diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000000000000000000000000000000000000..aa8227b142f77c731283cc23cb40abe0e7fdc490 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,11 @@ +.*\.git$ +.*\.gitignore$ +.*\.tar.gz$ +.*\.pdf$ +.*^(?!inst)\.nc$ +sample_data +README\.Rmd$ +README\.md$ +\..*\.RData$ +vignettes +.gitlab-ci.yml diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..26a2200ce258f2658c2328e321b49be5d8935268 --- /dev/null +++ b/.gitignore @@ -0,0 +1,18 @@ +.*.sw* +./*.nc +*.tar.gz +*.Rcheck +.Rd2pdf* +*~ +*.Rhistory +\#*\# +build_output.txt +check_output.txt +checkout_output.txt +merge_output.txt +master_pull.txt +*.eps +README.Rmd +*.ps +Rplots.pdf +.nfs* diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..ee4c80918fa3999a444af9367d700aee1652ca4c --- /dev/null +++ b/.gitlab-ci.yml @@ -0,0 +1,10 @@ +stages: + - build +build: + stage: build + script: + - module load R +# - module load CDO + - R CMD build --resave-data . + - R CMD check --as-cran --no-manual --run-donttest s2dv_*.tar.gz + - R -e 'covr::package_coverage()' diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000000000000000000000000000000000000..6780c83d1760c794b0289f671433edacbab07636 --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,64 @@ +Package: s2dverification +Title: Set of Common Tools for Forecast Verification +Version: 2.8.6 +Authors@R: c( + person("BSC-CNS", role = c("aut", "cph")), + person("Virginie", "Guemas", , "virginie.guemas@bsc.es", role = "aut"), + person("Nicolau", "Manubens", , "nicolau.manubens@bsc.es", role = "aut"), + person("An-Chi", "Ho", , "an.ho@bsc.es", role = c("ctb", "cre")), + person("Nuria", "Perez-Zanon", , "nuria.perez@bsc.es", role = "ctb"), + person("Javier", "Garcia-Serrano", , "javier.garcia@bsc.es", role = "aut"), + person("Neven", "Fuckar", , "neven.fuckar@bsc.es", role = "aut"), + person("Louis-Philippe", "Caron", , "louis-philippe.caron@bsc.es", role = "aut"), + person("Omar", "Bellprat", , "omar.bellprat@bsc.es", role = "aut"), + person("Luis", "Rodrigues", , "lrodrigues@ic3.cat", role = "aut"), + person("Veronica", "Torralba", , "veronica.torralba@bsc.es", role = "aut"), + person("Alasdair", "Hunter", , "alasdair.hunter@bsc.es", role = "aut"), + person("Chloe", "Prodhomme", , "chloe.prodhomme@bs.es", role = "aut"), + person("Martin", "Menegoz", , "martin.menegoz@bsc.es", role = "aut"), + person("Domingo", "Manubens", , "domingo.manubens@bsc.es", role = "ctb"), + person("Constantin", "Ardilouze", , "constantin.ardilouze@meteo.fr", role = "ctb"), + person("Lauriane", "Batte", , "lauriane.batte@meteo.fr", role = "ctb"), + person("Fabian", "Lienert", , "fabian.lienert@bsc.es", role = "ctb"), + person("Julia", "Giner", , "julia.giner@bsc.es", role = "ctb"), + person("Jean-Philippe", "Baudouin", , "jean.baudouin@bsc.es", role = "ctb"), + person("Nube", "Gonzalez", , "nube.gonzalez@bsc.es", role = "ctb"), + person("Ludovic", "Auger", , "ludovic.auger@meteo.fr", role = "ctb"), + person("Nicola", "Cortesi", , "nicola.cortesi@bsc.es", role = "ctb"), + person("Eleftheria", "Exarchou", , "eleftheria.exarchou@bsc.es", role = "ctb"), + person("Ruben", "Cruz", , "ruben.cruzgarcia@bsc.es", role = "ctb"), + person("Isabel", "Andreu-Burillo", , "isabel.andreu.burillo@ic3.cat", role = "ctb"), + person("Ramiro", "Saurral", , "ramiro.saurral@ic3.cat", role = "ctb")) +Description: Set of tools to verify forecasts through the computation of typical + prediction scores against one or more observational datasets or reanalyses (a + reanalysis being a physical extrapolation of observations that relies on the + equations from a model, not a pure observational dataset). Intended for seasonal + to decadal climate forecasts although can be useful to verify other kinds of + forecasts. The package can be helpful in climate sciences for other purposes + than forecasting. +Depends: + maps, + methods, + R (>= 2.14.1) +Imports: + abind, + bigmemory, + GEOmap, + geomapdata, + mapproj, + NbClust, + ncdf4, + parallel, + plyr, + SpecsVerification (>= 0.5.0), + multiApply (>= 2.0.0) +Suggests: + easyVerification, + testthat +License: LGPL-3 +URL: https://earth.bsc.es/gitlab/es/s2dverification/wikis/home +BugReports: https://earth.bsc.es/gitlab/es/s2dverification/issues +LazyData: true +SystemRequirements: cdo +Encoding: UTF-8 +RoxygenNote: 5.0.0 diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000000000000000000000000000000000000..83b3be15f431f25977506d0247015710a623e42a --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,132 @@ +# Generated by roxygen2: do not edit by hand + +export(.BrierScore) +export(.RatioRMS) +export(.RatioSDRMS) +export(ACC) +export(Alpha) +export(AnimateMap) +export(Ano) +export(Ano_CrossValid) +export(ArrayToNetCDF) +export(BrierScore) +export(CDORemap) +export(Clim) +export(Cluster) +export(ColorBar) +export(Composite) +export(ConfigAddEntry) +export(ConfigApplyMatchingEntries) +export(ConfigEditDefinition) +export(ConfigEditEntry) +export(ConfigFileCreate) +export(ConfigFileOpen) +export(ConfigFileSave) +export(ConfigRemoveDefinition) +export(ConfigRemoveEntry) +export(ConfigShowDefinitions) +export(ConfigShowSimilarEntries) +export(ConfigShowTable) +export(Consist_Trend) +export(Corr) +export(EOF) +export(Enlarge) +export(Eno) +export(EnoNew) +export(Filter) +export(FitAcfCoef) +export(FitAutocor) +export(GenSeries) +export(Histo2Hindcast) +export(IniListDims) +export(InsertDim) +export(LeapYear) +export(Load) +export(Mean1Dim) +export(MeanListDim) +export(NAO) +export(Plot2VarsVsLTime) +export(PlotACC) +export(PlotAno) +export(PlotBoxWhisker) +export(PlotClim) +export(PlotEquiMap) +export(PlotLayout) +export(PlotMatrix) +export(PlotSection) +export(PlotStereoMap) +export(PlotVsLTime) +export(ProbBins) +export(ProjectField) +export(RMS) +export(RMSSS) +export(RatioRMS) +export(RatioSDRMS) +export(Regression) +export(SVD) +export(Season) +export(SelIndices) +export(Smoothing) +export(Spectrum) +export(Spread) +export(StatSeasAtlHurr) +export(Subset) +export(ToyModel) +export(Trend) +export(UltimateBrier) +export(clim.colors) +export(clim.palette) +import(GEOmap) +import(NbClust) +import(SpecsVerification) +import(abind) +import(bigmemory) +import(geomapdata) +import(graphics) +import(mapproj) +import(maps) +import(methods) +import(multiApply) +import(ncdf4) +import(parallel) +import(plyr) +importFrom(abind,adrop) +importFrom(grDevices,bmp) +importFrom(grDevices,col2rgb) +importFrom(grDevices,colorRampPalette) +importFrom(grDevices,dev.cur) +importFrom(grDevices,dev.new) +importFrom(grDevices,dev.off) +importFrom(grDevices,gray) +importFrom(grDevices,jpeg) +importFrom(grDevices,pdf) +importFrom(grDevices,png) +importFrom(grDevices,postscript) +importFrom(grDevices,rainbow) +importFrom(grDevices,rgb) +importFrom(grDevices,svg) +importFrom(grDevices,tiff) +importFrom(stats,IQR) +importFrom(stats,acf) +importFrom(stats,confint) +importFrom(stats,cor) +importFrom(stats,kmeans) +importFrom(stats,lm) +importFrom(stats,mad) +importFrom(stats,median) +importFrom(stats,na.fail) +importFrom(stats,na.omit) +importFrom(stats,na.pass) +importFrom(stats,pf) +importFrom(stats,predict) +importFrom(stats,pt) +importFrom(stats,qnorm) +importFrom(stats,qt) +importFrom(stats,quantile) +importFrom(stats,rnorm) +importFrom(stats,runif) +importFrom(stats,sd) +importFrom(stats,setNames) +importFrom(stats,spectrum) +importFrom(stats,ts) +importFrom(stats,window) diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000000000000000000000000000000000000..a12ca5094ea62b663c817d84595d53a600bd99fb --- /dev/null +++ b/NEWS.md @@ -0,0 +1,145 @@ +# s2dv 0.0.1 (Release date: 2020-02-) +- The package is the advanced version of package 's2dverification', adopting the regime of package 'multiApply' for all the analytic