widely used in Climate Services, #'such as: #'\itemize{ -#' \code{WSDI}{Warm Spell Duration Index that count the total number of days -#' with at least 6 consecutive days when the daily temperature -#' maximum exceeds its 90th percentile.} +#' \item{'WSDI', Warm Spell Duration Index that count the total number of days +#' with at least 6 consecutive days when the daily temperature +#' maximum exceeds its 90th percentile.} #'} #'This function requires the data and the threshold to be in the same units. The #'90th percentile can be translate into absolute values given a reference diff --git a/R/TotalTimeExceedingThreshold.R b/R/TotalTimeExceedingThreshold.R index fa57208..15b822c 100644 --- a/R/TotalTimeExceedingThreshold.R +++ b/R/TotalTimeExceedingThreshold.R @@ -9,15 +9,15 @@ #'Providing maximum temperature daily data, the following agriculture #'indices for heat stress can be obtained by using this function: #'\itemize{ -#' \item\code{SU35}{Total count of days when daily maximum temperatures exceed -#' 35°C in the seven months from the start month given (e.g. -#' from April to October for start month of April).} -#' \item\code{SU36}{Total count of days when daily maximum temperatures exceed -#' 36 between June 21st and September 21st} -#' \item\code{SU40}{Total count of days when daily maximum temperatures exceed -#' 40 between June 21st and September 21st} -#' \item\code{Spr32}{Total count of days when daily maximum temperatures exceed -#' 32 between April 21st and June 21st} +#' \item{'SU35', Total count of days when daily maximum temperatures exceed +#' 35°C in the seven months from the start month given (e.g. from April +#' to October for start month of April).} +#' \item{'SU36', Total count of days when daily maximum temperatures exceed +#' 36 between June 21st and September 21st.} +#' \item{'SU40', Total count of days when daily maximum temperatures exceed +#' 40 between June 21st and September 21st.} +#' \item{'Spr32', Total count of days when daily maximum temperatures exceed +#' 32 between April 21st and June 21st.} #'} #' #'@param data An 's2dv_cube' object as provided function \code{CST_Start} or @@ -157,15 +157,15 @@ CST_TotalTimeExceedingThreshold <- function(data, threshold, op = '>', #'Providing maximum temperature daily data, the following agriculture #'indices for heat stress can be obtained by using this function: #'\itemize{ -#' \item\code{SU35}{Total count of days when daily maximum temperatures exceed -#' 35°C in the seven months from the start month given (e.g. -#' from April to October for start month of April).} -#' \item\code{SU36}{Total count of days when daily maximum temperatures exceed -#' 36 between June 21st and September 21st} -#' \item\code{SU40}{Total count of days when daily maximum temperatures exceed -#' 40 between June 21st and September 21st} -#' \item\code{Spr32}{Total count of days when daily maximum temperatures exceed -#' 32 between April 21st and June 21st} +#' \item{'SU35', Total count of days when daily maximum temperatures exceed +#' 35°C in the seven months from the start month given (e.g. from April +#' to October for start month of April).} +#' \item{'SU36', Total count of days when daily maximum temperatures exceed +#' 36 between June 21st and September 21st.} +#' \item{'SU40', Total count of days when daily maximum temperatures exceed +#' 40 between June 21st and September 21st.} +#' \item{'Spr32', Total count of days when daily maximum temperatures exceed +#' 32 between April 21st and June 21st.} #'} #' #'@param data A multidimensional array with named dimensions. diff --git a/man/AccumulationExceedingThreshold.Rd b/man/AccumulationExceedingThreshold.Rd index cf6c8df..976c967 100644 --- a/man/AccumulationExceedingThreshold.Rd +++ b/man/AccumulationExceedingThreshold.Rd @@ -78,8 +78,8 @@ use a percentile as a scalar, the function \code{Threshold} or following agriculture indices for heat stress can be obtained by using this function: \itemize{ - \item\code{GDD}{Summation of daily differences between daily average - temperatures and 10°C between April 1st and October 31st} + \item{'GDD', Summation of daily differences between daily average + temperatures and 10°C between April 1st and October 31st.