diff --git a/.Rbuildignore b/.Rbuildignore index c0e2736124c33fe6ccadcad4604bb76ac738da0f..83f840f062b3f6d4dcdc548e6458946c58f1bf70 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,5 +1,6 @@ .*\.git$ .*\.gitignore$ +.*\.gitlab$ .*\.tar.gz$ .*\.pdf$ ./.nc$ diff --git a/DESCRIPTION b/DESCRIPTION index b716d5d55a89680136ab85df0e6f7473f8df8cb5..98fecac842870eb8bc56bcfb6379228bf67f9314 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")), @@ -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: diff --git a/NEWS.md b/NEWS.md index 44285d2f5c49d8a63ca79ed8ce235d6ee3c1dacd..c3047f968328c38145628e7111e5cdcb9a0d5d8c 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 +- 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. +- Include new publication in documentation. +- Change to testthat edition 3. + # 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/R/AccumulationExceedingThreshold.R b/R/AccumulationExceedingThreshold.R index feee031aef0cee3387ad08d38ab6c70ae118c1d1..b8ae9ae798909c22d8a9ee4b4804ed09af63ac0c 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 56c3c3deddb7b0e2bbd4633f2ec36bb07faf1e6a..6d9fd6e88104d58c871254ac52171b4e4fce115d 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 60245b6bdc06fe8192b2084ad8cf35de7e1389eb..8986e3ff97e070c87550fb8c4c840617f1d2b55f 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 8c56156a73d2f063b90bb63f4e91be1ead6ac5a2..3ae23ec4d519572de99059183cc980fb5e40df57 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 9106927edf7a3c446a31f7f5da3ef3374582312a..f58bbeb27c9fc1e12efd8de06b058efd3be737be 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 74547cc7e609d4f46d227048c2aebf57faa2d4b5..99ce8016a76fca9d80920abb2b44cf89094ad79d 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 f95b8e4e5033e39704934a1670eca8ca2c94f313..4e1e93e89181fe40b8aa903ec4df8d7fd6a371f4 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 cd2676e0f1d71585de7cb71ff1867b7adfa29cbe..14507036558203064f334eeef869b8cc4dd51214 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 fa57208fe4309955c682bc2c0fc2ccd144981218..15b822c6ee37a8aea19c9f0c12d4cd91710cde44 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 cf6c8df02caae07775840bd1a5d00d1b6ca2db66..976c967f82e56354b5553c7197705d828e6473dd 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 0bea015823d0b08ecfa65db23385c6bf8c190aec..ceb9ad74b4bce72f675b055709b6c9651ad9ae7d 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 983291216727a47f9965ef0bda1e77055503afb6..b95ef79881cdb87a27bf5033c2877680d6a14e81 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 4d71ff3d17d56e3828673b61fdf72422ed02becf..c1b4a1ccd73d9938d4cebc11cf51a7205241a9e5 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 a372a1d8bb52ee97153157f75398b771ec0a2e9e..3c760ba2a0cd2573b413d20069fcd4a4619bf7a1 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 323adae91e962df2f10fe09496d7ac76b10d5bb8..3f510418f91418fceac18676036f7e4e76d0d0a3 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 9d3833f4937576a39e8b0b97dd6205511b538e4c..97caa6e060a3a837060a65053bc4632a96b19040 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 b04b4ed03fd1298e16163fe185d2326c76e52e08..4d789ddde3f07486b2a7bdde7786a3f9ee67dad3 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 831bf2cf9f3af2f549fff3f64734bd065ac6b52a..89d2fb2d4ab090c253e9c004c6871e71dcc63d35 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 db9a3d6cabff166e688ce90ab2db93ab9ebb4834..e0b8ed4521c2cb84bc8b5b078136bb2609c55fdc 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 81cda03ecbcfb1f45f1ec6da990152bc44cc8c31..e524ead2aec6c58ae859f37e329133b3ba199ecc 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 ca01c205a3fc912b0c18cc98f89e395651932fd5..71b7d73ae391bbd8c09213e74845125dc6c3d951 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 cb776d24cb9d308153cb1f230cab81ce3831828a..762b3c902dba912ac9b25d46010da7144b06b515 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 9637d58f54a4cc5b2362438d348cc44b9f4accf0..b639d0936b38c19501344037f8c2fdb8bdf86735 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 154acf0872b04ca1e2de993ceeaa94cf7b36975a..597421c4ccb4104f1851fd0430168ff2f21da2b7 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 e1e8d7cd6137accd0d8fdfaf704470246b8a272d..9155c4b41009c0af2915fd9b35050adae549a370 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 ea1a6aba15bfaff698e9b504b39028fa33cf1789..d7815bfab02725637bdddba304b18a5604b88dc1 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 31f3161d59b1a91ac779ad518bae842b80d94c20..5b9627e75d52687c567be6c34fa8c82923ed916f 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{