functions. Most of the other functions for plotting and data retrieval in 's2dverification' are also preserved in this package. +- Because of the adoption of 'multiApply' regime, the functions work well with package 'startR'. +- All the packages mentioned above are developed by BSC-CNS. + +# s2dverification 2.8.6 (Release date: 2019-10-17) +- Apply Roxygen2 format to all the files. +- Bug fix in Composite(). +- Bug fix in Ano(). Recommend to assign the dimensions by name to avoid confusion when the dimensions have same length. +- Trend() documentation error fix. +- Introduce new function PlotMatrix(). + +# s2dverification 2.8.0 (Release date: 2017-02-13) +- Change licence from GPL-3 to LGPL-3. +- New veriApply compatible score functions (.BrierScore, .Corr, .RMS, .RMSSS, .RatioRMS, .RatioSDRMS and .Trend). +- New function CDORemap to interpolate R arrays with CDO. +- New function ArrayToNetCDF to save R arrays with metadata in NetCDF files. +- Enhance plot_timeseries.R and plot_maps.R example scripts to work with file-per-chunk data, for auto-ecearth v3.2.1a. +- Add colour-blind colour bars for the map plots. +- Add warning in Load when extrapolating data. +- Bug fix in ProbBins when called with cross-validation. +- Enhance documentation. +- Adapt UltimateBrier to SpecsVerification 0.5-0. +- Enhancements to adjust size and resolution in plotting functions. +- Solve PlotEquiMap bug when values equal to the lower limit. +- Bug fix in Ano. +- Bug fix in PlotVsLTime. +- Small update in the configuration file. + +# s2dverification 2.7.0 (Release date: 2016-08-24) +Enhanced PlotEquiMap() and PlotStereoMap() with lots of new options and fixed issues: +- Colour bar with triangle ends and lots of new features. +- Margins, labels, ticks, colour bar, titles now arranged properly. +- Now possibile to adjust colour and border of continents, size, colour and type of contour lines, size of labels, ticks and margins, colour and width of boxes, etc. +- Draw multiple superimposed dot/symbol layers. +- Draw boxes in PlotStereoMap(). +- PlotStereoMap() with bounding circle. +- Add function PlotLayout() to automatically generate complex figure layouts and populate with plots from multi-dimensional arrays. +- Fix and updated corrupted example scripts (required for new auto-ecearth releases to work). +- Add function Subset() to easily take chunks of data arrays. +- Fix bug in Load() under some particular configurations. +- Enhance margins in PlotAno(). +- Update sample data to be together with metadata as provided by Load(). +- Update and fix in the BSC Load() configuration file. + +# s2dverification 2.6.0 (Release date: 2016-06-06) +- Update configuration file. +- Functions to compute variability modes and project data on EOF() and ProjectField(). +- Function to compute co·variability modes: SVD(), by Javi. +- Function to compute the NAO: NAO(), by Fabian, Virginie, Lauriane, Martin. +- Brier score/skill score accounting for small ensemble/start date sample size: UltimateBrier(). +- K-means spatial clustering: Cluster(). +- Synthetic data generator: ToyModel(). +- Tropical cyclone downscaling: StatSeasAtlHurr(). +- Function to composite fields: Composite(). +- Function to generate map animations: AnimateMap(). +- Function to plot time series with box-and-whisker plots: PlotBoxWhisker(). +- Possible to disable computation of confidence intervals or p-values in ACC(), Corr(), RatioRMS(), RatioSDRMS(), RMS(), RMSSS(), Spread() and Trend(). +- Possible to adjust confidence level in all functions that provide confidence intervals: ACC(), Corr(), RMS(), Spread() and Trend(). +- Possible to plot arrows in PlotEquiMap(). +- Possible to save plots in multiple formats, to file or onscreen from all plot functions. +- Objects returned by Load() are now closer to the format in downscaleR. The initial and end date of each time step is provided now. +- Enhancements in Smoothing(). +- Load() now stops if the tag $START_DATE$/$YEAR$+$MONTH$+$DAY$ is not in the path pattern of any of the experiments. + +# s2dverification 2.5.0 (Release date: 2016-01-04) +- Fix bugs when using masks in Load() +- Able to specify masks with paths to NetCDF files + +# s2dverification 2.4.7 (Release date: 2015-11-15) +- Update plot_timeseries.R to new paths and to 'ncdf4'. +- Improve performance when retrieving subsets of data (regions of earth or time periods). +- Add possibility to use Load() without a configuration file. See details on parameters 'exp' and 'obs' in ?Load + +Load() now returns plenty of metadata. Highlighted: +- Paths to all loaded files +- Paths to not found files +- Stamp with all the provided parameters to exactly reproduce any Load() call +- The name of the common grid (if any), following CDO's naming conventions + +Other enhancements in Load(): +- Enhance error handling and error messages +- Add “progress bar” +- Detect automatically grid of the files. No need to specify it +- Detect automatically if the requested variable is 2-dimensional or global mean. No need to specify it +- Possibility to load observations only, from a limited period of time only +- Possibility to load NetCDF files with disordered dimensions +- Remove system dependency of 's2dverification' to NCO and some GNU tools +- Simplify configuration file: removed lists of variables and reduced from 5 tables to 2, one for experimental datasets and one for observational datasets. You can convert old configuration files to the new format with the script in /shared/earth/software/scripts/convertConfig.R as follows: /shared/earth/software/scripts/convertConfig.R /path/to/configfile.conf +- Fix and updated the sample script plot_timeseries.R +- Fix wrong entries in BSC configuration file for some ice variables. + +# s2dverification 2.4.0 (Release date: 2015-07-27) +- Option to draw rectangles in PlotEquiMap() +- Motification of Corr() to accomodate ranked correlation +- Add the possibility to load the second set of HadCM3 decadal data (i3p1) +- Add functions to assist in manipulating the configuration file +- Improve examples that use extremely reduced experimental and observational datasets +- Uniformize documentation style +- Add possibility to configure dimension names to look for inside NetCDF files +- Add the possibility to load ESA observations from SMHI +- Fix bug that happened in some cases when a common grid is not specified + +# s2dverification 2.3.2 (Release date: 2015-04-23) +- New CRPS() function to compute the continuous ranked probability score for ensemble forecasts. +- New ProbBins() function to compute probabilistic information of a forecast relative to a threshold or a quantile. +- Load() stops and warns if the masks provided are not in the correct grid. +- Load() didn't apply, as expected, the same masks in observations as in experiments when possible. Now fixed. +- Enhancement in Clim() documentation. +- Enhancements in Load() and configuration file documentation. +- HadSLP dataset is now loadable + +# s2dverification 2.3.1 (Release date: 2015-03-09) +- Loading observations only fixed +- Loading only one leadtime fixed +- Loading a 2D variable when the first observation was not stored in file-per-dataset format fixed +- Parameter 'ncores' changed to 'nprocs' +- Improvements in configuration file mechanism and documentation + +# s2dverification 2.3.0 (Release date: 2015-03-02) +- Configuration file mechanism to specify new dataset or variable paths, grids, etc. +- New parameters in Load() to specify maximum and minimum values. +- New supported dataset formats. See '?Load' in R after loadings2dverificationfor more information. +- More efficient memory usage in Load() and usage of multiple parallel processes (faster). +- NetCDF4 + OPeNDAP support + +# s2dverification 2.2.0 (Release date: 2014-12-16) +- ACC