} } } \examples{ diff --git a/man/CST_AccumulationExceedingThreshold.Rd b/man/CST_AccumulationExceedingThreshold.Rd index 0bea015..ceb9ad7 100644 --- a/man/CST_AccumulationExceedingThreshold.Rd +++ b/man/CST_AccumulationExceedingThreshold.Rd @@ -79,8 +79,8 @@ use a percentile as a scalar, the function \code{Threshold} or following agriculture indices for heat stress can be obtained by using this function: \itemize{ - \item\code{GDD}{Summation of daily differences between daily average - temperatures and 10°C between April 1st and October 31st} + \item{'GDD', Summation of daily differences between daily average + temperatures and 10°C between April 1st and October 31st.} } } \examples{ diff --git a/man/CST_MergeRefToExp.Rd b/man/CST_MergeRefToExp.Rd index 9832912..b95ef79 100644 --- a/man/CST_MergeRefToExp.Rd +++ b/man/CST_MergeRefToExp.Rd @@ -120,5 +120,5 @@ Chou, C., R. Marcos-Matamoros, L. Palma Garcia, N. Pérez-Zanón, M. Teixeira, S. Silva, N. Fontes, A. Graça, A. Dell'Aquila, S. Calmanti and N. González-Reviriego (2023). Advanced seasonal predictions for vine management based on bioclimatic indicators tailored to the wine sector. -Climate Services, 30, 100343, \doi{doi.org/10.1016/j.cliser.2023.100343}. +Climate Services, 30, 100343, \doi{10.1016/j.cliser.2023.100343}. } diff --git a/man/CST_PeriodAccumulation.Rd b/man/CST_PeriodAccumulation.Rd index 4d71ff3..c1b4a1c 100644 --- a/man/CST_PeriodAccumulation.Rd +++ b/man/CST_PeriodAccumulation.Rd @@ -77,10 +77,10 @@ Period Accumulation computes the sum (accumulation) of a given variable in a period. Providing precipitation data, two agriculture indices can be obtained by using this function: \itemize{ - \item\code{SprR}{Spring Total Precipitation: The total precipitation from - April 21th to June 21st} - \item\code{HarR}{Harvest Total Precipitation: The total precipitation from - August 21st to October 21st} + \item{'SprR', Spring Total Precipitation: The total precipitation from + April 21th to June 21st.} + \item{'HarR', Harvest Total Precipitation: The total precipitation from + August 21st to October 21st.} } } \details{ diff --git a/man/CST_PeriodMax.Rd b/man/CST_PeriodMax.Rd index a372a1d..3c760ba 100644 --- a/man/CST_PeriodMax.Rd +++ b/man/CST_PeriodMax.Rd @@ -52,13 +52,12 @@ element. Period Max computes the maximum (max) of a given variable in a period. Two bioclimatic indicators can be obtained by using this function: \itemize{ - \item\code{BIO5}{(Providing temperature data) Max Temperature of Warmest - Month. The maximum monthly temperature occurrence over a - given year (time-series) or averaged span of years - (normal).} - \item\code{BIO13}{(Providing precipitation data) Precipitation of Wettest - Month. This index identifies the total precipitation - that prevails during the wettest month.} + \item{'BIO5', (Providing temperature data) Max Temperature of Warmest + Month. The maximum monthly temperature occurrence over a + given year (time-series) or averaged span of years (normal).} + \item{'BIO13', (Providing precipitation data) Precipitation of Wettest + Month. This index identifies the total precipitation + that prevails during the wettest month.} } } \examples{ diff --git a/man/CST_PeriodMean.Rd b/man/CST_PeriodMean.Rd index 323adae..3f51041 100644 --- a/man/CST_PeriodMean.Rd +++ b/man/CST_PeriodMean.Rd @@ -54,10 +54,10 @@ Period Mean computes the average (mean) of a given variable in a period. Providing temperature data, two agriculture indices can be obtained by using this function: \itemize{ - \item\code{GST}{Growing Season average Temperature: The average temperature - from April 1st to Octobe 31st} - \item\code{SprTX}{Spring Average Maximum Temperature: The average daily - maximum temperature from April 1st to May 31st} + \item{'GST', Growing Season average Temperature: The average temperature + from April 1st to Octobe 31st.