# HYPEtools NEWS

## HYPEtools 1.6.5
*Enhancements and bug fixes*

#### Highlights
* Fix bug in AllUpstreamSubids() that resulted in incorrect upstream SUBIDs when MAINPART == 0 in BranchData.txt
* Add plots for modeled organic carbon in PlotBasinOutput() and PlotBasinSummary()
* Update ReadGeoData() to check and warn for duplicate column names
* Add check to PlotSubbasinRouting() to ensure that "map" and "gd" have shared SUBIDs and add handling for if SUBIDs in "map" and "gd" are not identical
* Allow for custom line colors and weights in PlotSubbasinRouting()
* Add RunHYPE() function

## HYPEtools 1.6.4 (2024-11-27)
*Enhancements and bug fixes*

#### Highlights
* Update ReadDescription() to read information about point source types
* Allow adding comment line to WriteObs()
* Ensure that first column is named "DATE" in ReadObs()
* Update datetime formatting for ReadXobs()

## HYPEtools 1.6.3 (2024-09-04)
*Enhancements and bug fixes*

#### Highlights
* Add warning message to PlotPerformanceByAttribute() if multiple column names are present in both subass and attributes
* Fix group colors in PlotPerformanceByAttribute()
* Update allowable "types" in CompareFiles() to fix bug preventing comparison of certain HYPE file types
* Update WriteHarmonizedData() and WriteHarmonizedSpatialDescription() to prevent error caused when writing file without loading data.table package
* Add reference to HYPEtools reference paper
* Add package anchors in help text links

## HYPEtools 1.6.2 (2024-05-24)
*Enhancements and bug fixes*

#### Highlights
* Update ScalePar() function to properly handle recession coefficients
* Add ScaleAquiferData() function to scale RETRATE recession coefficient
* Add example AquiferData.txt and FloodData.txt files to demo model; taken from HYPE wiki:
  * http://hype.smhi.net//wiki/doku.php?id=start:hype_file_reference:aquiferdata.txt
  * http://hype.smhi.net//wiki/doku.php?id=start:hype_file_reference:flooddata.txt
* Add ScaleFloodData() function to scale recession cofficients
* Add ReadFloodData() and WriteFloodData() functions
* Update CompareFiles() function to warn if "type" argument is not in the supported list of options
* Update links to HYPEtools Wiki

## HYPEtools 1.6.1 (2024-01-12)
*Enhancements and bug fixes*

#### Highlights
* Add cbind option for adding groups in PlotPerformanceByAttribute()
* Handle NA values when scaling axes in PlotPerformanceByAttribute()
* Handle group IDs as strings in PlotPerformanceByAttribute()
* Add argument to adjust spacing between plots and summary table in PlotPerformanceByAttribute()
* Add warning for non-standard column names when using ReadGeoData()
* Update default info columns for VariableLookup functions
* Add jitter to points with duplicate geometries in PlotMapPoints()
* Hide label group by default for Leaflet maps in MapRegionalSources()
* Allow SUBIDs with many digits in SortGeoData()
* Update PlotSimObsRegime() to ignore NA values and to fix percentile polygons when using log scale with negative/zero values (Issue #61)
* Create distinctColorPalette() function and update PlotSubbasinRouting() and MapRegionalSources() to allow setting a seed so palettes can be reproduced
* Update MapRegionalSources() to allow specifying different connection groups with different colors
* Various updates to help text

## HYPEtools 1.6.0 (2023-10-18)
*Enhancements*

#### Highlights
* Remove hydroGOF and hydroTSM dependencies because packages are being archived by CRAN due to not updating to remove dependencies on retired r-spatial packages
* Various updates to help text

## HYPEtools 1.5.2 (2023-10-06)
*Enhancements and bug fixes*

#### Highlights
* Fix ReadObs() so date/time format works when importing as a data.table object
* Prevent scientific notation when writing files
* Add ReadClassData() function
* Add argument to control date/time format for x-axis in PlotBasinOutput()

## HYPEtools 1.5.1 (2023-08-24)
*Enhancements and bug fixes*

#### Highlights
* Fix broken @docTYPE package documentation (package?pkgname) as described here: https://github.com/r-lib/roxygen2/issues/1491
* Update PlotMapOutput() and PlotMapPoints() to allow for missing SUBIDs in MapOutput or GIS files
* Update PlotMapOutput() and PlotMapPoints() functions so "map"/"sites" and "map.subid.column"/"sites.subid.column" arguments are interchangeable

## HYPEtools 1.5.0 (2023-08-14)
*Enhancements and bug fixes*

#### Highlights
* Add basic MergeObs() function
* Allow users to change polygon outline colors in in PlotMapOutput()
* Fix bug in PlotMapOutput() that ignored user defined col.breaks
* Allow users to specify custom labels for PlotMapPoint() legends
* Remove ggspatial dependency because the package is set to be archived by CRAN due to unaddressed check problems

