Recent Releases of rSFSW2

rSFSW2 - v4.3.0

Tilted radiation, gridMET, MACA, and other improvements

  • updated code to support new SOILWAT2 v6.0.0 that overhauled estimation of solar radiation with a particular improvement for tilted surfaces (https://github.com/DrylandEcology/SOILWAT2/releases/tag/v6.0.0)
  • moved supporting functionality to new R package "rSW2utils" (https://github.com/DrylandEcology/rSW2utils)
  • moved code of the sagebrush regeneration model (Schlaepfer et al. 2014) to new R package "rSW2funs" (https://github.com/DrylandEcology/rSW2funs)
  • moved code to estimate vegetation composition and biomass from climate relationships to R package "rSOILWAT2" and completely redesigned much of the functions
  • added functionality to extract daily meteorological data from gridMET
  • added functionality to extract daily scenario climate dataset CMIP5_MACAv2metdata_USA
  • improved handling of yearly atmospheric CO2-concentration time-series
  • several bug fixes and other improvements

Natural Resources - Soil and Land - R
Published by dschlaep over 4 years ago

rSFSW2 - v4.1.0

  • new functions to deal with the output database: dbOutput_add_calculated_field, dbOut_read_variables_from_scenario
  • new functions for circular arithmetic: circ_add, circ_minus
  • other new functions: trewartha_climate, rbind_2cols_nonoverlapping
  • upgraded to rSOILWAT2 v3.1.3
  • several bug fixes
  • upgraded to lintr v2.0.0

Natural Resources - Soil and Land - R
Published by dschlaep over 5 years ago

rSFSW2 - v4.0.0

  • Updates to reflect new interception equations in SOILWAT2 v5.0.0 and rSOILWAT v3.0.0
  • Moved several functions to rSOILWAT2:
    • Vegetation-climate functions and associated time functions
    • Functions related to soil moisture/temperature conditions and regimes, resilience and resistance categories, and associated functions

Natural Resources - Soil and Land - R
Published by dschlaep almost 6 years ago

rSFSW2 - v3.1.5

Addressing changes in interfaces of dependencies:

  • roxygen2 v6.1.1
  • devtools v2.0.1
  • R-devel (upcoming v3.6.0)
  • lintr (incompatible with R-devel)

Natural Resources - Soil and Land - R
Published by dschlaep about 6 years ago

rSFSW2 - v3.1.4

  • Updated to 'estimate_PotNatVeg_composition' function to account for Tree PFT

Natural Resources - Soil and Land - R
Published by CaitlinA about 6 years ago

rSFSW2 - v3.1.3

  • requiring a new version of rSOILWAT2 v2.3.5 (to fix a REAL/INTEGER bug related to transpiration regions)
  • fixed DayMet unit tests
  • fixed netCDF unit tests

Natural Resources - Soil and Land - R
Published by dschlaep about 6 years ago

rSFSW2 - v3.1.2

Function dbOutput_subset: gains capability to subset records

Natural Resources - Soil and Land - R
Published by dschlaep over 6 years ago

rSFSW2 - v3.1.1

Several bug fixes

Natural Resources - Soil and Land - R
Published by dschlaep over 6 years ago

rSFSW2 - v3.1.0

  • New functionality to check agreement among two output databases, to update values in one from another output database (e.g., fixing output affected by some fixed bug), and to subset an output database to a smaller set of tables and variables
  • Improved organization of unit tests: more consistent behavior controlled by environmental variables RSFSW2_ALLTESTS, RSFSW2_SAVETESTS, NOT_CRAN (not set consistently), TRAVIS, APPVEYOR, and TESTTHAT
  • Improved linters
  • Improved README

Natural Resources - Soil and Land - R
Published by dschlaep over 6 years ago

rSFSW2 - v3.0.0

Natural Resources - Soil and Land - R
Published by dschlaep over 6 years ago

rSFSW2 - v2.7.4

  • fixes bug that caused all aggregated output that was using snow to be incorrect for scenarios > ambient (#307)
  • expanded unit test project and fixed newly identified bugs arising from more thorough testing

Natural Resources - Soil and Land - R
Published by dschlaep almost 7 years ago

rSFSW2 - v2.7.3

  • under-the-hood updates to SOILWAT2 and rSOILWAT2

Natural Resources - Soil and Land - R
Published by dschlaep about 7 years ago

rSFSW2 -

fixed daymet functions

Natural Resources - Soil and Land - R
Published by CaitlinA about 7 years ago

rSFSW2 - v2.7.1

Fixed code so that projects that use weather folders lookups run again

Natural Resources - Soil and Land - R
Published by dschlaep about 7 years ago

rSFSW2 - v2.7.0

Bug fixes

  • Fixes to function recreate_dbWork
  • Fixes to aggregation periodicVWCmatricFirstLayer
  • Fixes to aggregation yearlyTranspirationBySoilLayer
  • Fixes to aggregation dailySnowpack
  • Fixes to function check_rSFSW2_project_input_data for "prj_todos"