} + \item{'SprTX', Spring Average Maximum Temperature: The average daily + maximum temperature from April 1st to May 31st.} } } \examples{ diff --git a/man/CST_PeriodMin.Rd b/man/CST_PeriodMin.Rd index 9d3833f..97caa6e 100644 --- a/man/CST_PeriodMin.Rd +++ b/man/CST_PeriodMin.Rd @@ -52,13 +52,12 @@ element. Period Min computes the average (min) of a given variable in a period. Two bioclimatic indicators can be obtained by using this function: \itemize{ - \item\code{BIO6}{(Providing temperature data) Min Temperature of Coldest - Month. The minimum monthly temperature occurrence over a - given year (time-series) or averaged span of years - (normal).} - \item\code{BIO14}{(Providing precipitation data) Precipitation of Driest - Month. This index identifies the total precipitation - that prevails during the driest month.} + \item{'BIO6', (Providing temperature data) Min Temperature of Coldest + Month. The minimum monthly temperature occurrence over a + given year (time-series) or averaged span of years (normal).} + \item{'BIO14', (Providing precipitation data) Precipitation of Driest + Month. This index identifies the total precipitation + that prevails during the driest month.} } } \examples{ diff --git a/man/CST_PeriodVariance.Rd b/man/CST_PeriodVariance.Rd index b04b4ed..4d789dd 100644 --- a/man/CST_PeriodVariance.Rd +++ b/man/CST_PeriodVariance.Rd @@ -52,17 +52,16 @@ element. Period Variance computes the average (var) of a given variable in a period. Two bioclimatic indicators can be obtained by using this function: \itemize{ - \item\code{BIO4}{(Providing temperature data) Temperature Seasonality - (Standard Deviation). The amount of temperature variation - over a given year (or averaged years) based on the standard - deviation (variation) of monthly temperature averages. } - \item\code{BIO15}{(Providing precipitation data) Precipitation Seasonality - (CV). This is a measure of the variation in - monthly precipitation totals over the course of the year. - This index is the ratio of the standard deviation of the - monthly total precipitation to the mean monthly total - precipitation (also known as the coefficient of variation) - and is expressed as a percentage} + \item{'BIO4', (Providing temperature data) Temperature Seasonality + (Standard Deviation). The amount of temperature variation + over a given year (or averaged years) based on the standard + deviation (variation) of monthly temperature averages.} + \item{'BIO15', (Providing precipitation data) Precipitation Seasonality + (CV). This is a measure of the variation in monthly precipitation + totals over the course of the year. This index is the ratio of the + standard deviation of the monthly total precipitation to the mean + monthly total precipitation (also known as the coefficient of + variation) and is expressed as a percentage.} } } \examples{ diff --git a/man/CST_TotalSpellTimeExceedingThreshold.Rd b/man/CST_TotalSpellTimeExceedingThreshold.Rd index 831bf2c..89d2fb2 100644 --- a/man/CST_TotalSpellTimeExceedingThreshold.Rd +++ b/man/CST_TotalSpellTimeExceedingThreshold.Rd @@ -71,9 +71,9 @@ exceed) a threshold are calculated with \code{TotalSpellTimeExceedingThreshold}. This function allows to compute indicators widely used in Climate Services, such as: \itemize{ -\code{WSDI}{Warm Spell Duration Index that count the total number of days - with at least 6 consecutive days when the daily temperature - maximum exceeds its 90th percentile.} + \item{'WSDI', Warm Spell Duration Index that count the total number of days + with at least 6 consecutive days when the daily temperature + maximum exceeds its 90th percentile.