## HYPEtools 1.4.1 (2023-06-30)
*Enhancements and bug fixes*

#### Highlights
* Add option in SubidAttributeSummary() to summarize landuse, soil, and crop fractions for just subbasin areas (not upstream areas)
* Add PartyParrot() Easter Egg
* Fix example for PlotSubbasinRouting() which was not working

## HYPEtools 1.4.0 (2023-05-17)
*New functions and bug fixes*

#### Highlights
* Fix bug in checking of PlotMapPoints() and PlotMapOutput() legend positions
* Fix bug in PlotMapPoints() where custom color breaks were ignored
* Add option to reverse color palette in PlotMapPoints()
* Add pseudo-log scale to PlotPerformanceByAttribute() if any zero or negative values exist
* Add options for boxplot density plots and common y-axis in PlotPerformanceByAttribute()
* Allow for specifying only number of rows or columns in PlotPerformanceByAttribute()
* Add "-9999" as NA string in ReadSubass()
* Fix bug in PlotBasinOutput() where line plots would not get generated if NA values were present
* Update plotting functions to replace usage of deprecated ggplot2 aes_string() function

## HYPEtools 1.3.0 (2023-04-05)
*New functions and bug fixes*

#### Highlights
* Fix bug in PlotMapPoints() and PlotMapOutput() that would prevent plots from being generated if "x" was e.g. a tibble
* Fix bug in PlotMapPoints() that would prevent plots from being generated with user defined color scale if NA values were present
* Update warning text in WriteObs()
* Add VisualizeMapOutput() and VisualizeMapPoints() Shiny apps
* Add ScalePar() to scale par files to different model time steps
* Add comparison threshold for numeric values in CompareFiles()

## HYPEtools 1.2.0 (2023-02-10)
*New functions and bug fixes*

#### Highlights
* Added "exact" mode to ReadInfo() to read info.txt files with exact info.txt file structure
* Added AddInfoLine(), RemoveInfoLine(), and WriteInfo() functions to help with info.txt file manipulation
* Added AllSimToPar() and BestSimsToPar() functions to update a par.txt file with parameter values from an allsim.txt or bestsims.txt file
* Updated CompareFiles() to include options for Simass and Subass files and to use ReadObs() instead of ReadPTQobs()
* Add error message to CompareFiles() to handle if compare.order = FALSE and by = NULL.
* Update ReadSubass() to be able to read Subass files with zero rows and add na.strings argument.
* Updated PlotMapOutput() and PlotMapPoints() to generate ggplot maps by default
* Updated WriteXobs() to include !! at beginning of comment line
* Added CITATION.cff file
* Updated WriteObs() to allow for appending data to existing file
* Fix bugs in ignore.cols for WriteHarmonizedData() and WriteHarmonizedSpatialDescription() to allow for lower case values and to format dates with times correctly
* Update GroupSLCClasses() to allow for multiple values for type argument
* Added WriteGlacierData()

## HYPEtools 1.1.0 (2022-10-26)
*New functions and bug fixes*

#### Highlights
* Fixed bug in PlotMapPoints() that prevented plot from displaying for default plots with geographic coordinate systems
* Added ability to toggle on/off display of point groups in PlotMapPoints() Leaflet maps
* Fixed TS plots in PlotBasinSummary() to use simulated discharge (cout) with reTS instead of using observed discharge (rout)
* Added SubidAttributeSummary() and PlotPerformanceByAttribute() functions to plot model performance by subbasin attributes
* Added WriteHarmonizedData() and WriteHarmonizedSpatialDescription() functions to help with HYPEObsMetadataTools workflow.

#### Notable Shortcomings
* See issue tracker on HYPEtools' [GitHub development page](https://github.com/rcapell/HYPEtools/issues)

## HYPEtools 1.0.0 (2022-08-22)
*New functions and bug fixes*

#### Highlights
* Initial CRAN Submission
* Added vignettes to package
* Updated functions to use sf package instead of sp package for spatial processing
* Fixed bug in SortGeoData()
* Various bug fixes and small improvements

#### Notable Shortcomings
* See issue tracker on HYPEtools' [GitHub development page](https://github.com/rcapell/HYPEtools/issues)

#### New Functions
* IsHeadwater: Quickly query vectors of HYPE SUBIDs to identify if they are headwater subbasins
* IsOutlet: Quickly query vectors of HYPE SUBIDs to identify if they are outlet subbasins
* ReadInfo: Import a HYPE model settings information file as list into R
* ReadUpdate: Import HYPE "update.txt" files as data frames into R

