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update main!#86

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CeresBarros merged 195 commits intomainPredictiveEcology/Biomass_core:mainfrom developmentPredictiveEcology/Biomass_core:developmentCopy head branch name to clipboardJun 7, 2024

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Commits on Mar 2, 2022

• allow sppNameVector

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Commits on Mar 9, 2022

• Merge branch 'development' into sppNameVector

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Commits on Mar 13, 2022

• bugfix when cohortDefinitionCols has B (e.g., partial mortality)

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Commits on Mar 29, 2022

• minor improvement to example setup

  

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• spell out LBSE in header

  

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• Merge branch 'addManualRmd' into development

  

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• Merge branch 'development' into initialBglobal

  

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• rm dot from P(sim)$initialB & check value across modules

  

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Commits on Apr 6, 2022

• knitr cache is only logical now

  

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Commits on Apr 7, 2022

• change pipe table to list

  

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• fixes for latex

  

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• Merge branch 'addManualRmd' into initialBglobal

  

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• need LandR@LANDISinitialB to pass initialB = NA/NULL

  

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Commits on Apr 12, 2022

• use LandR::sppHarmonize to make sppEquiv etc.

  

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• minor

  

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• Merge pull request #59 from PredictiveEcology/sppNameVector

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• Merge remote-tracking branch 'upstream/development' into development

  

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• bump LandR version

  

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• Merge branch 'development' into initialBglobal

  

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• bump LandR version

  

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• bump LandR

  

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• add assertSppVectors

  

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• bump LandR

  

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• add missing dependency

  

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Commits on Apr 13, 2022

• add assertSppVectors

  

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• add missing dependency

  

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• Merge branch 'temp' into sppNameVector

  

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• Merge pull request #63 from PredictiveEcology/sppNameVector

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• Merge remote-tracking branch 'upstream/development' into development

  

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Commits on Apr 14, 2022

• merge branch from usptream

  

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Commits on Apr 21, 2022

• bugfix: sppEquivCol is a parameter

  

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• Merge pull request #64 from PredictiveEcology/sppNameVector

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• Merge remote-tracking branch 'upstream/development' into development

  

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• Merge remote-tracking branch 'upstream/development' into initialBglobal

  

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Commits on Apr 22, 2022

• bugfix, can't assign to P(sim) (duh!)

  

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• Merge pull request #65 from CeresBarros/bugfix

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Commits on May 2, 2022

• Merge remote-tracking branch 'upstream/development' into sppNameVector

  

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• bugfix: pass studyArea to sppHarmonize

  

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• Merge pull request #66 from CeresBarros/sppNameVector

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Commits on May 3, 2022

• minor cleanup

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Commits on May 5, 2022

• Merge remote-tracking branch 'upstream/development' into development

  

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Commits on May 27, 2022

• fix figure size -manual

  

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• Merge pull request #67 from CeresBarros/manualFix

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• Merge remote-tracking branch 'upstream/development' into development

  

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Commits on Jun 2, 2022

• table fixes -- not finished

  

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• Merge branch 'manualFixes' into development

  

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• manual edits: minor

  

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• manual edits: add sppNamesVector

  

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• re-knit

  

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Commits on Jun 21, 2022

• use LandR from PredictiveEcology instead of CeresBarros

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• Update Biomass_core.R

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• Merge branch 'development' into initialBglobal

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• Merge pull request #62 from CeresBarros/initialBglobal

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• bump min LandR version reqd

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• Merge remote-tracking branch 'upstream/development' into development

  

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Commits on Jun 29, 2022

• need latest LandR

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Commits on Jun 30, 2022

• v minor

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Commits on Sep 7, 2022

• remove RandomFields dependency

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Commits on Sep 8, 2022

• httr::config(ssl_verify) controlled by module param

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Commits on Sep 9, 2022

• metadata description formatting

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• use latest LandR pkg

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Commits on Oct 14, 2022

• Merge remote-tracking branch 'upstream/development' into development

  

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• Merge remote-tracking branch 'origin/development' into development

  

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• fix GitHub Actions wrkflow: need bookdown

  

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Commits on Oct 18, 2022

• simplify GHA workflow to rubild Rmd

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• GHA: render rmd needs bookdown

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• sslVerify as integer

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• Merge remote-tracking branch 'origin/development' into development

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Commits on Oct 19, 2022

• Update render-module-rmd.yaml

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• Re-build Biomass_core.Rmd

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• Merge remote-tracking branch 'upstream/development' into development

  

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• metadata cleanup

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• fix assertions during plotting (close #73)

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• need latest LandR (with prev and #73)

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• Re-build Biomass_core.Rmd

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• Merge remote-tracking branch 'upstream/development' into development

  

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• Merge pull request #61 from CeresBarros/development

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• temporary: example trait/parameter tables for manual

  

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• Merge remote-tracking branch 'upstream/development' into development

  

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Commits on Nov 3, 2022

• [skip-ci] GHActions: improved worfklow

  

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• metadata: pkg bumps and re-organisation

  

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• metadata: .sslVerify needs to be integer

  

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• bugfix: need Plots(..., usePlot = TRUE, fn = NULL)

  

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• bump to v1.3.10

  

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• manual changes: formatting and rendering updates

  

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• manual: clean up old code

  

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• manual: fix conflict between master & development

  

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• manual: revamp working example

  

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• manual: minor textual change

  

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• manual: render

  

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Commits on Nov 4, 2022

• manual: fix table formatting

  

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• Merge pull request #76 from PredictiveEcology/resync-devel

