gisler / rphosfate Goto Github PK

Define test concept and prepare data

• Test concept (tinytest)
  • Add tests for low level interface
  • Add tests for high level interface
  • Add tests for getters and setters
• Test data (HOAL catchment)
  • Use open government data were possible (DEM, channels, roads, fields)
  • Add data to "inst" folder
  • Make plausible assumptions about soil and related data as well as loads (update test data and parameters in examples etc.)
  • Manually check test data

Efficient interface for SS and PP

• Add inheritance for substance classes
• Revise relevant functions using PP as default substance for backward compatibility
  • emission()
  • transport()
  • firstRun()
  • calibrationQuality()
  • subsequentRun()

Implement function argument sanity checks utilising checkmate

• autoCalibrate()
• calibrationQuality()
• DEMrelatedInput()
• emission()
• firstRun()
• subsequentRun()
• transport()

Write and read parameters from a YAML instead of RDS file

• Test functionality from yaml package: test successful
• Replace parameters.rds with parameters.yaml
  • Write YAML file
  • Read YAML file and allow for overrides via arguments
• Check for existence of parameters.rds and add parameters.yaml on catchment initialisation for backward compatibility if only the RDS file exists

Write best practice model handbook

• Decide on language(s): en_GB
• Decide on platform: website utilising GitHub Pages
• pkgdown + bookdown
• Write handbook

This package depends on (depends, imports or suggests) raster and one or more of the retiring packages rgdal, rgeos or maptools (https://r-spatial.org/r/2022/04/12/evolution.html). Since raster 3.6.3, all use of external FOSS library functionality has been transferred to terra, making the retiring packages very likely redundant. It would help greatly if you could remove dependencies on the retiring packages as soon as possible.

Add inlet transfer coefficient for SS

• Update class RPhosFateParameters2
• Update relevant code
• Use PP as default when converting parameters.rds

Implememt getters and setters

• getLayer()
• getParameter()
• setParameter()
  • Add prototype list to the RPhosFateParameters2 class
  • Add class sanity checks (setValidity() and validObject())

As chances are high hydroTSM won't be ready in time (see #17), hydroGOF functions shall be replaced with own code.

Write help files utilising roxygen2

• Document RPhosFate class
• Document constructors
• Document methods
• Document DEMrelatedInput()
• Add demoProject() function providing training data
• Document demonstration project data
• Add examples utilising \dontrun{}
• Add "example.R" script, which allows for checking if examples are working

Concept for and implementation of automatic model calibration

• Prepare calibrationQuality() for use with optimisation algorithm
• Choose approach and optimisation algorithm
  • Two-stage calibration: first ns_dep_ovl (overland deposition rate) for SS and then nv_enr_rto (enrichment ratio) for all other substances (no calibration of ns_dep_cha (channel deposition rate))
  • Algorithm for one dimensional optimisation without derivatives as implemented in stats::optimize() (combination of golden section search and successive parabolic interpolation)
  • Allow for manual override of the default calibration parameter so that ns_dep_cha alternatively can be used for SS or, for example, ns_dep_ovl for PP
• Implement feature