## HYPEtools 0.5.1 (2021-08-27)
*New functions and bug fixes*

#### Highlights
* Further leaflet plotting functionality, with PlotMapPoints
* Various improvements and bug fixes in existing functions

#### Notable Shortcomings
* SortGeoData sorting with branches not yet fixed.

#### New Functions
* ReadObs: Replaces ReadPTQObs and now supports more HYPE input data types
* CompareFiles: Compare imported HYPE files for differences, typically used in quality control
* PlotSubbasinRouting: Plot routing of subbasins for a HYPE model on an interactive map
* VariableInfo and VariableSearch: Lookup information (e.g. Name, Units) for a specific HYPE variable ID, or find HYPE variable information for a search term.

## HYPEtools 0.5.0 (2021-05-13)
*New functions and bug fixes*

#### Highlights
* PlotMapOutput now offers plotting to Leaflet maps
* Rudimentary netCDF file support in ReadTimeOutput (to be extended in coming releases)
* Targeted summary method for GeoData.txt files
* New S3 class for HypeGeoData with summary and merge methods

#### Notable Shortcomings
* SortGeoData sorting with branches not yet fixed.

#### New Functions
* HypeAttrAccess: HYPE data-specific attribute assign/access helpers
* OutletNearObs: Find outlet-near observations in HYPE observation data files
* ReadOutregions/WriteOutRegions: Read/Write 'Outregions.txt' files
* ReadSimass: Read 'simass.txt' files
* RescaleSLCClasses: Rescale SLC classes in a GeoData data frame

## HYPEtools 0.4.6 (2019-09-02)
*Bug fixes and improvements*

#### Highlights
* PlotBasinOutput and PlotBasinSummary now with default printing to pdf file, and new argument 'driver'
* PlotMapOutput now with argument 'col' instead of 'col.ramp.fun', accepts vectors of colors in addition to color ramp functions
* Numerous bug fixes and small improvements

## HYPEtools 0.4.5 (2018-02-20)
*Bug fixes and improvements*

#### Highlights
* Bug fixes in ReadMapOutput, WriteMapOutput, ReadTimeOutput, PlotMapOutput, PlotMapPoints, AnnualRegime
* Export functions updated to data.table's fwrite
* Better performance of AnnualRegime

#### New Functions
* ExtractStats: Calculate aggregated statistics from long-term time series, typically imported HYPE time output files

## HYPEtools 0.4.4 (2017-08-31)
*New functions and bug fixes*

#### Highlights
* Bug fixes

#### New Functions
* WriteMapOutput: Export a HYPE map output file

## HYPEtools 0.4.3 (2016-11-10)
*New functions and bug fixes*

#### Highlights
* Bug fixes, among them a critical one in PlotBasinSummary(), where upstream loads were partly wrong
* Optimised classes are no longer included as elements in optpar lists, but can now be inspected using OptimisedClasses()

#### New Functions
* CreateOptpar: Create a list representing a HYPE optpar.txt file from an imported par.txt file and a selection of parameters
* GwRetention: Calculate nutrient load retention fractions in groundwater parts of HYPE, i.e. after rootzone retention
* OptimisedClasses: Check which classes (land use or soil) of parameters in an imported optpar list are actually optimized, i.e. have a min/max range larger than zero
* ReadForcKey: Import HYPE ForcKey files
* WriteForcKey: Write HYPE ForcKey files
* WriteOptpar: Write a HYPE parameter optimization list to a file

## HYPEtools 0.4.2 (2016-10-05)
*Bug fixes*

#### Highlights
* Div. improvements to PlotBasinSummary()
* Div. bug fixes
* ReadDescription() updated, not backwards-compatible

## HYPEtools 0.4.1 (2016-09-02)
*New functions and bug fixes*

#### Highlights
* Bug fixes and improvements in various functions, changes to ReadDescription() are not backwards-compatible

#### New Functions
* BarplotUpstreamClasses: Plot upstream-averaged landscape property classes of one or several sub-basins as bar plots, e.g. land use or soils
* PlotSimObsRegime: Combined plot for annual regimes with box plot elements for observed variables and ribbon elements for simulated variables
* PlotBasinSummary: Plot a standard suite of plots summarizing properties of a sub-basin including upstream area and model performance for discharge and concentrations of nutrients, sediment, and tracers
* CustomColors: Custom color ramp functions

