rcapell/HYPEtools: HYPEtools 1.6.0

HYPEtools 1.6.0

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 (2022-08-22)

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

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