1.5.3

Fixes

• read.output now accepts date-times for start.year and end.year argument (#1887)
• read.output no longer assumes timestamps are in days since the beginning of the year
• Fixed xss issue in setup folder, now require users to login before accessing the setup folder scripts.
• Fixed issue where in website not all sites are shown #1884
• Fixed status page, should now be run from cronjob, creates static page
• Fixed bug that overwrote remote met file paths with local file paths
• PEcAnRTM:
  • Remove non-portable extensions from src/Makevars. This should make the package Windows-compatible.
• Fixed BrownDog shiny issues of removing site without geometry; fixing sites.length==0; removing old map markers when change input$type; fixing agreement bug when change input$type

Added

• Functionality to read pft-specific outputs and to run sensitivity analysis on pft-specific outputs.
• Ability to allow for insecure sync using -k flag
• Added information on how to join slack
• PEcAn.BIOCRO now supports BioCro version 1.0. BioCro 0.9x models should still work as before, but note parameter and weather format changes in the Changed section below.
• Added new model package (PEcAn.dvmdostem) and initial wrappers for integration of the DVM-DOS-TEM model and tested.
• PEcAn now supports PFTs whose members are cultivars rather than species, and will automatically restrict the meta-analysis to matching records, e.g. runs with a PFT containing only Panicum virgatum 'Cave-In-Rock' will not use observations from Panicum virgatum 'Alamo', but a PFT containing the whole species will use observations from both. However, there is not yet any BETYdb interface to create cultivar-PFTs other than manual SQL.
• New base package PEcAn.workflow, for functions used to perform the each major step of the analysis. These were previously scattered in other base packages.
• Added PR review time estimate to PR template
• New set of PEcAn.logger functions similar to stopifnot to facilitate assertive programming: severeifnot, errorifnot, warnifnot, infoifnot, debugifnot
• PEcAnRTM:
  • Exposed PROSPECT absorption coefficients and gpm() function ("generalized plate model"), facilitating experimentation with different absorption coefficients
  • Added spectra S3 class and methods for subsetting (e.g. myspec[[400:700]]), plotting (plot() and matplot()), and combining spectra by wavelength.
  • Added resample functions for quickly resampling spectra (and, more generally, vectors and functions) to different dimensions.
  • EDR API has been revised. Setup has been refactored from EDR via new setup_edr function, which relies on the ED utilities (see PEcAn.ED2 below), and the EDR function now focuses only on execution. Also, added new params2edr function to make it easy to convert complex EDR parameters list to flat parameter vector required by invert_bt (or other optimization functions).
• PEcAn.ED2:
  • New set of utilities for working with ED meteorology and vegetation inputs, and the ED2IN file. Existing PEcAn code has been revised to use these utilities.
• PEcAn.data.atmosphere:
  • New utilities for efficiently downloading NARR time series using THREDDS/OpenDAP

Removed

• Removed deprecated copies of PEcAn.utils::SafeList, PEcAn.utils::listToXml (both moved to PEcAn.settings in v 1.5.2), and PEcAn.utils::fqdn (moved to PEcAn.remote in 1.5.2). This fixes the masses of deprecation warnings in otherwise normal run logs (#1719).

Changed

• Updated wrappers for FATES model to work with recent CLM5 release. Updated write.config, job.template, and other associated files to work with CLM5 inputs and met drivers
• Updated model2netcdf.MAAT to use ncdf4::ncvar_def to define netCDF variables
• Fixed an remote code execution discovered by NCSA security team.
• Column name changes for newly generated biocromet csvs: SolarR is now solar and WS is now windspeed. Previously generated met files with the old names will still work for BioCro 0.9 runs, but will need to be renamed before using them with BioCro 1.0.
• write.configs.BIOCRO now requires a model version specification so that it can format parameters to match your version of BioCro. Set it in your Bety model record or in the model$revision field of your pecan.xml.
• When using BioCro 1.0 and no parameter file is given, PEcAn will make an attempt to find default parameters for your genus in the datasets provided by the BioCro package. Note that the default parameter files provided in models/biocro/inst/extdata/defaults will not work when using BioCro 1.0.
• Added documentation how to submit a run from the command line
• Updated models/maat to provide support for latest model code updates
• PEcAn.DB function rename.jags.columns renamed to rename_jags_columns to avoid conflict with S3 method naming conventions
• Replaced rhdf5 library with hdf5r, a more modern alternative that is available on CRAN.
• PEcAn.DB function runModule.get.trait.data has been moved to the new PEcAn.workflow package to avoid a circular package dependency between PEcAn.DB and PEcAn.settings.
• Major documentation refactoring. The documentation names are now directly tied to the order in which they are rendered, and all Rmd files in all subdirectories of the documentation source are rendered by default. The overall structure of the documentation has been revised for clarity and cohesiveness.
• Edited met2model.ED2 to not enforce leap years.
• Integrate demo 1 into basic user guide