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Commits on Nov 18, 2022

• Re-build Biomass_core.Rmd

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Commits on Feb 22, 2023

• metadata cleanup

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• metadata formatting

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• Re-build Biomass_core.Rmd

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• fix typo (partial matching) in plotting

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• Merge branch 'development' of ssh://github.com/PredictiveEcology/Biomass_core into development

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• Re-build Biomass_core.Rmd

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Commits on Mar 9, 2023

• Merge remote-tracking branch 'upstream/development' into development

  

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• metadata cleanup and improvement (minor)

  

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• Re-build Biomass_core.Rmd

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• Re-build Biomass_core.Rmd

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Commits on Jul 24, 2023

• rm reproducible deprecated args

  

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Commits on Jul 26, 2023

• Merge remote-tracking branch 'upstream/development' into deprecatedArgs

  

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• metadata: RasterLayer -> SpatRaster

  

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• metadata: SPDF -> sfc

  

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• compareRaster -> .compareRas

  

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• compareCRS -> .compareCRS

  

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• spTransform -> projectInputs

  

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• ras[]/getValues(ras) -> as.vector(ras[])/as.vector(values(ras))

  

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• raster::mask/projection-> mask/crs

  

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• use new methods flow to make RTM

  

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Commits on Jul 27, 2023

• do rawBiomassMap and RTM steps if needRTM==TRUE

  

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• rm unused object

  

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Commits on Aug 1, 2023

• add Biomass_sspParameters to loadOrder

  

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Commits on Aug 4, 2023

• document functions

  

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• minorissimo

  

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• more documenting

  

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• add stage arg checks

  

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• minor: more code readability

  

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• minor: metadata desc

  

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• compareRaster -> .compareRas

  

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• more param checks and organize code

  

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• bugfix: .compareRas argument

  

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Commits on Aug 21, 2023

• arg name changed in .compareRas

  

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• add LANDIS ref

  

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• minor: metadata improvements

  

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Commits on Sep 14, 2023

• Merge remote-tracking branch 'upstream/development' into development

  

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• rm unused objs/args

  

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• export first simulatedBiomassMap (init) to sim

  

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• use verbose arg in dispersal functions

  

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• minorissimo

  

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Commits on Sep 16, 2023

• Merge branch 'cleanup' into terra-migration

  

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Commits on Sep 21, 2023

• cleanup + fix sections for use with Rstudio

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• use figurePath()

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Commits on Sep 26, 2023

• update SpaDES.core

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• Merge remote-tracking branch 'upstream/terra-migration' into terra-migration

  

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Commits on Sep 27, 2023

• add terra to module pkgDeps

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• Merge branch 'terra-migration' of ssh://github.com/PredictiveEcology/Biomass_core into terra-migration

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Commits on Oct 12, 2023

• add function prefix to allow building of manual

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• citation cleanup + add Scheller et al. 2007

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Commits on Oct 21, 2023

• more terra-izing

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Commits on Nov 10, 2023

• don't use "mod$groupSize"... just groupSize

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• calculateSumB -- add "verbose" so can limit noisiness

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• tags -- use OtherFunction instead of function

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• Re-build Biomass_core.Rmd

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• otherFunctions

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• Merge remote-tracking branch 'origin/development' into development

  

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• Re-build Biomass_core.Rmd

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Commits on Dec 2, 2023

• can't use mask; may be diff crs

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• Re-build Biomass_core.Rmd

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Commits on Jan 22, 2024

• cohortDefinitionCols -- rm ad hoc addition; must be in metadata

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• Re-build Biomass_core.Rmd

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Commits on Apr 19, 2024

• use inputPath instead of dataPath per latest best practices

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• Re-build Biomass_core.Rmd

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Commits on May 7, 2024

• minor metadata formatting

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• Re-build Biomass_core.Rmd

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Commits on May 10, 2024

• [v1.4.0] use latest LandR with assertSpeciesTable

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Commits on May 17, 2024

• minor metadata formatting

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• Merge branch 'development' of ssh://github.com/PredictiveEcology/Biomass_core into development

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Commits on May 29, 2024

• switch to stable versions of pkgs where possible

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• bump v1.4.1

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Commits on May 30, 2024

• bump reproducible

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• minor

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Commits on May 31, 2024

• bump SpaDES.core & rm figurePath()

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• Re-build Biomass_core.Rmd

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• speciesLayers may not yet exist during .inputObjects

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• one .compareRas needs stopOnError = FALSE

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Commits on Jun 4, 2024

• bump v1.4.1.9001

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Commits on Jun 5, 2024

• LandR@development -> LandR

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• bump v1.4.1.9002

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• minor

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• assert spp vectors/sppEquiv/species earlier

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• filter sppEquiv/sppColorV/sppNameVect to simulated species

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• minor

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• use mo$sppEquiv throughout

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• bump v1.4.1.9003

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• Re-build Biomass_core.Rmd

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Commits on Jun 6, 2024

• Merge remote-tracking branch 'upstream/development' into bugfixes

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• Update Biomass_core.R LandR@development >=1.1.3

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• 2 cohorts become identical ... cohort 1 = 14 B and 2 = 15 B at start of yr

  

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• Merge branch 'development' into bugfixes

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• Merge pull request #84 from CeresBarros/bugfixes

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• Merge branch 'development' into LandRAssertionFix

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• Merge pull request #85 from PredictiveEcology/LandRAssertionFix

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• Re-build Biomass_core.Rmd

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• allow mixedType = 0 with latest LandR

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Commits on Jun 7, 2024

• Merge remote-tracking branch 'upstream/main' into development

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• rm development from GHA manual render

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