} } This function requires the data and the threshold to be in the same units. The 90th percentile can be translate into absolute values given a reference dataset diff --git a/man/CST_TotalTimeExceedingThreshold.Rd b/man/CST_TotalTimeExceedingThreshold.Rd index db9a3d6..e0b8ed4 100644 --- a/man/CST_TotalTimeExceedingThreshold.Rd +++ b/man/CST_TotalTimeExceedingThreshold.Rd @@ -76,15 +76,15 @@ variable units, i.e. to use a percentile as a scalar, the function Providing maximum temperature daily data, the following agriculture indices for heat stress can be obtained by using this function: \itemize{ - \item\code{SU35}{Total count of days when daily maximum temperatures exceed - 35°C in the seven months from the start month given (e.g. - from April to October for start month of April).} - \item\code{SU36}{Total count of days when daily maximum temperatures exceed - 36 between June 21st and September 21st} - \item\code{SU40}{Total count of days when daily maximum temperatures exceed - 40 between June 21st and September 21st} - \item\code{Spr32}{Total count of days when daily maximum temperatures exceed - 32 between April 21st and June 21st} + \item{'SU35', Total count of days when daily maximum temperatures exceed + 35°C in the seven months from the start month given (e.g. from April + to October for start month of April).} + \item{'SU36', Total count of days when daily maximum temperatures exceed + 36 between June 21st and September 21st.} + \item{'SU40', Total count of days when daily maximum temperatures exceed + 40 between June 21st and September 21st.} + \item{'Spr32', Total count of days when daily maximum temperatures exceed + 32 between April 21st and June 21st.} } } \examples{ diff --git a/man/MergeRefToExp.Rd b/man/MergeRefToExp.Rd index 81cda03..e524ead 100644 --- a/man/MergeRefToExp.Rd +++ b/man/MergeRefToExp.Rd @@ -120,5 +120,5 @@ Chou, C., R. Marcos-Matamoros, L. Palma Garcia, N. Pérez-Zanón, M. Teixeira, S. Silva, N. Fontes, A. Graça, A. Dell'Aquila, S. Calmanti and N. González-Reviriego (2023). Advanced seasonal predictions for vine management based on bioclimatic indicators tailored to the wine sector. -Climate Services, 30, 100343, \doi{doi.org/10.1016/j.cliser.2023.100343}. +Climate Services, 30, 100343, \doi{10.1016/j.cliser.2023.100343}. } diff --git a/man/PeriodAccumulation.Rd b/man/PeriodAccumulation.Rd index ca01c20..71b7d73 100644 --- a/man/PeriodAccumulation.Rd +++ b/man/PeriodAccumulation.Rd @@ -72,10 +72,10 @@ Period Accumulation computes the sum (accumulation) of a given variable in a period. Providing precipitation data, two agriculture indices can be obtained by using this function: \itemize{ - \item\code{SprR}{Spring Total Precipitation: The total precipitation from - April 21th to June 21st} - \item\code{HarR}{Harvest Total Precipitation: The total precipitation from - August 21st to October 21st} + \item{'SprR', Spring Total Precipitation: The total precipitation from + April 21th to June 21st.} + \item{'HarR', Harvest Total Precipitation: The total precipitation from + August 21st to October 21st.} } } \details{ diff --git a/man/PeriodMax.Rd b/man/PeriodMax.Rd index cb776d2..762b3c9 100644 --- a/man/PeriodMax.Rd +++ b/man/PeriodMax.Rd @@ -51,13 +51,12 @@ indicator in the element \code{data}. Period max computes the average (max) of a given variable in a period. Two bioclimatic indicators can be obtained by using this function: \itemize{ - \item\code{BIO5}{(Providing temperature data) Max Temperature of Warmest - Month. The maximum monthly temperature occurrence over a - given year (time-series) or averaged span of years - (normal).} - \item\code{BIO13}{(Providing precipitation data) Precipitation of Wettest - Month. This index identifies the total precipitation - that prevails during the wettest month.} + \item{'BIO5', (Providing temperature data) Max Temperature of Warmest + Month. The maximum monthly temperature occurrence over a + given year (time-series) or averaged span of years (normal).