From 01780d4d06b7f9a2718979ceddca95160ac5fbf8 Mon Sep 17 00:00:00 2001 From: Eva Rifa Date: Thu, 19 Oct 2023 16:08:50 +0200 Subject: [PATCH] Add startR namespace in CST_Start calls --- DESCRIPTION | 2 +- NEWS.md | 5 +++ R/CST_Start.R | 5 ++- R/sample_data_st.R | 34 +++++++-------- man/CST_Start.Rd | 5 ++- man/lonlat_prec_st.Rd | 10 ++--- man/lonlat_temp_st.Rd | 24 +++++------ vignettes/Analogs_vignette.Rmd | 54 ++++++++++++------------ vignettes/Data_Considerations.Rmd | 26 ++++++------ vignettes/MostLikelyTercile_vignette.Rmd | 24 +++++------ vignettes/MultiModelSkill_vignette.Rmd | 26 ++++++------ vignettes/MultivarRMSE_vignette.Rmd | 54 ++++++++++++------------ vignettes/PlotForecastPDF.Rmd | 10 ++--- vignettes/WeatherRegimes_vignette.Rmd | 20 ++++----- 14 files changed, 156 insertions(+), 143 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 14cd34f6..3af5dcb1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: CSTools Title: Assessing Skill of Climate Forecasts on Seasonal-to-Decadal Timescales -Version: 5.1.0 +Version: 5.1.1 Authors@R: c( person("Nuria", "Perez-Zanon", , "nuria.perez@bsc.es", role = "aut", comment = c(ORCID = "0000-0001-8568-3071")), person("Louis-Philippe", "Caron", , "louis-philippe.caron@bsc.es", role = "aut", comment = c(ORCID = "0000-0001-5221-0147")), diff --git a/NEWS.md b/NEWS.md index f2f8f099..25041008 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# CSTools 5.1.1 (Release date: 19-10-2023) + +### Fixes +- Added startR namespace in all CST_Start calls of the vignettes and sample data. + # CSTools 5.1.0 (Release date: 17-10-2023) ### Fixes diff --git a/R/CST_Start.R b/R/CST_Start.R index 722568cc..bc688557 100644 --- a/R/CST_Start.R +++ b/R/CST_Start.R @@ -9,7 +9,10 @@ #'`s2dv_cube` object. #' #'It receives any number of parameters (`...`) that are automatically forwarded -#'to the `startR::Start` function. See details in `?startR::Start`. +#'to the `startR::Start` function. See details in `?startR::Start`. The +#'auxiliary functions used to define dimensions need to be called within the +#'startR namespace (e.g. startR::indices(), startR::values(), startR::Sort(), +#'startR::CircularSort(), startR::CDORemapper(), ...). #' #'@param ... Parameters that are automatically forwarded to the `startR::Start` #' function. See details in `?startR::Start`. diff --git a/R/sample_data_st.R b/R/sample_data_st.R index cd33ee06..ee766b7a 100644 --- a/R/sample_data_st.R +++ b/R/sample_data_st.R @@ -25,13 +25,13 @@ #' latmin <- 27 #' lonlat_temp_st$exp <- CST_Start(dataset = repos_exp, #' var = 'tas', -#' member = indices(1:15), +#' member = startR::indices(1:15), #' sdate = sdates, -#' ftime = indices(1:3), -#' lat = values(list(latmin, latmax)), -#' lat_reorder = Sort(decreasing = TRUE), -#' lon = values(list(lonmin, lonmax)), -#' lon_reorder = CircularSort(0, 360), +#' ftime = startR::indices(1:3), +#' lat = startR::values(list(latmin, latmax)), +#' lat_reorder = startR::Sort(decreasing = TRUE), +#' lon = startR::values(list(lonmin, lonmax)), +#' lon_reorder = startR::CircularSort(0, 360), #' synonims = list(lon = c('lon', 'longitude'), #' lat = c('lat', 'latitude'), #' member = c('member', 'ensemble'), @@ -54,19 +54,19 @@ #' lonlat_temp_st$obs <- CST_Start(dataset = path.obs, #' var = 'tas', #' date = unique(format(dates, '%Y%m')), -#' ftime = values(dates), +#' ftime = startR::values(dates), #' ftime_across = 'date', #' ftime_var = 'ftime', #' merge_across_dims = TRUE, #' split_multiselected_dims = TRUE, -#' lat = values(list(latmin, latmax)), -#' lat_reorder = Sort(decreasing = TRUE), -#' lon = values(list(lonmin, lonmax)), -#' lon_reorder = CircularSort(0, 360), +#' lat = startR::values(list(latmin, latmax)), +#' lat_reorder = startR::Sort(decreasing = TRUE), +#' lon = startR::values(list(lonmin, lonmax)), +#' lon_reorder = startR::CircularSort(0, 360), #' synonims = list(lon = c('lon', 'longitude'), #' lat = c('lat', 'latitude'), #' ftime = c('ftime', 'time')), -#' transform = CDORemapper, +#' transform = startR::CDORemapper, #' transform_extra_cells = 2, #' transform_params = list(grid = 'r360x181', #' method = 'conservative'), @@ -119,13 +119,13 @@ NULL #' #' lonlat_prec_st <- CST_Start(dataset = path, #' var = 'prlr', -#' member = indices(1:6), +#' member = startR::indices(1:6), #' sdate = sdates, #' ftime = 121:151, -#' lat = values(list(latmin, latmax)), -#' lat_reorder = Sort(decreasing = TRUE), -#' lon = values(list(lonmin, lonmax)), -#' lon_reorder = CircularSort(0, 360), +#' lat = startR::values(list(latmin, latmax)), +#' lat_reorder = startR::Sort(decreasing = TRUE), +#' lon = startR::values(list(lonmin, lonmax)), +#' lon_reorder = startR::CircularSort(0, 360), #' synonims = list(lon = c('lon', 'longitude'), #' lat = c('lat', 'latitude'), #' ftime = c('time', 'ftime'), diff --git a/man/CST_Start.Rd b/man/CST_Start.Rd index 6069f0c8..b286bf18 100644 --- a/man/CST_Start.Rd +++ b/man/CST_Start.Rd @@ -21,7 +21,10 @@ multidimensional distributed data sets. Then, the output is transformed into } \details{ It receives any number of parameters (`...`) that are automatically forwarded -to the `startR::Start` function. See details in `?startR::Start`. +to the `startR::Start` function. See details in `?startR::Start`. The +auxiliary functions used to define dimensions need to be called within the +startR namespace (e.g. startR::indices(), startR::values(), startR::Sort(), +startR::CircularSort(), startR::CDORemapper(), ...). } \examples{ \dontrun{ diff --git a/man/lonlat_prec_st.Rd b/man/lonlat_prec_st.Rd index 81715631..981c64aa 100644 --- a/man/lonlat_prec_st.Rd +++ b/man/lonlat_prec_st.Rd @@ -30,13 +30,13 @@ extracted from forecast data available in the MEDSCOPE internal archive. lonlat_prec_st <- CST_Start(dataset = path, var = 'prlr', - member = indices(1:6), + member = startR::indices(1:6), sdate = sdates, ftime = 121:151, - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), ftime = c('time', 'ftime'), diff --git a/man/lonlat_temp_st.Rd b/man/lonlat_temp_st.Rd index 8dc554f2..f538d07a 100644 --- a/man/lonlat_temp_st.Rd +++ b/man/lonlat_temp_st.Rd @@ -31,13 +31,13 @@ next. Note that `CST_Start` internally calls `startR::Start` and then uses latmin <- 27 lonlat_temp_st$exp <- CST_Start(dataset = repos_exp, var = 'tas', - member = indices(1:15), + member = startR::indices(1:15), sdate = sdates, - ftime = indices(1:3), - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + ftime = startR::indices(1:3), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), member = c('member', 'ensemble'), @@ -60,19 +60,19 @@ next. Note that `CST_Start` internally calls `startR::Start` and then uses lonlat_temp_st$obs <- CST_Start(dataset = path.obs, var = 'tas', date = unique(format(dates, '%Y%m')), - ftime = values(dates), + ftime = startR::values(dates), ftime_across = 'date', ftime_var = 'ftime', merge_across_dims = TRUE, split_multiselected_dims = TRUE, - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), ftime = c('ftime', 'time')), - transform = CDORemapper, + transform = startR::CDORemapper, transform_extra_cells = 2, transform_params = list(grid = 'r360x181', method = 'conservative'), diff --git a/vignettes/Analogs_vignette.Rmd b/vignettes/Analogs_vignette.Rmd index de4594e8..6f63174c 100644 --- a/vignettes/Analogs_vignette.Rmd +++ b/vignettes/Analogs_vignette.Rmd @@ -135,11 +135,11 @@ dates <- as.POSIXct(seq(start, end, by = "year"), format = '%Y%m%d', 'UTC') Using the `CST_Start` function from **CSTools package**, the data available in our data store can be loaded. The following lines show how this function can be used. The experimental datasets are interpolated to the ERA5 grid by specifying the 'grid' parameter while ERA5 doesn't need to be interpolated. While dimension 'time' is set to 1 for the experimental dataset, it is set to 31 for the observations, returning the daily observations for October for the years requested in 'sdate' (2000-2006). Download the data to run the recipe under the HTTPS: downloads.cmcc.bo.it/d_chaves/ANALOGS/data_for_Analogs.Rdat or ask carmen.alvarez-castro at cmcc.it or nuria.perez at bsc.es. -``` +```r exp_path <- paste0('/esarchive/exp/ecmwf/system4_m1/daily_mean/', - '$var$_f6h/$var$_$sdate$.nc') + '$var$_f6h/$var$_$sdate$.nc') obs_path <- paste0('/esarchive/recon/ecmwf/era5/daily_mean/', - '$var$_f1h-r1440x721cds/$var$_$sdate$.nc') + '$var$_f1h-r1440x721cds/$var$_$sdate$.nc') date_exp <- '20001001' lonmax <- 50 @@ -149,18 +149,18 @@ latmin <- 22 expTAS <- CST_Start(dataset = exp_path, var = 'tas', - member = indices(1:15), + member = startR::indices(1:15), sdate = '20001001', - ftime = indices(15), - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + ftime = startR::indices(15), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), member = c('member', 'ensemble'), ftime = c('ftime', 'time')), - transform = CDORemapper, + transform = startR::CDORemapper, transform_params = list(grid = 'r1440x721', method = 'bilinear'), transform_vars = c('lat', 'lon'), @@ -170,18 +170,18 @@ expTAS <- CST_Start(dataset = exp_path, expPSL <- CST_Start(dataset = exp_path, var = 'psl', - member = indices(1:15), + member = startR::indices(1:15), sdate = '20001001', - ftime = indices(15), - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + ftime = startR::indices(15), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), member = c('member', 'ensemble'), ftime = c('ftime', 'time')), - transform = CDORemapper, + transform = startR::CDORemapper, transform_params = list(grid = 'r1440x721', method = 'bilinear'), transform_vars = c('lat', 'lon'), @@ -192,11 +192,11 @@ expPSL <- CST_Start(dataset = exp_path, obsTAS <- CST_Start(dataset = obs_path, var = 'tas', sdate = unique(format(dates, '%Y%m')), - ftime = indices(1:31), - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + ftime = startR::indices(1:31), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), ftime = c('ftime', 'time')), @@ -207,11 +207,11 @@ obsTAS <- CST_Start(dataset = obs_path, obsPSL <- CST_Start(dataset = obs_path, var = 'psl', sdate = unique(format(dates, '%Y%m')), - ftime = indices(1:31), - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + ftime = startR::indices(1:31), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), ftime = c('ftime', 'time')), diff --git a/vignettes/Data_Considerations.Rmd b/vignettes/Data_Considerations.Rmd index a07f6aeb..91214985 100644 --- a/vignettes/Data_Considerations.Rmd +++ b/vignettes/Data_Considerations.Rmd @@ -114,7 +114,7 @@ c(exp, obs) %<-% CST_Load(var = 'sfcWind', ``` ### 5. CST_Start example -``` +```r path_exp <- paste0('/esarchive/exp/meteofrance/system6c3s/monthly_mean/', '$var$_f6h/$var$_$sdate$.nc') @@ -126,13 +126,13 @@ latmax <- 79.5 latmin <- 0 exp <- CST_Start(dataset = path_exp, var = 'sfcWind', - ensemble = indices(1:9), + ensemble = startR::indices(1:9), sdate = sdates, - time = indices(1:3), - latitude = values(list(latmin, latmax)), - latitude_reorder = Sort(decreasing = TRUE), - longitude = values(list(lonmin, lonmax)), - longitude_reorder = CircularSort(0, 360), + time = startR::indices(1:3), + latitude = startR::values(list(latmin, latmax)), + latitude_reorder = startR::Sort(decreasing = TRUE), + longitude = startR::values(list(lonmin, lonmax)), + longitude_reorder = startR::CircularSort(0, 360), synonims = list(longitude = c('lon', 'longitude'), latitude = c('lat', 'latitude')), return_vars = list(latitude = NULL, @@ -145,14 +145,14 @@ dates <- as.POSIXct(sdates, format = '%Y%m%d', 'UTC') obs <- CST_Start(dataset = path_obs, var = 'sfcWind', sdate = unique(format(dates, '%Y%m')), - time = indices(2:4), - latitude = values(list(latmin, latmax)), - latitude_reorder = Sort(decreasing = TRUE), - longitude = values(list(lonmin, lonmax)), - longitude_reorder = CircularSort(0, 360), + time = startR::indices(2:4), + latitude = startR::values(list(latmin, latmax)), + latitude_reorder = startR::Sort(decreasing = TRUE), + longitude = startR::values(list(lonmin, lonmax)), + longitude_reorder = startR::CircularSort(0, 360), synonims = list(longitude = c('lon', 'longitude'), latitude = c('lat', 'latitude')), - transform = CDORemapper, + transform = startR::CDORemapper, transform_extra_cells = 2, transform_params = list(grid = 'r360x181', method = 'conservative'), diff --git a/vignettes/MostLikelyTercile_vignette.Rmd b/vignettes/MostLikelyTercile_vignette.Rmd index ded05182..66d9029b 100644 --- a/vignettes/MostLikelyTercile_vignette.Rmd +++ b/vignettes/MostLikelyTercile_vignette.Rmd @@ -82,18 +82,18 @@ repos_exp <- paste0('/esarchive/exp/ecmwf/system5c3s/monthly_mean/', '$var$_f6h/$var$_$sdate$.nc') exp <- CST_Start(dataset = repos_exp, var = clim_var, - member = indices(1:10), + member = startR::indices(1:10), sdate = dateseq, - ftime = indices(2:4), - lat = values(list(lat_min, lat_max)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lon_min, lon_max)), - lon_reorder = CircularSort(0, 360), + ftime = startR::indices(2:4), + lat = startR::values(list(lat_min, lat_max)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lon_min, lon_max)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), member = c('member', 'ensemble'), ftime = c('ftime', 'time')), - transform = CDORemapper, + transform = startR::CDORemapper, transform_extra_cells = 2, transform_params = list(grid = 'r256x128', method = 'bilinear'), @@ -118,14 +118,14 @@ obs <- CST_Start(dataset = repos_obs, var = clim_var, date = date_arr, split_multiselected_dims = TRUE, - lat = values(list(lat_min, lat_max)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lon_min, lon_max)), - lon_reorder = CircularSort(0, 360), + lat = startR::values(list(lat_min, lat_max)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lon_min, lon_max)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), ftime = c('ftime', 'time')), - transform = CDORemapper, + transform = startR::CDORemapper, transform_extra_cells = 2, transform_params = list(grid = 'r256x128', method = 'bilinear'), diff --git a/vignettes/MultiModelSkill_vignette.Rmd b/vignettes/MultiModelSkill_vignette.Rmd index dd35e256..145c0402 100644 --- a/vignettes/MultiModelSkill_vignette.Rmd +++ b/vignettes/MultiModelSkill_vignette.Rmd @@ -73,14 +73,16 @@ exp <- CST_Start(dataset = list(list(name = 'glosea5c3s', path = repos1), list(name = 'ecmwf/system4_m1', path = repos2), list(name = 'meteofrance/system5_m1', path = repos3)), var = clim_var, - member = indices(1:4), sdate = dateseq, ftime = indices(2:4), - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + member = startR::indices(1:4), + sdate = dateseq, + ftime = startR::indices(2:4), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), member = c('member', 'ensemble'), ftime = c('ftime', 'time')), - transform = CDORemapper, + transform = startR::CDORemapper, transform_extra_cells = 2, transform_params = list(grid = 'r256x128', method = 'bilinear'), transform_vars = c('lat', 'lon'), @@ -92,19 +94,19 @@ repos_obs <- "/esarchive/recon/ecmwf/erainterim/monthly_mean/$var$/$var$_$date$. obs <- CST_Start(dataset = list(list(name = 'erainterim', path = repos_obs)), var = clim_var, date = unique(format(dates_exp, '%Y%m')), - ftime = values(dates_exp), + ftime = startR::values(dates_exp), ftime_across = 'date', ftime_var = 'ftime', merge_across_dims = TRUE, split_multiselected_dims = TRUE, - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), ftime = c('ftime', 'time')), - transform = CDORemapper, + transform = startR::CDORemapper, transform_extra_cells = 2, transform_params = list(grid = 'r256x128', method = 'bilinear'), diff --git a/vignettes/MultivarRMSE_vignette.Rmd b/vignettes/MultivarRMSE_vignette.Rmd index 73f08fe3..a9f00799 100644 --- a/vignettes/MultivarRMSE_vignette.Rmd +++ b/vignettes/MultivarRMSE_vignette.Rmd @@ -76,18 +76,18 @@ repos1 <- "/esarchive/exp/glosea5/glosea5c3s/monthly_mean/$var$_f6h/$var$_$sdate exp_T <- CST_Start(dataset = list(list(name = 'glosea5c3s', path = repos1)), var = temp, - member = indices(1:9), + member = startR::indices(1:9), sdate = dateseq, - ftime = indices(2:4), - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + ftime = startR::indices(2:4), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), member = c('member', 'ensemble'), ftime = c('ftime', 'time')), - transform = CDORemapper, + transform = startR::CDORemapper, transform_extra_cells = 2, transform_params = list(grid = 'r256x128', method = 'bilinear'), @@ -100,19 +100,19 @@ repos2 <- "/esarchive/recon/ecmwf/erainterim/monthly_mean/$var$/$var$_$date$.nc" obs_T <- CST_Start(dataset = list(list(name = 'erainterim', path = repos2)), var = temp, date = unique(format(dates_exp, '%Y%m')), - ftime = values(dates_exp), + ftime = startR::values(dates_exp), ftime_across = 'date', ftime_var = 'ftime', merge_across_dims = TRUE, split_multiselected_dims = TRUE, - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), ftime = c('ftime', 'time')), - transform = CDORemapper, + transform = startR::CDORemapper, transform_extra_cells = 2, transform_params = list(grid = 'r256x128', method = 'bilinear'), @@ -126,18 +126,18 @@ repos3 <- "/esarchive/exp/glosea5/glosea5c3s/monthly_mean/$var$_f24h/$var$_$sdat exp_P <- CST_Start(dataset = list(list(name = 'glosea5c3s', path = repos3)), var = precip, - member = indices(1:9), + member = startR::indices(1:9), sdate = dateseq, - ftime = indices(2:4), - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + ftime = startR::indices(2:4), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), member = c('member', 'ensemble'), ftime = c('ftime', 'time')), - transform = CDORemapper, + transform = startR::CDORemapper, transform_extra_cells = 2, transform_params = list(grid = 'r256x128', method = 'bilinear'), @@ -148,20 +148,20 @@ exp_P <- CST_Start(dataset = list(list(name = 'glosea5c3s', path = repos3)), dates_exp <- exp_P$attrs$Dates obs_P <- CST_Start(dataset = list(list(name = 'erainterim', path = repos2)), var = precip, - date = unique(format(dates_exp, '%Y%m')), - ftime = values(dates_exp), + date = unique(format(dates_exp, '%Y%m')), + ftime = startR::values(dates_exp), ftime_across = 'date', ftime_var = 'ftime', merge_across_dims = TRUE, split_multiselected_dims = TRUE, - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), ftime = c('ftime', 'time')), - transform = CDORemapper, + transform = startR::CDORemapper, transform_extra_cells = 2, transform_params = list(grid = 'r256x128', method = 'bilinear'), diff --git a/vignettes/PlotForecastPDF.Rmd b/vignettes/PlotForecastPDF.Rmd index 34bcb223..d754df16 100644 --- a/vignettes/PlotForecastPDF.Rmd +++ b/vignettes/PlotForecastPDF.Rmd @@ -18,7 +18,7 @@ Library *CSTools*, should be installed from CRAN and loaded: library(CSTools) ``` -### 1.