provides confidence intervals obtained with bootstrap method +- Function to plot ACC score +- Function to plot variables on a polar stereographic projection +- Possibility of loading observations only +- Possibility to load more ice variables +- Adjustable significance level in the Corr function +- Adjustable number size in ColorBar + +# s2dverification 2.1.0 (Release date: 2014-01-23) +- Demo scripts 'plot_timeseries.R' and 'plot_maps.R' available in the 'inst/doc' directory in thes2dverificationrepository. +- Documentation on how to specify the grids and masks to the function Load() has been added to its help page, code and package manual. + +# s2dverification 2.0.0 (Release date: 2013-08-02) +- Use of the standard R package structure. +- Use of the google's R style guide. +- Functions that involved RClim set of funcions have been kept apartfrom the package (AnimVsLTime, BlueRed, PlotMap, ProjMap) as well as the authors. +- New functions have been added: Alpha, EnoNew, Filter, FitAcfCoef, FitAutocor, GenSeries, Spectrum. +- Extended help. diff --git a/inst/config/BSC.conf b/inst/config/BSC.conf new file mode 100644 index 0000000000000000000000000000000000000000..aca91dbb44fbb0fc2212fbcecfa06ef3cd2a0f0a --- /dev/null +++ b/inst/config/BSC.conf @@ -0,0 +1,100 @@ +# s2dverification configuration file +# +# Check ?ConfigFileOpen after loading s2dverification for detailed +# documentation on this configuration file. + +############# +!!definitions +############# +# Mandatory defaults +DEFAULT_EXP_MAIN_PATH = /es*/exp/*/$EXP_NAME$/ +DEFAULT_EXP_FILE_PATH = $STORE_FREQ$$SUFFIX$/$VAR_NAME$$FILE_GRID$*/$EXP_FILE$ +DEFAULT_OBS_MAIN_PATH = /es*/obs/*/$OBS_NAME$/ +DEFAULT_OBS_FILE_PATH = $STORE_FREQ$$SUFFIX$/$VAR_NAME$*/$OBS_FILE$ +DEFAULT_NC_VAR_NAME = $VAR_NAME$ +DEFAULT_SUFFIX = _mean +DEFAULT_VAR_MIN = -1e19 +DEFAULT_VAR_MAX = 1e19 +DEFAULT_DIM_NAME_LONGITUDES = longitude +DEFAULT_DIM_NAME_LATITUDES = latitude +DEFAULT_DIM_NAME_MEMBERS = ensemble + +# Helper variables +EXP_FILE = $VAR_NAME$_*$START_DATE$*.nc +OBS_FILE = $VAR_NAME$_$YEAR$$MONTH$*.nc +RECON_LIST = (20thcr_v2|copernicus012|ds083.2|ecco|era40|era40-erainterim|eraclim|erainterim|erainterim-lores|eraland|gecco_v2|gfs|glorys2_v1|glorys2_v3|glosea5|ishii-kimoto|jra55|merra|merra_v2|ncep-reanalysis|oaflux|oi_v2|orap5|piomas|seaice-lim2|sst|tropflux|nemovar_system4|era5) + +# Defaults for extra variables from Load +DEFAULT_FILE_GRID = + +###################### +!!table of experiments +###################### +#exp_name, var_name[, exp_main_path[, exp_file_path[, nc_var_name[, suffix[, var_min[, var_max]]]]]] +# By default, any pair (var, exp) is associated to the default values +# As experiment name, the user is expected to provide model/expid +.*, .*, *, *, *, *, *, * +# But we also want to allow that they provide expid only +.*/.*, .*, /es*/exp/$EXP_NAME$/, *, *, *, *, * +# If the requested experiment is in the list of reconstructions, it will be fetched in recon +$RECON_LIST$, .*, /es*/recon/*/$EXP_NAME$/, *, *, *, *, * +.*/$RECON_LIST$, .*, /es*/recon/$EXP_NAME$/, *, *, *, *, * +# If the variable is of the kind varname_whatever it will be fetched in the monthly/daily_statistics instead of _mean +.*, .*_.*, *, *, *, _statistics, *, * +# Ocean variables follow special conventions +.*, psi, *, *, sobarstf, *, *, * +.*, .*heatc, *, $STORE_FREQ$_mean/heatc/$EXP_FILE$, thc, *, *, * +.*, moc_.*, *, $STORE_FREQ$_mean/moc/$EXP_FILE$, zomsfatl, *, *, * +.*, max_moc_.*, *, $STORE_FREQ$_mean/moc/$EXP_FILE$, maxmoc, *, *, * +.*, .*Pac_stc_.*, *, $STORE_FREQ$_mean/moc/$EXP_FILE$, zomsfpac, *, *, * +.*, .*Atl_stc_.*, *, $STORE_FREQ$_mean/moc/$EXP_FILE$, zomsfatl, *, *, * +.*, sal_.*, *, $STORE_FREQ$_mean/saltc/$EXP_FILE$, vertmeansal, *, *, * +.*, temp_.*, *, $STORE_FREQ$_mean/sections/$EXP_FILE$, votemper, *, *, * +.*, sian, *, $STORE_FREQ$$SUFFIX$/ice/siasiesiv_N*$START_DATE$*.nc, sia, *, *, * +.*, sien, *, $STORE_FREQ$$SUFFIX$/ice/siasiesiv_N*$START_DATE$*.nc, sie, *, *, * +.*, sivn, *, $STORE_FREQ$$SUFFIX$/ice/siasiesiv_N*$START_DATE$*.nc, siv, *, *, * +.*, sias, *, $STORE_FREQ$$SUFFIX$/ice/siasiesiv_S*$START_DATE$*.nc, sia, *, *, * +.*, sies, *, $STORE_FREQ$$SUFFIX$/ice/siasiesiv_S*$START_DATE$*.nc, sie, *, *, * +.*, sivs, *, $STORE_FREQ$$SUFFIX$/ice/siasiesiv_S*$START_DATE$*.nc, siv, *, *, * +.*, sia_.*, *, $STORE_FREQ$_mean/ice/sia_Arcticreg1*$START_DATE$*.nc, *, *, *, * +.*, sie_.*, *, $STORE_FREQ$_mean/ice/sie_Arcticreg1*$START_DATE$*.nc, *, *, *, * +.*, siv_.*, *, $STORE_FREQ$_mean/ice/siv_Arcticreg1*$START_DATE$*.nc, *, *, *, * + +####################### +!!table of observations +####################### +#obs_name, var_name[, obs_main_path[, obs_file_path[, nc_var_name[, suffix[, var_min[, var_max]]]]]] +# By default, any pair (var, obs) is associated to the default values +# As observation name, the user is expected to provide obsid +.*, .*, *, *, *, *, *, * +# But we also want to allow institution/obsid +.*/.*, .*, /es*/obs/$OBS_NAME$/, *, *, *, *, * +# If the requested observation is in the list of reconstructions, it will be fetched in recon +$RECON_LIST$, .*, /es*/recon/*/$OBS_NAME$/, *, *, *, *, * +.*/$RECON_LIST$, .*, /es*/recon/$OBS_NAME$/, *, *, *, *, * +# As in experiments, we associate all variables of the kind varname_whatever to the folder _statistics instead of _mean +.*, .*_.*, *, *, *, _statistics, *, * +.*, (tos|tas|prlr), *, *, *, *, -999, 599 +# file per dataset experiments +(ecmwf/)?nemovar-s4, moc_.*, /es*/exp/ecmwf/nemovar-s4/, $STORE_FREQ$_mean/moc/$VAR_NAME$_nemovar_s4_19570901_fc0-4_195709_201212.nc, zomsfatl, *, *, * +", max_moc_.*, ", ", maxmoc, *, *, * +", .*Pac_stc_.*, ", $STORE_FREQ$_mean/mon/$VAR_NAME$_nemovar_s4_19570901_fc0-4_195709_201108.nc, zomsfpac, *, *, * +", .*Atl_stc_.*, ", ", zomsfatl, *, *, * +", heatc, ", $STORE_FREQ$_mean/heatc/$VAR_NAME$_nemovar_s4_19570901_fc0-4_195709_201212.nc, thc, *, *, * +", .*_heatc, ", ", thc, *, *, * +# file per dataset observations +(ukmo/)?hadisst_v1.1,sien, *, $STORE_FREQ$_mean/ice/ice_hadisst_N.nc, sie, *, *, * +", sian, *, ", sia, *, *, * +", sies, *, $STORE_FREQ$_mean/ice/ice_hadisst_S.nc, sie, *, *, * +", sias, *, ", sia, *, *, * +", si(a|e|v)_.*, *, $STORE_FREQ$_mean/ice/siasie_HadISST.nc,*, *, *, * +(nasa/)?nsidc-siasie, sien, *, $STORE_FREQ$_mean/ice/ice_nsidc_N.nc, sie, *, *, * +", sian, *, ", sia, *, *, * +", sies, *, $STORE_FREQ$_mean/ice/ice_nsidc_S.nc, sie, *, *, * +", sias, *, ", sia, *, *, * +", si(a|e|v)_.*, *, $STORE_FREQ$_mean/ice/siasie_NSIDC.nc, *, *, *, * +# file per dataset reconstructions +glorys2_v1, .*heatc, *, $STORE_FREQ$_mean/heatc/$VAR_NAME$_*_19930101_fc0-0_199301_200912.nc, thc +(ucl/)?seaice-lim2, sivn, *, $STORE_FREQ$_mean/ice/siasiesiv_N_ucl_fc0-0_19790101_197901_200712.nc, siv, *, *, * +", sivs, *, $STORE_FREQ$_mean/ice/siasiesiv_S_ucl_fc0-0_19790101_197901_200712.nc, siv, *, *, * +(psc/)?piomas, sivn, *, $STORE_FREQ$_mean/ice/sivN_piomas.nc, sivN, *, *, * diff --git a/inst/config/template.conf b/inst/config/template.conf new file mode 100644 index 0000000000000000000000000000000000000000..b6f727eef3235fedd5a31879811e7eac122d2756 --- /dev/null +++ b/inst/config/template.conf @@ -0,0 +1,44 @@ +# s2dverification configuration file +# +# Check ?LoadConfigurationFile after loading s2dverification for detailed +# documentation on this configuration file. + +################# +!!definitions +################# +DEFAULT_EXP_MAIN_PATH = /data/exp/$EXP_NAME$/ +DEFAULT_EXP_FILE_PATH = $VAR_NAME$/$START_DATE$.nc +DEFAULT_GRID = t106grid +DEFAULT_NC_VAR_NAME = $VAR_NAME$ +DEFAULT_SUFFIX = +DEFAULT_VAR_MIN = -1e19 +DEFAULT_VAR_MAX = 1e19 +DEFAULT_OBS_MAIN_PATH = /data/$OBS_NAME$/ +DEFAULT_OBS_FILE_PATH = $VAR_NAME$/$YEAR$$MONTH$.nc + +DEFAULT_DIM_NAME_LONGITUDES = longitude +DEFAULT_DIM_NAME_LATITUDES = latitude +DEFAULT_DIM_NAME_MEMBERS = ensemble + +###################### +!!table of experiments +###################### +#exp_name, var_name[, exp_main_path[, exp_file_path[, nc_var_name[, suffix[, var_min[, var_max]]]]]]] +.