## HYPEtools 0.4.0 (2016-06-12)
*New functions and bug fixes*

#### Highlights
* Much-improved import of large files, thanks to fread() from package data.table
  - ReadPTQobs(), ReadXobs(), ReadGeoData() updated
  - Option to import as data.table object to make use of the speedier data handling for that class
* New S3 classes HypeMultiVar and HypeXobs, improvements to HypeSingleVar
* Attribute preservation when sub-setting
* PBIAS(), Pearson's R (r()), and summary() methods for HypeSingleVar
* New map plot function PlotMapPoints(), mostly for quickly plotting performance measures at measurement points on a map
* New import function for text files with HYPE land use, soil, and crop class descriptions, for easier label plotting: ReadDescription() (the imported file is not a HYPE file, file structure described in ReadDescription help entry)
* New import function for optpar.txt files, imports optpar contents into a list structure which makes it easier to create and update optpar files
* New trivial import/export functions for HYPE files: ReadAllsim(), ReadDamData(), ReadGlacierData(), ReadSubass(), WriteCropData(), WriteDamData(), WriteMgmtData(), WritePointSourceData()
* Numerous bug fixes since last release

## HYPEtools 0.3.9 (2016-02-10)
*Bug fixes*

## HYPEtools 0.3.8 (2015-11-06)
*New functions and bug fixes*

#### Highlights
* Bug fixes in PlotBasinOutput() after testing the initial 0.3-7 release version
* New function ReadWsOutput() to import MC results
* First HYPE-specific S3 class HypeSingleVar, for (multiple) time and map output files, relates to the new import function
* New sub-setting and NSE calculation (for hydroGOF::NSE generic) methods for the new class
* Several other bug fixes and internal updates

## HYPEtools 0.3.7 (2015-10-20)
*New functions and bug fixes*

#### New Functions
* PlotBasinOutput: Plot a standard suite of time series plots from a basin output file, typically used for model performance inspection and/or during manual calibration
* PlotAnnualRegime: Convenience wrapper function for a combined line plot with polygon variation ranges

## HYPEtools 0.3.6 (2015-08-14)
*Bug fixes*

## HYPEtools 0.3.5 (2015-06-30)
*New functions and bug fixes*

#### New Functions
* ReadPointSourceData: Read HYPE PointSourceData file
* UpstreamPointSources: Calculate point source emissions over all upstream areas of a vector of SUBIDs or all SUBIDs in a GeoData table

## HYPEtools 0.3.4 (2015-06-10)
*Bug fixes*

## HYPEtools 0.3.3 (2015-06-09)
*New functions and bug fixes*

#### Highlights
* Update for DirectUpstreamSubids()
* Bug fixes

#### New Functions
* SortGeoData: Sort an imported GeoData.txt file in downstream order, so that all upstream sub-basins are listed in rows above downstream sub-basins

## HYPEtools 0.3.2 (2015-06-04)
*New functions and bug fixes*

#### New Functions
* UpstreamGeoData: Calculate upstream sums and averages for selected variables of imported GeoData.txt files
* UpstreamGroupSLCClasses: Calculate averages of grouped SLC class fractions calculated from imported GeoData.txt and GeoClass.txt or any other user-defined grouping
* EquallySpacedObs: Create equally spaced time series with missing observations from a data frame with irregular observations

## HYPEtools 0.3.1 (2015-01-28)
*New functions and bug fixes*

#### Highlights
* Added new functions, mostly small helper functions: AnnualRegime, HeadwaterSubids, MapRegionalSources, OutletSubids, ReadAquiferdata, WriteAquiferdata, ReadMgmtData, WriteMgmtData
* Various small bug fixes

## HYPEtools 0.3.0 (2014-11-21)
*New functions and bug fixes*

#### Highlights
* Bug fixes
* Read and write functions for pmsf.txt files
* Write function for lake data
* New function UpstreamObs() for extracting upstream average forcing, includes fortran code

## HYPEtools 0.2.5 (2014-10-22)
*New functions and bug fixes*

#### Highlights
* New attribute "timestep" in ReadBasinOutput()
* Extended functionality of ConvertDischarge()
* Bug fixes

#### New Functions
* AllDownstreamSubids: Find all SUBIDs of downstream sub-catchments along the main stem for a single sub-catchment
* OutletIds: Find the identifier of model domain outlets, i.e. the "downstream" ID of outlet catchments, in a GeoData file
* MergeXobs: Merge two Xobs data frames, with handling of overlapping time periods and time periods gaps as well as merging of common columns

## HYPEtools 0.2.4 (2014-08-18)
*New functionalities and bug fixes*

## HYPEtools 0.2.3 (2014-07-14)
*New functionalities and bug fixes*

## HYPEtools 0.2.2 (2014-07-08)
*New functionalities and bug fixes*

## HYPEtools 0.2.1 (2014-05-18)
*Improved functionality*

#### Highlights
* Several functions were added to the package, most noteworthy the first plot function, PlotMapOutput()

## HYPEtools 0.1.2 (2014-02-10)
*Import/Export for common HYPE files complete*
