NEWS

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HYPEtools 1.6.3.9000

Development Version

Highlights

• Update ReadDescription() to read information about point source types
• Allow adding comment line to WriteObs()

HYPEtools 1.6.3 (2024-09-05)

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 (2024-05-23)

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

HYPEtools 1.0.0 (2022-09-05)

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

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

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

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

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

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

New functions and bug fixes

Highlights

• Bug fixes

New Functions

• WriteMapOutput: Export a HYPE map output file

HYPEtools 0.4.3

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

Bug fixes

Highlights

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

HYPEtools 0.4.1

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

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

Bug fixes

HYPEtools 0.3.8

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

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

Bug fixes

HYPEtools 0.3.5

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

Bug fixes

HYPEtools 0.3.3

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

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

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

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

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

New functionalities and bug fixes

HYPEtools 0.2.3

New functionalities and bug fixes

HYPEtools 0.2.2

New functionalities and bug fixes

HYPEtools 0.2.1

Improved functionality

Highlights

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

HYPEtools 0.1.2

Import/Export for common HYPE files complete