*, .* +#grid exception for some experiments +ecmwf, .*, *, * +#nc variable name exception for some variables +.*, sia(N|S), *, *, sia +.*, sie(N|S), *, *, sie +.*, siv(N|S), *, *, siv +#special file paths for some variables in some experimental datasets +ecmwf, tasmax, *, statistics/$VAR_NAME$/$START_DATE$.nc + +####################### +!!table of observations +####################### +#obs_name, var_name[, obs_main_path[, obs_file_path[, nc_var_name[, suffix[, var_min[, var_max]]]]]] +.*, .* +#special nc variable name for some variables in some observational datasets +UCL, sivN, *, *, siv +UCL, sivS, *, *, siv diff --git a/inst/sample_data/README.txt b/inst/sample_data/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc4cb21fcb084f19eaa249e11793582a382c104 --- /dev/null +++ b/inst/sample_data/README.txt @@ -0,0 +1,3 @@ +These data sets provide data in function of longitudes and latitudes for the variable 'tos', i.e. sea surface temperature, over the world from the decadal climate prediction experiment run at IC3 in the context of the CMIP5 project. The experimental data belongs to an experiment named 'i00k' in the IC3 local database. +The observational data used for verification is the 'ERSST' observational dataset, in this example. +The resolutions of the experimental and observational datasets have been drastically reduced so as to make it on CRAN. The original resolution names (under CDO conventions) were t106grid and r180x89 respectively. 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new file mode 100644 index 0000000000000000000000000000000000000000..a7dec961977515915d829f763b67f71ad23ccd14 --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,4 @@ +library(testthat) +library(s2dv) + +test_check("s2dv") diff --git a/tests/testthat/test-Clim.R b/tests/testthat/test-Clim.R new file mode 100644 index 0000000000000000000000000000000000000000..d9617a95272f3d151473c18409229f0b97feb668 --- /dev/null +++ b/tests/testthat/test-Clim.R @@ -0,0 +1,194 @@ +context("s2dverification::Clim tests") + +############################################## + # dat1 + set.seed(1) + exp1 <- array(rnorm(360), dim = c(dataset = 1, member = 3, sdate = 5, + ftime = 3, lon = 2, lat = 4)) + set.seed(2) + obs1 <- array(rnorm(120), dim = c(dataset = 1, member = 1, + ftime = 3, lon = 2, lat = 4, sdate = 5)) + # dat2 + exp2 <- exp1 + set.seed(1) + na <- floor(runif(5, min = 1, max = 360)) + exp2[na] <- NA + obs2 <- obs1 + set.seed(2) + na <- floor(runif(30, min = 1, max = 120)) + obs2[na] <- NA + +############################################## +test_that("1. Input checks", { + + expect_error( + Clim(c(), c()), + "Parameter 'exp' and 'obs' cannot be NULL." + ) + expect_error( + Clim(c('b'), c('a')), + "Parameter 'exp' and 'obs' must be a numeric array." + ) + expect_error( + Clim(c(1:10), c(2:4)), + paste0("Parameter 'exp' and 'obs' must be at least two dimensions ", + "containing time_dim and dat_dim.") + ) + expect_error( + Clim(array(1:10, dim = c(2, 5)), array(1:4, dim = c(2, 2))), + "Parameter 'exp' and 'obs' must have dimension names." + ) + expect_error( + Clim(array(1:10, dim = c(a = 2, c = 5)), array(1:4, dim = c(a = 2, b = 2))), + "Parameter 'exp' and 'obs' must have same dimension name" + ) + expect_error( + Clim(exp1, obs1, method = TRUE), + "Parameter 'method' must be one of 'clim', 'kharin' or 'NDV'." + ) + expect_error( + Clim(exp1, obs1, time_dim = c('sdate','ftime')), + "Parameter 'time_dim' must be a character string." + ) + expect_error( + Clim(exp1, obs1, time_dim = 'asd'), + "Parameter 'time_dim' is not found in 'exp' or 'obs' dimension." + ) + expect_error( + Clim(exp1, obs1, dat_dim = c(1,2)), + "Parameter 'dat_dim' must be a character vector." + ) + expect_error( + Clim(exp1, obs1, dat_dim = c('member', 'dat')), + "Parameter 'dat_dim' is not found in 'exp' or 'obs' dimension." + ) + expect_error( + Clim(exp1, obs1, ftime_dim = 4), + "Parameter 'ftime_dim' must be a character string." + ) + expect_error( + Clim(exp1, obs1, ftime_dim = 'f'), + "Parameter 'ftime_dim' is not found in 'exp' or 'obs' dimension." + ) + expect_error( + Clim(exp1, obs1, memb_dim = c('dataset', 'member')), + "Parameter 'memb_dim' must be a character string." + ) + expect_error( + Clim(exp1, obs1, memb_dim = 'memb'), + "Parameter 'memb_dim' is not found in 'exp' or 'obs' dimension." + ) + expect_error( + Clim(exp1, obs1, memb = 'member'), + "Parameter 'memb' must be one logical value." + ) + expect_error( + Clim(exp1, obs1, na.rm = na.omit), + "Parameter 'na.rm' must be one logical value." + ) + expect_error( + Clim(exp1, obs1, ncores = T), + "Parameter 'ncores' must be a positive integer." + ) + expect_error( + Clim(array(1:10, dim = c(dataset = 2, member = 5, sdate = 4, ftime = 3)), + array(1:4, dim = c(dataset = 2, member = 2, sdate = 5, ftime = 3))), + paste0("Parameter 'exp' and 'obs' must have same length of ", + "all dimension expect 'dat_dim'.") + ) + +}) + +############################################## +test_that("2. Output checks: dat1", { + + expect_equal( + dim(Clim(exp1, obs1)$clim_exp), + c(dataset = 1, member = 3, ftime = 3, lon = 2, lat = 4) + ) + expect_equal( + dim(Clim(exp1, obs1, memb = FALSE)$clim_exp), + c(dataset = 1, ftime = 3, lon = 2, lat = 4) + ) + expect_equal( + dim(Clim(exp1, obs1, time_dim = 'lon')$clim_exp), + c(dataset = 1, member = 3, sdate = 5, ftime = 3, lat = 4) + ) + expect_equal( + dim(Clim(exp1, obs1, method = 'kharin')$clim_exp), + c(sdate = 5, dataset = 1, member = 3, ftime = 3, lon = 2, lat = 4) + ) + expect_equal( + dim(Clim(exp1, obs1, method = 'NDV')$clim_exp), + c(sdate = 5, dataset = 1, member = 3, ftime = 3, lon = 2, lat = 4) + ) + expect_equal( + dim(Clim(exp1, obs1)$clim_obs), + c(dataset = 1, member = 1, ftime = 3, lon = 2, lat = 4) + ) + expect_equal( + dim(Clim(exp1, obs1, method = 'kharin')$clim_obs), + c(dataset = 1, member = 1, ftime = 3, lon = 2, lat = 4) + ) + expect_equal( + dim(Clim(exp1, obs1, method = 'NDV')$clim_obs), + c(dataset = 1, member = 1, ftime = 3, lon = 2, lat = 4) + ) + expect_equal( + (Clim(exp1, obs1)$clim_obs)[1:5], + c(0.14831161, -0.60462627, 0.06609153, -0.23378059, 0.50553522), + tolerance = 0.001 + ) + expect_equal( + (Clim(exp1, obs1, memb = FALSE)$clim_exp)[1:5], + c(0.10084284, 0.06407350, 0.09028584, 0.17526332, 0.18004387), + tolerance = 0.001 + ) + expect_equal( + max(Clim(exp1, obs1)$clim_exp, na.rm = T), + 1.026186, + tolerance = 0.001 + ) + expect_equal( + max(Clim(exp1, obs1, method = 'kharin')$clim_exp, na.rm = T), + 2.282634, + tolerance = 0.001 + ) + expect_equal( + min(Clim(exp1, obs1, method = 'NDV')$clim_exp, na.rm = T), + -4.025745, + tolerance = 0.001 + ) + +}) + +############################################## +test_that("3. Output checks: dat2", { + + expect_equal( + (Clim(exp2, obs2)$clim_obs)[1:5], + c(0.23142987, -0.60462627, -0.03669491, -0.14193572, 0.61163024), + tolerance = 0.001 + ) + expect_equal( + (Clim(exp2, obs2)$clim_exp)[1:5], + c(0.01054951, -0.04744191, -0.03533071, 0.14149945, 0.02359945), + tolerance = 0.001 + ) + expect_equal( + length(which(is.na(Clim(exp2, obs2, na.rm = FALSE)$clim_exp))), + 57 + ) + expect_equal( + length(which(is.na(Clim(exp2, obs2, na.rm = FALSE)$clim_obs))), + 19 + ) + expect_equal( + length(which(is.na(Clim(exp2, obs2)$clim_obs))), + 0 + ) + +}) + +############################################## + diff --git a/tests/testthat/test-Corr.R b/tests/testthat/test-Corr.R new file mode 100644 index 0000000000000000000000000000000000000000..490f5e72ec624a938b9ee74920debdf648f4c8ca --- /dev/null +++ b/tests/testthat/test-Corr.R @@ -0,0 +1,165 @@ +context("s2dverification::Corr tests") + +############################################## + # dat1 + set.seed(1) + exp1 <- array(rnorm(240), dim = c(dataset = 1, member = 2, sdate = 5, + ftime = 3, lat = 2, lon = 4)) + + set.seed(2) + obs1 <- array(rnorm(120), dim = c(dataset = 1, member = 1, sdate = 5, + ftime = 3, lat = 2, lon = 4)) + set.seed(2) + na <- floor(runif(10, min = 1, max = 120)) + obs1[na] <- NA + +############################################## +test_that("1. Input checks", { + + expect_error( + Corr(c(), c()), + "Parameter 'exp' and 'obs' cannot be NULL." + ) + expect_error( + Corr(c('b'), c('a')), + "Parameter 'exp' and 'obs' must be a numeric array." + ) + expect_error( + Corr(c(1:10), c(2:4)), + paste0("Parameter 'exp' and 'obs' must be at least two dimensions ", + "containing time_dim and memb_dim.") + ) + expect_error( + Corr(array(1:10, dim = c(2, 5)), array(1:4, dim = c(2, 2))), + "Parameter 'exp' and 'obs' must have dimension names." + ) + expect_error( + Corr(array(1:10, dim = c(a = 2, c = 5)), array(1:4, dim = c(a = 2, b = 2))), + "Parameter 'exp' and 'obs' must have same dimension name" + ) + expect_error( + Corr(exp1, obs1, memb_dim = 1), + "Parameter 'memb_dim' must be a character string." + ) + expect_error( + Corr(exp1, obs1, memb_dim = 'a'), + "Parameter 'memb_dim' is not found in 'exp' or 'obs' dimension." + ) + expect_error( + Corr(exp1, obs1, time_dim = c('sdate', 'a')), + "Parameter 'time_dim' must be a character string." + ) + expect_error( + Corr(exp1, obs1, time_dim = 'a'), + "Parameter 'time_dim' is not found in 'exp' or 'obs' dimension." + ) + expect_error( + Corr(exp1, obs1, comp_dim = c('sdate', 'ftime')), + "Parameter 'comp_dim' must be a character string." + ) + expect_error( + Corr(exp1, obs1, comp_dim = 'a'), + "Parameter 'comp_dim' is not found in 'exp' or 'obs' dimension." + ) + expect_error( + Corr(exp1, obs1, limits = c(1,3)), + "Paramter 'comp_dim' cannot be NULL if 'limits' is assigned." + ) + expect_error( + Corr(exp1, obs1, comp_dim = 'ftime', limits = c(1)), + paste0("Parameter 'limits' must be a vector of two positive ", + "integers smaller than the length of paramter 'comp_dim'.") + ) + expect_error( + Corr(exp1, obs1, conf.lev = -1), + "Parameter 'conf.lev' must be a numeric number between 0 and 1." + ) + expect_error( + Corr(exp1, obs1, method = 1), + "Parameter 'method' must be one of 'kendall', 'spearman' or 'pearson'." + ) + expect_error( + Corr(exp1, obs1, conf = 1), + "Parameter 'conf' must be one logical value." + ) + expect_error( + Corr(exp1, obs1, pval = 'TRUE'), + "Parameter 'pval' must be one logical value." + ) + expect_error( + Corr(exp1, obs1, ncores = 1.5), + "Parameter 'ncores' must be a positive integer." + ) + expect_error( + Corr(exp = array(1:10, dim = c(sdate = 1, member = 5, a = 1)), + obs = array(1:4, dim = c(a = 1, sdate = 2, member = 2))), + "Parameter 'exp' and 'obs' must have same length of all dimension expect 'memb_dim'." + ) + expect_error( + Corr(exp = array(1:10, dim = c(sdate = 2, member = 5, a = 1)), + obs = array(1:4, dim = c(a = 1, sdate = 2, member = 2))), + "The length of time_dim must be at least 3 to compute correlation." + ) + +}) + +############################################## +test_that("2. Output checks: dat1", { + + expect_equal( + dim(Corr(exp1, obs1)$corr), + c(n_exp = 2, n_obs = 1, dataset = 1, ftime = 3, lat = 2, lon = 4) + ) + expect_equal( + head(Corr(exp1, obs1)$corr), + c(0.11503859, -0.46959987, -0.64113021, 0.09776572, -0.32393603, 0.27565829), + tolerance = 0.001 + ) + expect_equal( + length(which(is.na(Corr(exp1, obs1)$p.val))), + 2 + ) + expect_equal( + max(Corr(exp1, obs1)$conf.lower, na.rm = T), + 0.6332941, + tolerance = 0.001 + ) + expect_equal( + length(which(is.na(Corr(exp1, obs1, comp_dim = 'ftime')$corr))), + 6 + ) + expect_equal( + length(which(is.na(Corr(exp1, obs1, comp_dim = 'ftime', limits = c(2, 3))$corr))), + 2 + ) + expect_equal( + summary(Corr(exp1, obs1, conf.lev = 0.99)$conf.upper)[1], + c(Min. = 0.2748), + tolerance = 0.0001 + ) + expect_equal( + length(Corr(exp1, obs1, conf = FALSE, pval = FALSE)), + 1 + ) + expect_equal( + length(Corr(exp1, obs1, conf = FALSE)), + 2 + ) + expect_equal( + length(Corr(exp1, obs1, pval = FALSE)), + 3 + ) + expect_equal( + head(Corr(exp1, obs1, method = 'spearman')$corr), + c(-0.3, -0.4, -0.6, 0.3, -0.3, 0.2) + ) + expect_equal( + range(Corr(exp1, obs1, method = 'spearman', comp_dim = 'ftime')$p.val, na.rm = T), + c(0.0, 0.5), + tolerance = 0.001 + ) + +}) + +############################################## + diff --git a/tests/testthat/test-Eno.R b/tests/testthat/test-Eno.R new file mode 100644 index 0000000000000000000000000000000000000000..1b85092c86c2d436e3d694a227a7097511498713 --- /dev/null +++ b/tests/testthat/test-Eno.R @@ -0,0 +1,89 @@ +context("s2dverification::Eno tests") + +############################################## + set.seed(1) + dat1 <- array(rnorm(800), dim = c(dataset = 1, member = 2, sdate = 4, + ftime = 4, lat = 10, lon = 10)) + set.seed(1) + na <- floor(runif(40, min = 1, max = 800)) + dat1[na] <- NA + + + dat2 <- array(c(-5, -7, -10:10, 12, 11, 7, 16), + dim = c(date = 13, ftime = 2)) + +############################################## +test_that("1. Input checks", { + + expect_error( + Eno(c()), + "Parameter 'data' cannot be NULL." + ) + expect_error( + Eno(data = 'a'), + "Parameter 'data' must be a numeric array." + ) + expect_error( + Eno(data = array(1:10, dim = c(2,5))), + "Parameter 'data' must have dimension names." + ) + expect_error( + Eno(data = 1:10, time_dim = 12), + "Parameter 'time_dim' must be a character string." + ) + expect_error( + Eno(data = array(1:10, dim = c(a = 2, b = 5))), + "Parameter 'time_dim' is not found in 'data' dimension." + ) + expect_error( + Eno(data = array(1:10, dim = c(a = 2, sdate = 5)), na.action = na.rm), + "Parameter 'na.action' must be a function either na.pass or na.fail." + ) + expect_error( + Eno(data = c(NA,1:19), na.action = na.fail), + paste0("Calculation fails because NA is found in paratemter 'data', ", + "which is not accepted when ", + "parameter 'na.action' = na.fail.") + ) + expect_error( + Eno(data = array(1:10, dim = c(a = 2, sdate = 5)), ncores = 0.5), + "Parameter 'ncores' must be a positive integer." + ) + +}) + +############################################## +test_that("2. Output checks: dat1", { + res <- Eno(dat1) + + expect_equal( + dim(res), + dim(array(dim = c(dataset = 1, member = 2, ftime = 4, lat = 10, lon = 10))) + ) + expect_equal( + length(res[which(is.na(res))]), + 1 + ) + expect_equal( + length(res[which(res != 4)]), + 37 + ) + expect_equal( + mean(res, na.rm = T), + 2.768103, + tolerance = 0.0001 + ) + +}) + +############################################## + +test_that("3. Output checks: dat2", { + + expect_equal( + Eno(dat2, time_dim = 'date'), + array(c(6.237689, 5.683186), dim = c(ftime = 2)), + tolerance = 0.0001 + ) + +}) diff --git a/tests/testthat/test-InsertDim.R b/tests/testthat/test-InsertDim.R new file mode 100644 index 0000000000000000000000000000000000000000..eb627fbcde965e4f19609bda69cbc4bd43416195 --- /dev/null +++ b/tests/testthat/test-InsertDim.R @@ -0,0 +1,99 @@ +context("s2dverification::InsertDim tests") + +############################################## + dat1 <- array(c(1:26), dim = c(dat = 1, sdate = 13, ftime = 2)) + dat2 <- array(c(1:24), dim = c(2, 3, c = 4)) +############################################## +test_that("1. Input checks", { + + expect_error( + InsertDim(c()), + "Parameter 'data' cannot be NULL." + ) + expect_error( + InsertDim(list(1:10), posdim = 1, lendim = 1), + "Parameter 'data' must be an array." + ) + expect_error( + InsertDim(1:10, posdim = 'a', lendim = 