NEWS.md

PAnEn 4.4.6

• Added missing packages when compiling on Windows

PAnEn 4.4.5

• From this version, only keeping notes for major and minor version. Notes for patches are dismissed.
• Introduced spatial analogs with PyTorch and deep learning
• Added a new class Grid and the Python API AnEnGrid
• Added a new command line tool, anen_transform
• Added a new option --no-norm for AI embeddings
• Moved Txt class from AnEnIO to the lower level class Grid
• Migrated from C++11 to C++14 for RAnEn to avoid compilation error from BH

PAnEn 4.3.1

• anen_netcdf can now accept reading from different subsets of observation and forecast stations.
• Fixed the inconsistency when writing AnEn results generated from AnEnSSEMS
• Added functionality for anen_grib and grib_convert so that input files can now be specified within a text file
• Added new argument --exclude-closest-location for SSE
• Added station subset by indices for anen_netcdf

PAnEn 4.3.0

• Added AnEnSSEMS for matching stations. This addition has also been ported to RAnEn.

PAnEn 4.2.7

• Added test time specification to C++ utility tools
• Added functionality to CAnEnMPI to deal with excessive processes

PAnEn 4.2.6

• Added multi-tokens to wind speed name conversion
• Fixed a bug when reading doubles with no decimal from an NetCDF file into R. The small error will be removed when reading.

PAnEn 4.2.5

• Added RAnEn::readNc2, RAnEn::readNcAttrs, RAnEn::mergeList
• Added recursive to RAnEn::print.list
• Added functions to unwrap observations when saving test observations (C++)
• Fixed a bug for multi-variate analogs when NAN indices are present

PAnEn 4.2.4

• Moved 'RAnEn::schaakeShuffle' to RAnEnExtra::schaakeShuffle
• Improve efficiency of AI inference

PAnEn 4.2.3

• Added reading root attributes to RAnEn::readNc
• Added RAnEn::formatForecasts and RAnEn::sortStations

PAnEn 4.2.2

• Added debug printing when parameters are missing
• Added functionality to read nc_STRING
• Added embedding support for 2-dimensional embedding (parameters, lead times)
• Added default embedding type
• Added complete messages
• Fixed a bug when reading configuration arguments with multiple tokens

PAnEn 4.2.1

• Separated AI models into an embedding model and a similarity model.
• Added OpenMP parallelization to embeddings
• RAnEn::readConfig now reads any *.cfg file into a list.

PAnEn 4.2.0

• Added AI functionality to C++ utilities
• Add copy operators to classes

PAnEn 4.1.3

• 'RAnEn::alignObservations' has been changed to be silent by default.
• 'RAnEn::schaakeShuffle' can find proper index for shuffling and added parameters.

PAnEn 4.1.2

• Minor fix. When similarity value is NAN, do not copy any results to output.

PAnEn 4.1.1

• Added RAnEn::writeNcVar
• Fixed partial reading check for station start and count
• Improve column-wise check

PAnEn 4.1.0

• Added anen_netcdf
• Fixed missing weight problem in anen_grib

PAnEn 4.0.10

• Fixed missing variable in RAnEn::writeNetCDF

PAnEn 4.0.9

• Avoid printing too much information for length-of-1 list in RAnEn::AnEn.

PAnEn 4.0.8

• Added thread control

PAnEn 4.0.7

• Removed profiling current memory
• Added sorting capability to RAnEn::formatObservations
• Added argument to read a subset of variables to RAnEn::readNc
• Bug fixed in RAnEn::formatObservations when X and Y column names are used
• Bug fixed in RAnEn::writeNetCDF when StationNames is empty

PAnEn 4.0.6

• Bug fixed. Analog values should not be saved when the similarity value is NAN. All other information (time and station index) will still be saved

PAnEn 4.0.5

• Added AnEnMPI
• Improved Profiler and added more profiling information
• Progress information will be displayed every 1%
• Improved documentation

PAnEn 4.0.4

• Changed MPI_Init to MPI_Init_thread for OpenMP programs
• Add progress information to AnEn computation
• Improved the distribution of files across nodes

PAnEn 4.0.3

• Added the regular expressions for forecast and analysis filenames separately
• Changed from boost::regex to boost::xpressive
• Added MPI support
• Fixed a bug when reading lat/lon from grib files
• Improved the file I/O functions in RAnEn
• Improved the printing functions for Forecasts and Observations

PAnEn 4.0.2

• Added test and search period checks to avoid calculating analogs over empty time periods
• Changed the tutorial on generating operational analogs
• Improve the performance of AnEnReadGrib by avoiding reading entire files