} + \item{'BIO13', (Providing precipitation data) Precipitation of Wettest + Month. This index identifies the total precipitation + that prevails during the wettest month.} } } \examples{ diff --git a/man/PeriodMean.Rd b/man/PeriodMean.Rd index 9637d58..b639d09 100644 --- a/man/PeriodMean.Rd +++ b/man/PeriodMean.Rd @@ -52,10 +52,10 @@ Period Mean computes the average (mean) of a given variable in a period. Providing temperature data, two agriculture indices can be obtained by using this function: \itemize{ - \item\code{GST}{Growing Season average Temperature: The average - temperature from April 1st to Octobe 31st} - \item\code{SprTX}{Spring Average Maximum Temperature: The average daily - maximum temperature from April 1st to May 31st} + \item{'GST', Growing Season average Temperature: The average temperature + from April 1st to Octobe 31st.} + \item{'SprTX', Spring Average Maximum Temperature: The average daily + maximum temperature from April 1st to May 31st.} } } \examples{ diff --git a/man/PeriodMin.Rd b/man/PeriodMin.Rd index 154acf0..597421c 100644 --- a/man/PeriodMin.Rd +++ b/man/PeriodMin.Rd @@ -51,13 +51,12 @@ indicator in the element \code{data}. Period Min computes the average (min) of a given variable in a period. Two bioclimatic indicators can be obtained by using this function: \itemize{ - \item\code{BIO6}{(Providing temperature data) Min Temperature of Coldest - Month. The minimum monthly temperature occurrence over a - given year (time-series) or averaged span of years - (normal).} - \item\code{BIO14}{(Providing precipitation data) Precipitation of Driest - Month. This index identifies the total precipitation - that prevails during the driest month.} + \item{'BIO6', (Providing temperature data) Min Temperature of Coldest + Month. The minimum monthly temperature occurrence over a + given year (time-series) or averaged span of years (normal).} + \item{'BIO14', (Providing precipitation data) Precipitation of Driest + Month. This index identifies the total precipitation + that prevails during the driest month.} } } \examples{ diff --git a/man/PeriodVariance.Rd b/man/PeriodVariance.Rd index e1e8d7c..9155c4b 100644 --- a/man/PeriodVariance.Rd +++ b/man/PeriodVariance.Rd @@ -51,17 +51,16 @@ indicator in the element \code{data}. Period Variance computes the average (var) of a given variable in a period. Two bioclimatic indicators can be obtained by using this function: \itemize{ - \item\code{BIO4}{(Providing temperature data) Temperature Seasonality - (Standard Deviation). The amount of temperature variation - over a given year (or averaged years) based on the standard - deviation (variation) of monthly temperature averages. } - \item\code{BIO15}{(Providing precipitation data) Precipitation Seasonality - (CV). This is a measure of the variation in - monthly precipitation totals over the course of the year. - This index is the ratio of the standard deviation of the - monthly total precipitation to the mean monthly total - precipitation (also known as the coefficient of variation) - and is expressed as a percentage} + \item{'BIO4', (Providing temperature data) Temperature Seasonality + (Standard Deviation). The amount of temperature variation + over a given year (or averaged years) based on the standard + deviation (variation) of monthly temperature averages.} + \item{'BIO15', (Providing precipitation data) Precipitation Seasonality + (CV). This is a measure of the variation in monthly precipitation + totals over the course of the year. This index is the ratio of the + standard deviation of the monthly total precipitation to the mean + monthly total precipitation (also known as the coefficient of + variation) and is expressed as a percentage.