2), + "Parameter 'posdim' must be a positive integer." + ) + expect_error( + InsertDim(1:10, posdim = 0, lendim = 2), + "Parameter 'posdim' must be a positive integer." + ) + expect_error( + InsertDim(1:10, posdim = 5, lendim = 2), + "Parameter 'posdim' cannot excess the number of dimensions of parameter 'data' plus 1" + ) + expect_error( + InsertDim(1:10, posdim = 1, lendim = 0.2), + "Parameter 'lendim' must be a positive integer." + ) + expect_error( + InsertDim(1:10, posdim = 1, lendim = T), + "Parameter 'lendim' must be a positive integer." + ) + expect_warning( + InsertDim(1:10, posdim = 1, lendim = 1), + "The name of new dimension is not given. Set the name as 'new'." + ) + expect_error( + InsertDim(1:10, posdim = 1, lendim = 1, name = 1), + "Parameter 'name' must be a character string." + ) + expect_error( + InsertDim(1:10, posdim = 1, lendim = 1, ncores = 'a'), + "Parameter 'ncores' must be a positive integer." + ) + expect_error( + InsertDim(1:10, posdim = 1, lendim = 1, ncores = 0), + "Parameter 'ncores' must be a positive integer." + ) + +}) + +############################################## +test_that("2. Output checks: dat1", { + + expect_equal( + dim(InsertDim(dat1, posdim = 1, lendim = 2)), + dim(array(dim = c(new = 2, dat = 1, sdate = 13, ftime = 2))) + ) + expect_equal( + dim(InsertDim(dat1, posdim = 3, lendim = c(d = 2))), + c(dat = 1, sdate = 13, d = 2, ftime = 2) + ) + expect_equal( + as.vector(InsertDim(dat1, posdim = 1, lendim = 2)[1,,,]), + as.vector(dat1) + ) + expect_equal( + as.vector(InsertDim(dat1, posdim = 1, lendim = 2)[2,,,]), + as.vector(dat1) + ) + +}) + +############################################## +test_that("3. Output checks: dat2", { + + expect_equal( + dim(InsertDim(dat2, posdim = 4, lendim = 2, name = 'd')), + c(2, 3, c = 4, d = 2) + ) + + expect_equal( + as.vector(InsertDim(dat2, posdim = 3, lendim = 1)[,,1,]), + as.vector(dat2) + ) + + expect_equal( + dim(InsertDim(InsertDim(dat2, posdim = 4, lendim = 2), posdim = 1, lendim = 4)), + dim(array(dim = c(new = 4, 2, 3, c = 4, new = 2))) + ) + +}) + +############################################## + diff --git a/tests/testthat/test-RMS.R b/tests/testthat/test-RMS.R new file mode 100644 index 0000000000000000000000000000000000000000..a0aaff65124bf2898241b2a1d16de98c898c93fc --- /dev/null +++ b/tests/testthat/test-RMS.R @@ -0,0 +1,150 @@ +context("s2dverification::RMS tests") + +############################################## + # dat1 + set.seed(1) + exp1 <- array(rnorm(120), dim = c(member = 3, sdate = 5, ftime = 2, lon = 1, lat = 4)) + + set.seed(2) + obs1 <- array(rnorm(80), dim = c(member = 2, sdate = 5, ftime = 2, lon = 1, lat = 4)) + set.seed(2) + na <- floor(runif(10, min = 1, max = 80)) + obs1[na] <- NA + +############################################## +test_that("1. Input checks", { + + expect_error( + RMS(c(), c()), + "Parameter 'exp' and 'obs' cannot be NULL." + ) + expect_error( + RMS(c('b'), c('a')), + "Parameter 'exp' and 'obs' must be a numeric array." + ) + expect_error( + RMS(c(1:10), c(2:4)), + paste0("Parameter 'exp' and 'obs' must be at least two dimensions ", + "containing time_dim and memb_dim.") + ) + expect_error( + RMS(array(1:10, dim = c(2, 5)), array(1:4, dim = c(2, 2))), + "Parameter 'exp' and 'obs' must have dimension names." + ) + expect_error( + RMS(array(1:10, dim = c(a = 2, c = 5)), array(1:4, dim = c(a = 2, b = 2))), + "Parameter 'exp' and 'obs' must have same dimension name" + ) + expect_error( + RMS(exp1, obs1, memb_dim = 1), + "Parameter 'memb_dim' must be a character string." + ) + expect_error( + RMS(exp1, obs1, memb_dim = 'a'), + "Parameter 'memb_dim' is not found in 'exp' or 'obs' dimension." + ) + expect_error( + RMS(exp1, obs1, time_dim = c('sdate', 'a')), + "Parameter 'time_dim' must be a character string." + ) + expect_error( + RMS(exp1, obs1, time_dim = 'a'), + "Parameter 'time_dim' is not found in 'exp' or 'obs' dimension." + ) + expect_error( + RMS(exp1, obs1, comp_dim = c('sdate', 'ftime')), + "Parameter 'comp_dim' must be a character string." + ) + expect_error( + RMS(exp1, obs1, comp_dim = 'a'), + "Parameter 'comp_dim' is not found in 'exp' or 'obs' dimension." + ) + expect_error( + RMS(exp1, obs1, limits = c(1,3)), + "Paramter 'comp_dim' cannot be NULL if 'limits' is assigned." + ) + expect_error( + RMS(exp1, obs1, comp_dim = 'ftime', limits = c(1)), + paste0("Parameter 'limits' must be a vector of two positive ", + "integers smaller than the length of paramter 'comp_dim'.") + ) + expect_error( + RMS(exp1, obs1, conf.lev = -1), + "Parameter 'conf.lev' must be a numeric number between 0 and 1." + ) + expect_error( + RMS(exp1, obs1, conf = 1), + "Parameter 'conf' must be one logical value." + ) + expect_error( + RMS(exp1, obs1, ncores = 1.5), + "Parameter 'ncores' must be a positive integer." + ) + expect_error( + RMS(exp = array(1:10, dim = c(sdate = 1, member = 5, a = 1)), + obs = array(1:4, dim = c(a = 1, sdate = 2, member = 2))), + "Parameter 'exp' and 'obs' must have same length of all dimension expect 'memb_dim'." + ) + expect_error( + RMS(exp = array(1:5, dim = c(sdate = 1, member = 5, a = 1)), + obs = array(1:2, dim = c(a = 1, sdate = 1, member = 2))), + "The length of time_dim must be at least 2 to compute RMS." + ) + + + +}) + +############################################## +test_that("2. Output checks: dat1", { + + expect_equal( + dim(RMS(exp1, obs1)$rms), + c(n_exp = 3, n_obs = 2, ftime = 2, lon = 1, lat = 4) + ) + expect_equal( + head(RMS(exp1, obs1)$rms), + c(1.2815677, 2.0832803, 1.1894637, 1.3000403, 1.4053807, 0.8157563), + tolerance = 0.001 + ) + expect_equal( + length(which(is.na(RMS(exp1, obs1)$conf.lower))), + 4 + ) + expect_equal( + max(RMS(exp1, obs1)$conf.lower, na.rm = T), + 1.399509, + tolerance = 0.001 + ) + expect_equal( + length(which(is.na(RMS(exp1, obs1, comp_dim = 'ftime')$rms))), + 0 + ) + expect_equal( + length(which(is.na(RMS(exp1, obs1, comp_dim = 'ftime')$conf.upper))), + 8 + ) + expect_equal( + length(which(is.na(RMS(exp1, obs1, comp_dim = 'lat')$conf.lower))), + 36 + ) + expect_equal( + length(which(is.na(RMS(exp1, obs1, comp_dim = 'lat', limits = c(1, 2))$conf.lower))), + 21 + ) + expect_equal( + summary(RMS(exp1, obs1, conf.lev = 0.99)$conf.upper)[1], + c(Min. = 1.406), + tolerance = 0.0001 + ) + expect_equal( + length(RMS(exp1, obs1, conf = FALSE)), + 1 + ) + + + +}) + +############################################## + diff --git a/tests/testthat/test-RMSSS.R b/tests/testthat/test-RMSSS.R new file mode 100644 index 0000000000000000000000000000000000000000..a73f90e71ce0ac67b4e9252dadb81d94e1fba9fe --- /dev/null +++ b/tests/testthat/test-RMSSS.R @@ -0,0 +1,142 @@ +context("s2dverification::RMSSS tests") + +############################################## + # case 0 + set.seed(1) + exp0 <- array(rnorm(15), dim = c(sdate = 3, member = 5)) + set.seed(2) + obs0 <- array(rnorm(6), dim = c(sdate = 3, member = 2)) + + # case 1 + set.seed(1) + exp1 <- array(rnorm(15), dim = c(time = 3, memb = 5)) + set.seed(2) + obs1 <- array(rnorm(6), dim = c(time = 3, memb = 2)) + + # case 2 + set.seed(3) + exp2 <- array(rnorm(120), dim = c(sdate = 10, dat = 1, lon = 3, lat = 2, member = 2)) + set.seed(4) + obs2 <- array(rnorm(60), dim = c(dat = 1, sdate = 10, member = 1, lat = 2, lon = 3)) + +############################################## + +test_that("1. Input checks", { + + expect_error( + RMSSS(c(), c()), + "Parameter 'exp' and 'obs' cannot be NULL." + ) + expect_error( + RMSSS('exp', 'obs'), + "Parameter 'exp' and 'obs' must be a numeric array." + ) + expect_error( + RMSSS(c(1:10), c(2:4)), + paste0("Parameter 'exp' and 'obs' must be at least two dimensions ", + "containing time_dim and memb_dim.") + ) + expect_error( + RMSSS(array(1:10, dim = c(2, 5)), array(1:4, dim = c(2, 2))), + "Parameter 