PAnEn 4.0.1

• Added RAnEn::generateSearchStations
• Updated document links

PAnEn 4.0.0 Pandora

• Changed Underlying data structure from boost to pointer for better performance
• Introduced functionalities like checks of searching into future
• Reduced memory consumption when using the R API
• Changed several configuration names in R
• Some functions are deprecated
• R API changed

PAnEn 3.7.1

• Introduced auto generation of HPC work flows using RAnEn::generateHPCWorkflow
• Fixed a bug during subseting observation times in RAnEn::plotAnalogTimeSeries
• Added operational in RAnEn::generateHPCWorkflow
• search_times_compare automatically changed when operational was used
• Changed RAnEn::writeConfiguration from ifelse to using the function if

PAnEn 3.7.0

• Negative values in indices were removed by default. Added a parameter debug for backward compatibility.
• Added function RAnEn::formatObservations
• Updated the docker image
• Change require to requireNamespace to avoid function name conflicts
• Added RAnEn::subsetStations
• Improve RAnEn name space management
• Added RAnEn::plotAnalogTimeSeries
• Changed default values for Configuration from NA to NULL when it is necessary

PAnEn 3.6.5

• Added reading forecast circular parameters in `RAnEn::readForecasts
• Added station subset function RAnEn::subsetCoordinates
• Minor document fix
• Added Github repository link on R documentation website
• Set up binder with RStudio and removed python notebooks

PAnEn 3.6.4

• Fixed environment issue for RAnEn::verify
• Bug fixed in RAnEn::plotAnEnSelection
• Updated the building process of gribConverter.
• Changed the spread skill verification function to slicing by FLTs.

PAnEn 3.6.3

• Fixed a bug in checking the configuration object in R
• Added instructions for package citation

PAnEn 3.6.2

• Changed the implementation of RAnEn::verifySpreadSkill
• Changed legal information
• Added checks and default values in RAnEn::generateSearchStation
• Resolved issues in tests
• Added a convenient function RAnEn::getAssociatedForecasts
• Used magrittr pipes to improve code readability
• Added the printing method for R class 'Configuration'

PAnEn 3.6.1

• Added RAnEn::generatePersistent
• Added function names when Done is printed

PAnEn 3.6.0

• Verification just became simpler. Added a caller function RAnEn::verify and helper function RAnEn::showVerificationMethods
• Resolved a variable missing bug in RAnEn::writeNetCDF

PAnEn 3.5.4

• Changed warnings of CAnEnIO from cout to cerr
• Reduced copies in RAnEn::AnEnC2R
• Added garbage collection mechanism to R file I/O functions

PAnEn 3.5.3

• Resolved a naming bug in RAnEn::schaakeShuffle
• Resolved a path bug in RAnEn::readAnEn
• Added RAnEn::writeConfiguration
• Added ParameterCirculars in function RAnEn::writeNetCDF
• Changed C++ test verbose levels

PAnEn 3.5.2

• Improved documentation for RAnEn::verifyBrier and RAnEn::verifyThreatScore
• Improved the printing information for 'class: AnEn list'

PAnEn 3.5.1

• Added the beta function RAnEn::schaakeShuffle.
• Added multiple variable support for windFieldCalculator.
• Added support for Forecasts in RAnEn::writeNetCDF.

PAnEn 3.5.0

• Added functions toDateTime, toForecastTime, val2Col, makeTransparent, and plotBackground.
• Improved verifyCRPS.
• Improved RAnEn function documentation.
• Added identification for cycle time in C++ utilities.
• Bug fixed in checking functions in RAnEn.
• Added grid checks in gribConverter for each file.
• Made classifier the parameter for extendedSearch only.
• Improved website and tutorials/posts.

PAnEn 3.4.2

• Added slicing tool fileSlice.
• Added R functions writeNetCDF, readForecasts, readObservations, readAnEn, AnEnC2R, verifyThreatScore, verifyBrier, and readConfig.
• Improved visualization. Fix the x plotting range of RAnEn figures.
• Changed analogGenerator code. Similarity output is sorted now.

PAnEn 3.4.1

• Added grid subset functionality to gribConverter for type Forecasts. This function has been tested.
• Fixed RAnEn installation script for C/C++ compilers.
• Fixed OpenMP shared object issue for runtime_error.

PAnEn 3.4.0

• Introducing SSE functionality based on classifiers. Search space can now be computed based on a classification map that only stations that belong to the same class will be considered when computing search space.
• SSE based on classification has been ported to R interfaces.
• Minor bugs fixed.