Improvements

  • Function check_rSFSW2_project_input_data gained checks for table lookups
  • Function check_outputDB_completeness now requires that all simulation runs have completed and all temporary output files have been moved to the database
  • Function recreate_dbWork doesn't overwrite anymore timing information when updating an existing work table
  • Improvements to dbWork functionality
  • dbOutput databases gained new indices for faster queries
  • To reduce parallel traffic jams, the call to dbWork_update_job for MPI-parallel backends was moved from workers to the loop on master
  • Completely re-written function move_temporary_to_outputDB reduced memory footprint by 20-40 fold and increased speed by about 20-100%

New functionality

  • New function move_output_to_dbOutput: can be used to move output to the database before all simulation runs have concluded
  • Function init_rSFSW2_project gained new argument update which calls update_project_paths to update an existing object SFSW2_prj_meta and it's representation SFSW2_project_descriptions.rds with the local path names (e.g., to move an ongoing project between computers)
  • New function dbOutput_update_OverallAggregationTable
  • New function generate_OverallAggregation_fields gathers information on the number and names of the selected overall aggregation output -- which is used under debugging runs by updated do_OneSite to check that requested and calculated output match up correctly

Changes to interface and demo code

  • Make demo code more robust
  • New demo code for moving temporary output files to the dbOutput
    database while the execution of runs continues

Natural Resources - Soil and Land - R
Published by dschlaep about 7 years ago

rSFSW2 - v2.6.4

Small fixes

Natural Resources - Soil and Land - R
Published by dschlaep about 7 years ago

rSFSW2 - v2.6.3

Additional aggregation outputs available in the "aggregation_overall_mean" and "aggregation_overall_sd" tables of dbTables.sqlite3 database.

New optionality allows users to set "doy_ranges" for aggregating variables (instead of for the entire year).

Natural Resources - Soil and Land - R
Published by CaitlinA about 7 years ago

rSFSW2 - v2.6.0

  • new output option yearlyTranspirationBySoilLayer: transpiration for
    each soil layer and each vegetation type (and total)

Natural Resources - Soil and Land - R
Published by dschlaep about 7 years ago

rSFSW2 - v2.5.8

  • Fix aggregation dailyFrostInSnowfreePeriod
  • Fix function check_rSFSW2_project_input_data

Natural Resources - Soil and Land - R
Published by dschlaep about 7 years ago

rSFSW2 - v2.5.7

  • checks that water balance is closed on test project
  • adds evaporation of ponded (surface) water as output field
  • fixes unit test issues arising from fixing dbWork

Natural Resources - Soil and Land - R
Published by dschlaep about 7 years ago

rSFSW2 - v2.5.6

  • fix failure on locked dbWork database

Natural Resources - Soil and Land - R
Published by dschlaep about 7 years ago

rSFSW2 - v2.5.5

  • v2.5.5: update interactions with rSOILWAT2's new vegetation structure

Natural Resources - Soil and Land - R
Published by dschlaep about 7 years ago

rSFSW2 - v2.5.0

  • simulation experiments that can use the CO2-concentration effects on biomass and water-use efficiency offered by SOILWAT2

Natural Resources - Soil and Land - R
Published by dschlaep over 7 years ago

rSFSW2 - v2.4.0

  • Weather database is created with maximal time period
  • Allow 1-year aggregation period
  • Handle runon and/or runoff from ponded water --> updated input files SWRuns_InputData_siteparam_v14.csv and SWRuns_InputData_ExperimentalDesign_v06.csv as well as updates to demo code SFSW2_project_descriptions.R
  • Run rSOILWAT2 silently
  • New script to generate SoilWat2_defaults input from rSOILWAT2 package --> completely updated default inputs 1_Data_SWInput/SoilWat2_defaults/

Natural Resources - Soil and Land - R
Published by dschlaep over 7 years ago

rSFSW2 - v2.3.14

  • Improved climate data extraction and downscaling
  • Allow projects with soil inputs from all sources mixed
  • Improved checks on soil input data; updated default SOILWAT2 soilsin input file such that default soil data less likely interfere with other input sources

Natural Resources - Soil and Land - R
Published by dschlaep over 7 years ago

rSFSW2 - v2.3.10

Natural Resources - Soil and Land - R
Published by dschlaep over 7 years ago

rSFSW2 - v2.3.9

Natural Resources - Soil and Land - R
Published by dschlaep over 7 years ago

rSFSW2 - v2.3.6

Changes since v2.3.0 include:

  • Added support for CMIP5 netCDF data with CF convention format which were accessed from one of the ESGF nodes
  • Consider 'Include_YN_*Sources' when extracting external data
  • Resuming with an existing dbWeather identifies correct sites and correct scenarios
  • Fix 'doQmapQUANT.default_drs' and 'doQmapQUANT_drs' when one month of each year in the reference data showed not variability (e.g., August of every year receives no precipitation)
  • Fix determination of 'include_YN_climscen'
  • Enhance input checks by querying available climate scenario data
  • Fix how worker IDs were determined
  • Fix idling MPI workers if call to 'do_OneSite' fails

Natural Resources - Soil and Land - R
Published by dschlaep over 7 years ago

rSFSW2 - v2.3.0

  • several fixes
  • improved unit tests
  • improved CIs

Natural Resources - Soil and Land - R
Published by dschlaep almost 8 years ago

rSFSW2 - v2.0.1

The wrapper is now a R package!