} } } \examples{ diff --git a/man/TotalSpellTimeExceedingThreshold.Rd b/man/TotalSpellTimeExceedingThreshold.Rd index ea1a6ab..d7815bf 100644 --- a/man/TotalSpellTimeExceedingThreshold.Rd +++ b/man/TotalSpellTimeExceedingThreshold.Rd @@ -71,9 +71,9 @@ exceed) a threshold are calculated with \code{TotalSpellTimeExceedingThreshold}. This function allows to compute indicators widely used in Climate Services, such as: \itemize{ -\code{WSDI}{Warm Spell Duration Index that count the total number of days - with at least 6 consecutive days when the daily temperature - maximum exceeds its 90th percentile.} + \item{'WSDI', Warm Spell Duration Index that count the total number of days + with at least 6 consecutive days when the daily temperature + maximum exceeds its 90th percentile.} } This function requires the data and the threshold to be in the same units. The 90th percentile can be translate into absolute values given a reference diff --git a/man/TotalTimeExceedingThreshold.Rd b/man/TotalTimeExceedingThreshold.Rd index 31f3161..5b9627e 100644 --- a/man/TotalTimeExceedingThreshold.Rd +++ b/man/TotalTimeExceedingThreshold.Rd @@ -75,15 +75,15 @@ variable units, i.e. to use a percentile as a scalar, the function Providing maximum temperature daily data, the following agriculture indices for heat stress can be obtained by using this function: \itemize{ - \item\code{SU35}{Total count of days when daily maximum temperatures exceed - 35°C in the seven months from the start month given (e.g. - from April to October for start month of April).} - \item\code{SU36}{Total count of days when daily maximum temperatures exceed - 36 between June 21st and September 21st} - \item\code{SU40}{Total count of days when daily maximum temperatures exceed - 40 between June 21st and September 21st} - \item\code{Spr32}{Total count of days when daily maximum temperatures exceed - 32 between April 21st and June 21st} + \item{'SU35', Total count of days when daily maximum temperatures exceed + 35°C in the seven months from the start month given (e.g. from April + to October for start month of April).} + \item{'SU36', Total count of days when daily maximum temperatures exceed + 36 between June 21st and September 21st.} + \item{'SU40', Total count of days when daily maximum temperatures exceed + 40 between June 21st and September 21st.} + \item{'Spr32', Total count of days when daily maximum temperatures exceed + 32 between April 21st and June 21st.} } } \examples{ -- GitLab From 33bf9d46dfebed96cba0138430749b6906ec19d2 Mon Sep 17 00:00:00 2001 From: Eva Rifa Date: Tue, 21 Nov 2023 17:29:09 +0100 Subject: [PATCH 6/6] Correct DESCRIPTION text with adding commas --- DESCRIPTION | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a54bf19..98fecac 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -16,16 +16,16 @@ Description: Set of generalised tools for the flexible computation of climate mathematical approach which is combined with the possibility to select an arbitrary time period to define the indicator. This enables a wide range of possibilities to tailor the most suitable indicator for each particular climate - service application (agriculture, food security, energy, water management…). + service application (agriculture, food security, energy, water management, ...). This package is intended for sub-seasonal, seasonal and decadal climate predictions, but its methods are also applicable to other time-scales, provided the dimensional structure of the input is maintained. Additionally, the outputs of the functions in this package are compatible with 'CSTools'. - This package is described in Pérez-Zanón et al. (2023) - and it was developed in the context of - H2020 MED-GOLD (776467) and S2S4E (776787) projects. See Lledó et al. (2019) - and Chou et al., 2023 - for details. + This package is described in 'Pérez-Zanón et al. (2023) + ' and it was developed in the context of + 'H2020 MED-GOLD' (776467) and 'S2S4E' (776787) projects. See 'Lledó et al. (2019) + ' and 'Chou et al., 2023 + ' for details. Depends: R (>= 3.6.0) Imports: -- GitLab