- A simple example +### 1. A simple example The first step is to put your forecasts in an appropriate format. For this vignette we generate some random values from two normal distributions. The PlotForecastPDF by default will plot the ensemble members, the estimated density distributions and the tercile probabilities. @@ -37,7 +37,7 @@ fcst <- array(rnorm(mean = 25, sd = 2, n = 90), dim = c(member = 30, 3)) PlotForecastPDF(fcst, tercile.limits = c(23, 27)) ``` -### 2.- Customizing the appearance of your plots +### 2. Customizing the appearance of your plots Some parameters allow to customize your plot by changing the title, the forecast labels, the variable name and units, or the colors. ```{r,fig.show = 'hide',warning=F} @@ -50,7 +50,7 @@ PlotForecastPDF(fcst, tercile.limits = c(20, 26), var.name = "Temperature (ºC)" ``` ![Example 2](./Figures/PlotForecastPDF_ex2.png) -### 3.- Adding extremes and observed values +### 3. Adding extremes and observed values Optionally, we can include the probability of extreme values or the actually observed values. The tercile limits, extreme limits and observation values can be specified for each panel separately. ```{r,fig.show = 'hide',warning=F} @@ -65,7 +65,7 @@ PlotForecastPDF(fcst, tercile.limits = rbind(c(20, 26), c(22, 28), c(15, 22)), ![Example 3](./Figures/PlotForecastPDF_ex3.png) -### 4.- Saving your plot to a file +### 4. Saving your plot to a file PlotForecastPDF uses ggplot2, so you can save the output of the function to a variable and operate with it as a ggplot2 object. For instance, you can save it to a file: ``` @@ -75,7 +75,7 @@ plot <- PlotForecastPDF(fcst, tercile.limits = c(23, 27)) ggsave("outfile.pdf", plot, width = 7, height = 5) ``` -### 5.- A reproducible example using lonlat_temp_st +### 5. A reproducible example using lonlat_temp_st This final example uses the sample lonlat data from CSTools. It is suitable for checking reproducibility of results. ```{r,fig.show = 'hide',warning=F} diff --git a/vignettes/WeatherRegimes_vignette.Rmd b/vignettes/WeatherRegimes_vignette.Rmd index 6e3655db..599b08f6 100644 --- a/vignettes/WeatherRegimes_vignette.Rmd +++ b/vignettes/WeatherRegimes_vignette.Rmd @@ -50,11 +50,11 @@ exp <- CST_Start(dataset = repos_exp, var = 'psl', member = "all", sdate = sdates, - ftime = indices(1:31), - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + ftime = startR::indices(1:31), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), member = c('member', 'ensemble'), @@ -69,15 +69,15 @@ repos_obs <-"/esarchive/recon/ecmwf/erainterim/daily_mean/$var$_f6h/$var$_$date$ obs <- CST_Start(dataset = repos_obs, var = 'psl', date = unique(format(dates0, '%Y%m')), - ftime = values(dates0), + ftime = startR::values(dates0), ftime_across = 'date', ftime_var = 'ftime', merge_across_dims = TRUE, split_multiselected_dims = TRUE, - lat = values(list(latmin, latmax)), - lat_reorder = Sort(decreasing = TRUE), - lon = values(list(lonmin, lonmax)), - lon_reorder = CircularSort(0, 360), + lat = startR::values(list(latmin, latmax)), + lat_reorder = startR::Sort(decreasing = TRUE), + lon = startR::values(list(lonmin, lonmax)), + lon_reorder = startR::CircularSort(0, 360), synonims = list(lon = c('lon', 'longitude'), lat = c('lat', 'latitude'), ftime = c('ftime', 'time')), -- GitLab