PAnEn 3.3.1

• Fix an indexing bug in RAnEn operational mode.
• Fix a parallelization bug in the internal verification function anen.mean.
• 'analogGenerator' accepts multiple test forecast files.
• Add partial reading feature in fileAggregate for Similarity and Analogs.
• Improve efficiency of verification functions. Some missing functions have been resolved.
• Add FLT_radius parameter to RAnEn

PAnEn 3.3.0

• Add parameters to restrict the number of similarities to keep. This can be very helpful to reduce the memory required. The C++ parameter is max-num-sims and the R parameter is max_num_sims.
• Change package name from Parallel Ensemble Forecast to Parallel Analog Ensemble.
• similarityCalculator, analogSelector, analogGenerator now accept multiple configuration files.
• Add along parameter check to AnEnIO.
• 'analogGenerator' accepts multiple search forecast and observation files.
• Add parallelization to verification functions.

PAnEn 3.2.6

• Add features to C++ tools that similarityCalculator and analogSelector now accept multiple file input.
• Add proper wall time profiling in C++ tools similarityCalculator and analogSelector.
• Change the profiling output messages.

PAnEn 3.2.5

• Add function RAnEn::plotAnalogSample and RAnEn::plotAnalogSelection.
• Add the feature for RAnEn to preserve standard deviations.
• Add tests for R and C++ for similarity calculation and standard deviation calculation.
• Add verification functions.
• Change R interface input parameters to constant references.
• Bug fixed for the RAnEn configuration parameter num_nearest and num_max_search_stations.
• Bug fixed in RAnEn::verifyCorrelation.
• Add mapping calculation feature to analog selector.

PAnEn 3.2.4

• Bug fixed for using weights.
• Bug fixed for using partial compare times from test and search. This was causing stack overflow.
• Change the onload message of RAnEn.
• Add density limit parameter for RAnEn::biasCorrectionInsitu.

PAnEn 3.2.3

• Port max_flt_nan and max_par_nan parameters to R function compute_analogs.
• Update R and C++ document.
• Add R configuration preserve_search_stations to independentSearch as well. Now, both independentSearch and extendedSearch support this configuration.
• Add RAnEn::alignObservations

PAnEn 3.2.2

• Improve backward compatibility of R function compute_analogs. This function now returns the analog member index in the 4D observations, rather than in the 3D observations.
• Add a cleaner version of configuration. Configuration now, by default, is the cleaner version. The old version can be accessed by using advanced parameter when generating a configuration.
• Remove some of the post contents to reduce redundant information. Tutorials are now only hosted on binder.
• Add MPI implementation for "MPI_UNIVERSE_SIZE" to limit the number of child spawned processes.
• Add unique identifier in SimilarityMatrices and Analogs to distinguish the reason for the NAN value.

PAnEn 3.2.1

• Remove computing sds outside the loops when operational search is used.
• Add demo for using operational search.
• Performance improved for computing similarity.
• Add default value in RAnEn for configuration$test_forecasts and configuration$test_times. If they are not specified, they are copied from configuration$search_forecasts and configuration$search_times respectively.
• Add default value for test-forecast-nc in analogGenerator and similarityCalculator. If they are not provided, the search file will be also used as a test file.
• When MPI is used, the reading function should automatically detect whether the file can be accessed with parallel processes.

PAnEn 3.2.0

• Synchronize versions of all components.
• Add similarity computing methods including SeparateTestSearch, LeaveOneOut, and OperationalSearch. This has brought an significant addition to similarity calculation function features.
• Add automatic removal of the overlapping test and search times. For example, if forecasts are 3 days ahead, the historical forecast for yesterday will not be compared to the forecast of today even if the yesterday forecast is included in the search times (which is considered as a mistaken input from the user).
• Add R function generateTimeMapping.

PAnEn 3.1.1

RAnEn

• Refactor Similarity Calculation core function and improve readability.
• Resolve the potential bug in the function biasCorrectionInsitu.
• Remove return_index option from computeSearchStations.
• Skip processing the similarity array if it is not preserved in the result.
• Update documentation.
• Update README file.

PAnEn 3.1.0

CAnEnIO

• Add MPI read functions for values only.
• Fix bug for MPI functions in reading.
• Add serial program limit to AnEn library.
• Add MPI read functions for strings.
• Speed up the station matching process.

RAnEn

• Reduce code size of the computeSimilarity function.
• Resolve a potential bug in computeSimilarity and introduce a new parameter extend_observations to this function. Now, extend_observations is supported by both computeSimilarity and selectAnalogs functions.
• Minor changes to RAnEn::biasCorrection.
• Introduce a new function for bias correction using a neural network.
• Change authors of the package.
• Update documentation.
• Change names of members from bias correction.
• Change import functions to suggested for parallel, nnet, and pbapply.

PAnEn 3.0.0

CAnEnIO

• Basic AnEn I/O functions.