'exp' and 'obs' must have dimension names." + ) + expect_error( + RMSSS(array(1:10, dim = c(a = 2, c = 5)), array(1:4, dim = c(a = 2, b = 2))), + "Parameter 'exp' and 'obs' must have same dimension name" + ) + expect_error( + RMSSS(exp1, obs1, time_dim = 1), + "Parameter 'time_dim' must be a character string." + ) + expect_error( + RMSSS(exp0, obs0, time_dim = 'a'), + "Parameter 'time_dim' is not found in 'exp' or 'obs' dimension." + ) + expect_error( + RMSSS(exp0, obs0, memb_dim = NA), + "Parameter 'memb_dim' must be a character string." + ) + expect_error( + RMSSS(exp0, obs0, memb_dim = 'memb'), + "Parameter 'memb_dim' is not found in 'exp' or 'obs' dimension." + ) + expect_error( + RMSSS(exp0, obs0, pval = c(T, T)), + "Parameter 'pval' must be one logical value." + ) + expect_error( + RMSSS(exp0, obs0, ncores = 1.4), + "Parameter 'ncores' must be a positive integer." + ) + expect_error( + RMSSS(exp = array(1:10, dim = c(sdate = 1, member = 5, a = 1)), + obs = array(1:4, dim = c(a = 1, sdate = 2, member = 2))), + "Parameter 'exp' and 'obs' must have same length of all dimension expect 'memb_dim'." + ) + expect_error( + RMSSS(exp = array(1:10, dim = c(sdate = 1, member = 5, a = 1)), + obs = array(1:4, dim = c(a = 1, sdate = 1, member = 2))), + "The length of time_dim must be more than 2 to compute RMSSS." + ) +}) + +############################################## +test_that("1. Output checks: case 1", { + + res1_1 <- RMSSS(exp1, obs1, time_dim = 'time', memb_dim = 'memb') + expect_equal( + dim(res1_1$rmsss), + c(nexp = 5, nobs = 2) + ) + expect_equal( + dim(res1_1$p.val), + c(nexp = 5, nobs = 2) + ) + expect_equal( + mean(res1_1$rmsss), + -0.5449538, + tolerance = 0.00001 + ) + + exp1_2 <- exp1 + exp1_2[2:4] <- NA + obs1_2 <- obs1 + obs1_2[1:2] <- NA + res1_2 <- RMSSS(exp1_2, obs1_2, time_dim = 'time', memb_dim = 'memb', pval = TRUE) + + expect_equal( + length(res1_2$rmsss[which(is.na(res1_2$rmsss))]), + 7 + ) + expect_equal( + range(res1_2$p.val, na.rm = T), + c(0.7159769, 0.8167073), + tolerance = 0.00001 + ) + +}) + + +############################################## +test_that("2. Output checks: case 2", { + + expect_equal( + dim(RMSSS(exp2, obs2)$rmsss), + c(nexp = 2, nobs = 1, dat = 1, lon = 3, lat = 2) + ) + expect_equal( + mean(RMSSS(exp2, obs2)$rmsss), + -0.3912208, + tolerance = 0.00001 + ) + expect_equal( + range(RMSSS(exp2, obs2)$p.val), + c(0.2627770, 0.9868412), + tolerance = 0.00001 + ) + +}) + +############################################## + + diff --git a/tests/testthat/test-Regression.R b/tests/testthat/test-Regression.R new file mode 100644 index 0000000000000000000000000000000000000000..c966fe929a2bc0eff9b96d368602e6f46fc8f050 --- /dev/null +++ b/tests/testthat/test-Regression.R @@ -0,0 +1,199 @@ +context("s2dverification::Regression tests") + +############################################## + # dat1 + set.seed(1) + datay1 <- array(c(-39:40) + rnorm(80), + dim = c(sdate = 5, ftime = 2, lon = 2, lat = 4)) + set.seed(2) + datax1 <- array(c(1:80) + rnorm(80), + dim = c(sdate = 5, ftime = 2, lon = 2, lat = 4)) + # dat2 + datay2 <- datay1 + set.seed(1) + na <- floor(runif(5, min = 1, max = 80)) + datay2[na] <- NA + datax2 <- datax1 + set.seed(2) + na <- floor(runif(5, min = 1, max = 80)) + datax2[na] <- NA + + # dat3 + set.seed(1) + datay3 <- array(c(-39:40) + rnorm(80), + dim = c(date = 5, ftime = 2, lon = 2, lat = 4)) + set.seed(2) + datax3 <- array(c(1:80) + rnorm(80), + dim = c(date = 5, lon = 2, lat = 4,ftime = 2)) + + +############################################## +test_that("1. Input checks", { + + expect_error( + Regression(c(), c()), + "Parameter 'datay' and 'datax' cannot be NULL." + ) + expect_error( + Regression(c('b'), c('a')), + "Parameter 'datay' and 'datax' must be a numeric array." + ) + expect_error( + Regression(c(1:10), c(2:4)), + "Parameter 'datay' and 'datax' must be at least one dimension 'time_dim'." + ) + expect_error( + Regression(array(1:10, dim = c(2, 5)), array(1:4, dim = c(2, 2))), + "Parameter 'datay' and 'datax' must have dimension names." + ) + expect_error( + Regression(array(1:10, dim = c(a = 2, c = 5)), array(1:4, dim = c(a = 2, b = 2))), + "Parameter 'datay' and 'datax' must have same dimension name" + ) + expect_error( + Regression(array(1:10, dim = c(a = 2, b = 5)), array(1:4, dim = c(a = 2, b = 2))), + "Parameter 'datay' and 'datax' must have same length of all dimensions." + ) + expect_error( + Regression(datay1, datax1, time_dim = 1), + "Parameter 'time_dim' must be a character string." + ) + expect_error( + Regression(datay1, datax1, time_dim = 'asd'), + "Parameter 'time_dim' is not found in 'datay' or 'datax' dimension." + ) + expect_error( + Regression(datay1, datax1, na.action = TRUE), + paste0("Parameter 'na.action' must be a function for NA values or ", + "a numeric indicating the number of NA values allowed ", + "before returning NA.") + ) + expect_error( + Regression(datay1, datax1, na.action = c(1,2)), + paste0("Parameter 'na.action' must be a function for NA values or ", + "a numeric indicating the number of NA values allowed ", + "before returning NA.") + ) + expect_error( + Regression(datay1, datax1, formula =T), + "Parameter 'formula' must the an object of class 'formula'." + ) + expect_error( + Regression(datay1, datax1, pval = 0.05), + "Parameter 'pval' must be one logical value." + ) + expect_error( + Regression(datay1, datax1, conf = 0.05), + "Parameter 'conf' must be one logical value." + ) + expect_error( + Regression(datay1, datax1, conf.lev = 1.5), + "Parameter 'conf.lev' must be a numeric number between 0 and 1." + ) + expect_error( + Regression(datay1, datax1, ncores = T), + "Parameter 'ncores' must be a positive integer." + ) +}) + + +############################################## +test_that("2. Output checks: dat1", { + + expect_equal( + dim(Regression(datay1, datax1)$regression), + c(stats = 2, ftime = 2, lon = 2, lat = 4) + ) + expect_equal( + head(Regression(datay1, datax1)$regression), + c(-39.0091480, 0.7290814, -39.1853129, 0.8623175, -37.4342099, 0.7844530), + tolerance = 0.001 + ) + expect_equal( + length(which(is.na(Regression(datay1, datax1)$conf.low))), + 0 + ) + expect_equal( + max(Regression(datay1, datax1)$conf.upper, na.rm = T), + 127.4267, + tolerance = 0.001 + ) + expect_equal( + length(Regression(datay1, datax1, conf = F)), + 3 + ) + expect_equal( + length(Regression(datay1, datax1, pval = F)), + 4 + ) + expect_equal( + length(Regression(datay1, datax1, pval = F, conf = F)), + 2 + ) + expect_equal( + range(Regression(datay1, datax1, conf.lev = 0.99)$conf.low, na.rm = T), + c(-380.888744, 0.220794), + tolerance = 0.001 + ) + expect_equal( + summary(Regression(datay1, datax1)$p.val)[1], + c(Min. = 0.005335), + tolerance = 0.0001 + ) + expect_equal( + summary(Regression(datay1, datax1, formula = y~poly(x, 2, raw = T))$p.val)[3], + c(Median = 0.22560), + tolerance = 0.0001 + ) +}) + +############################################## +test_that("3. Output checks: dat2", { + expect_equal( + length(which(is.na(Regression(datay2, datax2, na.action = 0)$conf.lower))), + 14 + ) + expect_equal( + length(which(is.na(Regression(datay2, datax2, na.action = 2)$conf.lower))), + 0 + ) + expect_equal( + length(which(is.na(Regression(datay2, datax2, na.action = 1)$p.val))), + 2 + ) + expect_equal( + length(which(is.na(Regression(datay2, datax2, na.action = na.pass)$p.val))), + 0 + ) + expect_equal( + which(is.na(Regression(datay2, datax2, na.action = 1)$p.val)), + c(3,15) + ) + expect_equal( + which(is.na(Regression(datay2, datax2, na.action = 1, + formula = y~poly(x, 2, raw = T))$p.val)), + c(3,15) + ) +}) + +############################################## +test_that("4. Output checks: dat3", { + + expect_equal( + dim(Regression(datay3, datax3, time_dim = 'date')$regression), + c(stats = 2, ftime = 2, lon = 2, lat = 4) + ) + expect_equal( + dim(Regression(datay3, datax3, time_dim = 'date')$conf.lower), + c(stats = 2, ftime = 2, lon = 2, lat = 4) + ) + expect_equal( + dim(Regression(datay3, datax3, time_dim = 'date')$p.val), + c(ftime = 2, lon = 2, lat = 4) + ) + + +}) + +############################################## + diff --git a/tests/testthat/test-Season.R b/tests/testthat/test-Season.R new file mode 100644 index 0000000000000000000000000000000000000000..b01b242b2bc23f8fc191339e246c5f10b2b14c66 --- /dev/null +++ b/tests/testthat/test-Season.R @@ -0,0 +1,122 @@ +context("s2dverification::Season tests") + +############################################## + # dat1 + set.seed(1) + dat1 <- array(rnorm(144*3), dim = c(member = 2, sdate = 12*3, ftime = 2, lon = 3)) + + # dat2 + dat2 <- dat1 + set.seed(2) + na <- floor(runif(30, min = 1, max = 144*3)) + dat2[na] <- NA + +############################################## +test_that("1. Input checks", { + + expect_error( + Season(c()), + "Parameter 'data' cannot be NULL." + ) + expect_error( + Season(c(NA, NA)), + "Parameter 'data' must be a numeric array." + ) + expect_error( + Season(list(a = array(rnorm(50), dim = c(dat = 5, sdate = 10)), b = c(1:4))), + "Parameter 'data' must be a numeric array." + ) + expect_error( + Season(array(1:10, dim = c(2, 5))), + "Parameter 'data' must have dimension names." + ) + expect_error( + Season(dat1, time_dim = 2), + "Parameter 'time_dim' must be a character string." + ) + expect_error( + Season(dat1, time_dim = 'a'), + "Parameter 'time_dim' is not found in 'data' dimension." + ) + expect_error( + Season(dat1, monini = 0, moninf = 1, monsup = 2), + "Parameter 'monini' must be a positive integer between 1 and 12." + ) + expect_error( + Season(dat1, monini = 1, moninf = 'jan', monsup = 2), + "Parameter 'moninf' must be a positive integer between 1 and 12." + ) + expect_error( + Season(dat1, monini = 1, moninf = 1, monsup = 'Jan'), + "Parameter 'monsup' must be a positive integer between 1 and 12." + ) + expect_error( + Season(dat1, monini = 1, moninf = 1, monsup = 2, method = 'mean'), + "Parameter 'method' should be an existing R function, e.g., mean or sum." + ) + expect_error( + Season(dat1, monini = 1, moninf = 1, monsup = 2, na.rm = na.omit), + "Parameter 'na.rm' must be one logical value." + ) + expect_error( + Season(dat1, monini = 1, moninf = 1, monsup = 2, ncores = T), + "Parameter 'ncores' must be a positive integer." + ) + +}) + +############################################## +test_that("2. Output checks: dat1", { + + expect_equal( + dim(Season(dat1, monini = 1, moninf = 1, monsup = 2)), + c(sdate = 3, member = 2, ftime = 2, lon = 3) + ) + expect_equal( + dim(Season(dat1, time_dim = 'lon', monini = 1, moninf = 1, monsup = 2)), + c(lon = 1, member = 2, sdate = 36, ftime = 2) + ) + expect_equal( + dim(Season(dat1, monini = 10, moninf = 12, monsup = 2)), + c(sdate = 3, member = 2, ftime = 2, lon = 3) + ) + expect_equal( + summary(Season(dat1, monini = 10, moninf = 12, monsup = 2))[3], + c(Median = 0.007925), + tolerance = 0.0001 + ) + expect_equal( + summary(Season(dat1, monini = 10, moninf = 2, monsup = 5, method = sum))[3], + c(Median = 0.2732), + tolerance = 0.0001 + ) + +}) + +############################################## +test_that("3. Output checks: dat2", { + + expect_equal( + summary(Season(dat2, monini = 10, moninf = 12, monsup = 2))[3], + c(Median = -0.01987), + tolerance = 0.0001 + ) + expect_equal( + summary(Season(dat2, monini = 10, moninf = 12, monsup = 2, na.rm = F))[3], + c(Median = 0.06207), + tolerance = 0.0001 + ) + res <- Season(dat2, monini = 10, moninf = 12, monsup = 2, na.rm = F) + expect_equal( + length(res[which(is.na(as.vector(res)))]), + 10 + ) + res <- Season(dat2, monini = 10, moninf = 12, monsup = 2) + expect_equal( + length(res[which(is.na(as.vector(res)))]), + 0 + ) +}) + +############################################## + diff --git a/tests/testthat/test-Trend.R b/tests/testthat/test-Trend.R new file mode 100644 index 0000000000000000000000000000000000000000..8843b9ed75bcc651826880ced57d8a4d1010e193 --- /dev/null +++ b/tests/testthat/test-Trend.R @@ -0,0 +1,143 @@ +context("s2dverification::Trend tests") + +############################################## + # dat1 + dat1 <- array(c(-5, -7, -10:10, 12, 11, 7, 16), + dim = c(dat = 1, sdate = 13, ftime = 2)) + + # dat2 + set.seed(10) + dat2 <- c(1:10) + rnorm(10) + + # dat3 + set.seed(1) + dat3 <- array(c(1:60) + rnorm(60), + dim = c(sdate = 5, lat = 2, lon = 3, lev = 2)) + set.seed(1) + na <- floor(runif(5, min = 1, max = 60)) + dat3[na] <- NA + +############################################## + +test_that("1. Input checks", { + + expect_error( + Trend(c()), + "Parameter 'data' cannot be NULL." + ) + expect_error( + Trend(c(NA, NA)), + "Parameter 'data' must be a numeric array." + ) + expect_error( + Trend(list(a = array(rnorm(50), dim = c(dat = 5, sdate = 10)), b = c(1:4))), + "Parameter 'data' must be a numeric array." + ) + expect_error( + Trend(array(1:10, dim = c(2, 5))), + "Parameter 'data' must have dimension names." + ) + expect_error( + Trend(dat1, time_dim = 'a'), + "Parameter 'time_dim' is not found in 'data' dimension." + ) + expect_error( + Trend(array(c(1:25), dim = c(dat = 1, date = 5, ftime = 5))), + "Parameter 'time_dim' is not found in 'data' dimension." + ) + expect_error( + Trend(dat1, time_dim = 2), + "Parameter 'time_dim' must be a character string." + ) + expect_error( + Trend(dat1, time_dim = c('a','sdate')), + "Parameter 'time_dim' must be a character string." + ) + expect_error( + Trend(dat1, interval = 0), + "Parameter 'interval' must be a positive number." + ) + expect_error( + Trend(dat1, conf = 3), + "Parameter 'conf' must be one logical value." + ) + expect_error( + Trend(dat1, polydeg = 3.5), + "Parameter 'polydeg' must be a positive integer." + ) + expect_error( + Trend(dat1, ncore = 3.5), + "Parameter 'ncores' must be a positive integer." + ) +}) + +############################################## +test_that("2. Output checks: dat1", { + + expect_equal( + Trend(dat1)$trend, + array(c(-9.7692308, 0.6593407, 0.9615385, 0.7967033), + dim = c(stats = 2, dat = 1, ftime = 2)), + tolerance = 0.0001 + ) + expect_equal( + Trend(dat1)$conf.upper, + array(c(-7.4735367, 0.9485709, 3.0167860, 1.0556402), + dim = c(stats = 2, dat = 1, ftime = 2)), + tolerance = 0.0001 + ) + expect_equal( + summary(Trend(dat1)$detrended)[3], + c(Median = 0.1154), + tolerance = 0.001 + ) + +}) + +############################################## +test_that("3. Output checks: dat2", { + + expect_equal( + Trend(dat2), + list(trend = array(c(-0.182, 0.944), dim = c(stats = 2)), + conf.lower = array(c(-1.316, 0.761), dim = c(stats = 2)), + conf.upper = array(c(0.953, 1.127), dim = c(stats = 2)), + detrended = array(c(0.257, 0.110, -1.021, -0.193, 0.757, 0.909, + -0.633, 0.267, -0.939, 0.487), dim = c(sdate = 10))), + tolerance = 0.001 + ) + expect_equal( + Trend(dat2, interval = 2), + list(trend = array(c(-0.182, 0.472), dim = c(stats = 2)), + conf.lower = array(c(-1.316, 0.381), dim = c(stats = 2)), + conf.upper = array(c(0.953, 0.563), dim = c(stats = 2)), + detrended = array(c(0.257, 0.110, -1.021, -0.193, 0.757, 0.909, + -0.633, 0.267, -0.939, 0.487), dim = c(sdate = 10))), + tolerance = 0.001 + ) + expect_equal( + length(Trend(dat2, conf = F)), + 2 + ) + expect_equal( + names(Trend(dat2, conf = F)), + c('trend', 'detrended') + ) + +}) + +############################################## +test_that("4. Output checks: dat3", { + + expect_equal( + summary(Trend(dat3)$trend)[3], + c(Median = 1.3680), + tolerance = 0.0001 + ) + expect_equal( + dim(Trend(dat3, polydeg = 2)$trend), + c(stats = 3, lat = 2, lon = 3, lev = 2) + ) + +}) +