Natural Resources - Soil and Land - R
Published by dschlaep almost 8 years ago

rSFSW2 - v1.12.0

  • redefine index ‘runIDs_total’ as “consecutive number of all possible (sites x exp) simulations” instead of “consecutive number of (included sites x exp) simulations”
  • incompatible with previous versions of 'dbWork'

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.11.0

  • fixing 'check' output database
  • fixing 'concatenation' of output database: works again for tables with soil layers
  • fixing code so that Rmpi works again
  • removed support for 'multicore'/'doMC' parallel backend and replaced 'snow' with base-package 'parallel'

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.10.0

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.9.2

if ‘saveRsoilwatOutput’ is TRUE, then output is not any more stored to disk for ‘runData’ but for each scenario ’runDataSC’ to ‘sw_output_scX.RData’ with X = scenario number

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.9.1

Much faster export to workers in parallel simulations

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.9.0_1

  • changes in folder structure
  • transfer of test projects to a dedicated rSWSFtools repository (using git-lfs for large reference databases)
  • eradicating test projects from history of SoilWat_R_Wrapper with BFG
    Repo-Cleaner

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.8.3

  • Fix memory issue in SOILWAT
  • Several minor bug fixes

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.8.2

Starts using Rcpp if available (for now for some of GISSM slowest functions)

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.8.1

  • simulation of sites with one soil layer is now possible (again)

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.8.0

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.7.0

  • new overall aggregation: dailyNRCS_Maestas2016_ResilienceResistance

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.6.4

  • Several bug fixes
  • Moved R code to folder R/ except for file p1

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.6.3

  • Bug fixes for certain date/time situations
  • Enables use by Rscript
  • Requires updated Rsoilwat which fixes same date/time bug

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.6.2

Several improvements and bug fixes

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.6.1

  • Bug fixes for parallelization, ExtendSoilDatafileToRequestedSoilLayers, and ExtractSoilDataFromISRICWISEv12_Global including 'get_prids'
  • Improvements to CalculateBareSoilEvaporationCoefficientsFromSoilTexture and soil information section of 'create' action
  • Updated GriddedDailyWeatherFromDayMet_NorthAmerica to DayMet version 3

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.6.0

Improved calculation of NRCS soil moisture / soil temperature regimes

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.5.1

  • Fixed running with MPI
  • Fixed export of R objects
  • Re-organized GISSM module

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.5.0

  • better control of debugging options
  • bug fix for exporting data to parallel workers

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.4.5

Bug fixes and other improvements

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.4.4

Important bug fixes including
- bugs in pedotransfer functions

Several speed improvements

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.4.3

Bug fix to GISSM, etc.

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.4.2

Bug fix for calculating NRCS soil moisture and soil temperature regimes

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.4.0

  • Important bug fixes
  • Improved interaction with test projects

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.3.1

Bug fixes for 'ExtendSoilDatafileToRequestedSoilLayers'

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.3.0

Functions defined in separate script file

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.2.2

Bug fix: Improved extraction control by preventing code from overwriting partially existing data with NAs

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.2.1

Faster and more stable 'CalculateBareSoilEvaporationCoefficientsFromSoilTexture'

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.2.0

Add new soil layers to soil datafile:
if ‘ExtendSoilDatafileToRequestedSoilLayers’ is TRUE, if simulation
input for soils is coming from the datafile.soils, and if requested_soil_layers are not existing in datafile.soillayers, then new soil layers are added and soil characteristics interpolated

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.1.5

Faster lookup tables: update affects treatment/experimental design options ‘LookupSnowDensityFromTable’, ‘LookupTranspRegionsFromTable’, and ‘LookupEvapCoeffFromTable’

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.1.4

Bug fix missing flag 'debug.dump.objects'

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.1.3

DB with more flexible field names

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.1.2

Bug fix for 'ExtractSkyDataFromNOAAClimateAtlas_USA'

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.1.1

Patched functionality in NRCS Soil and Temperature Regime Delineation (Agg #35a).

Natural Resources - Soil and Land - R
Published by CaitlinA over 8 years ago

rSFSW2 - v1.1.0

New version number to reflect merged branch with new overall
aggregation options (commit efdb360):

  • dailyWarmDays
  • dailyThermalDrynessStartEnd
  • dailyThermalSWPConditionCount
  • dailyThermalDrynessStress

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.0.2

Small fix to part 3 (data extractions) of code

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - v1.0.1

Natural Resources - Soil and Land - R
Published by dschlaep over 8 years ago

rSFSW2 - First full release on master

Natural Resources - Soil and Land - R
Published by dschlaep almost 9 years ago