Code

update main!#86

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Merged

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

+880-546

Commits

Commits on Mar 2, 2022

• allow sppNameVector

  eliotmcintire

  committed
  5609133

Commits on Mar 9, 2022

• Merge branch 'development' into sppNameVector

  eliotmcintire

  committed
  362c463

Commits on Mar 13, 2022

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

  eliotmcintire

  committed
  746a6b6

Commits on Mar 29, 2022

• minor improvement to example setup

  

  CeresBarros

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  3477d23

• spell out LBSE in header

  

  CeresBarros

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  94a25ab

• Merge branch 'addManualRmd' into development

  

  CeresBarros

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• Merge branch 'development' into initialBglobal

  

  CeresBarros

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  7fba9d5

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

  

  CeresBarros

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  f107a03

Commits on Apr 6, 2022

• knitr cache is only logical now

  

  CeresBarros

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  599d9a2

Commits on Apr 7, 2022

• change pipe table to list

  

  CeresBarros

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  2861039

• fixes for latex

  

  CeresBarros

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  327f883

• Merge branch 'addManualRmd' into initialBglobal

  

  CeresBarros

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  7d57cb6

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

  

  CeresBarros

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  a770a30

Commits on Apr 12, 2022

• use LandR::sppHarmonize to make sppEquiv etc.

  

  CeresBarros

  committed
  c9c35fb

• minor

  

  CeresBarros

  committed
  8e0a17d

• Merge pull request #59 from PredictiveEcology/sppNameVector

  Show description for 4a3c79e
  

  Ceres Barros

  authored
  4a3c79e

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

  

  CeresBarros

  committed
  8a8149f

• bump LandR version

  

  CeresBarros

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  50f278c

• Merge branch 'development' into initialBglobal

  

  CeresBarros

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  7aaa501

• bump LandR version

  

  CeresBarros

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  2aedd94

• bump LandR

  

  CeresBarros

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  2c0ed25

• add assertSppVectors

  

  CeresBarros

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  703ba7c

• bump LandR

  

  CeresBarros

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  258c157

• add missing dependency

  

  CeresBarros

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  d1dded6

Commits on Apr 13, 2022

• add assertSppVectors

  

  CeresBarros

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  832b8ce

• add missing dependency

  

  CeresBarros

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  ce6a18a

• Merge branch 'temp' into sppNameVector

  

  CeresBarros

  committed
  bfba27d

• Merge pull request #63 from PredictiveEcology/sppNameVector

  Show description for 8f228a4
  

  Ceres Barros

  authored
  8f228a4

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

  

  CeresBarros

  committed
  15b7be8

Commits on Apr 14, 2022

• merge branch from usptream

  

  CeresBarros

  committed
  5c50017

Commits on Apr 21, 2022

• bugfix: sppEquivCol is a parameter

  

  CeresBarros

  committed
  163421c

• Merge pull request #64 from PredictiveEcology/sppNameVector

  Show description for ab184fe
  

  Ceres Barros

  authored
  ab184fe

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

  

  CeresBarros

  committed
  bcf284a

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

  

  CeresBarros

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  790dac5

Commits on Apr 22, 2022

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

  

  CeresBarros

  committed
  8e035b2

• Merge pull request #65 from CeresBarros/bugfix

  Show description for bf382d8
  

  Ceres Barros

  authored
  bf382d8

Commits on May 2, 2022

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

  

  CeresBarros

  committed
  931e97b

• bugfix: pass studyArea to sppHarmonize

  

  CeresBarros

  committed
  e7f210a

• Merge pull request #66 from CeresBarros/sppNameVector

  Show description for 4d33156
  

  Ceres Barros

  authored
  4d33156

Commits on May 3, 2022

• minor cleanup

  achubaty

  committed
  ac032f1

Commits on May 5, 2022

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

  

  CeresBarros

  committed
  3d1bc4b

Commits on May 27, 2022

• fix figure size -manual

  

  CeresBarros

  committed
  cafee08

• Merge pull request #67 from CeresBarros/manualFix

  Show description for 2822d95
  

  Ceres Barros

  authored
  2822d95

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

  

  CeresBarros

  committed
  9876239

Commits on Jun 2, 2022

• table fixes -- not finished

  

  CeresBarros

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  7148674

• Merge branch 'manualFixes' into development

  

  CeresBarros

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  9fbf9d5

• manual edits: minor

  

  CeresBarros

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  75a092c

• manual edits: add sppNamesVector

  

  CeresBarros

  committed
  d9b51b5

• re-knit

  

  CeresBarros

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  179b15c

Commits on Jun 21, 2022

• use LandR from PredictiveEcology instead of CeresBarros

  achubaty

  authored
  657d8f0

• Update Biomass_core.R

  Show description for 025a0a0
  achubaty

  authored
  025a0a0

• Merge branch 'development' into initialBglobal

  achubaty

  authored
  bbc4662

• Merge pull request #62 from CeresBarros/initialBglobal

  Show description for c603c82
  achubaty

  authored
  c603c82

• bump min LandR version reqd

  achubaty

  committed
  9866b41

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

  

  CeresBarros

  committed
  236d7a7

Commits on Jun 29, 2022

• need latest LandR

  Show description for 4b02305
  achubaty

  committed
  4b02305

Commits on Jun 30, 2022

• v minor

  achubaty

  committed
  bc02fd8

Commits on Sep 7, 2022

• remove RandomFields dependency

  achubaty

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  12c4ad6

Commits on Sep 8, 2022

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

  achubaty

  committed
  adf7f3b

Commits on Sep 9, 2022

• metadata description formatting

  achubaty

  committed
  0fb4fae

• use latest LandR pkg

  achubaty

  committed
  31edabf

Commits on Oct 14, 2022

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

  

  CeresBarros

  committed
  bd93f35

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

  

  CeresBarros

  committed
  f949108

• fix GitHub Actions wrkflow: need bookdown

  

  CeresBarros

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  3530309

Commits on Oct 18, 2022

• simplify GHA workflow to rubild Rmd

  achubaty

  committed
  f72956c

• GHA: render rmd needs bookdown

  achubaty

  committed
  ba7303a

• sslVerify as integer

  achubaty

  committed
  5906930

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

  achubaty

  committed
  cadba84

Commits on Oct 19, 2022

• Update render-module-rmd.yaml

  Show description for 7861d43
  achubaty

  authored
  7861d43

• Re-build Biomass_core.Rmd

  actions-user

  committed
  edd5dbf

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

  

  CeresBarros

  committed
  17234ec

• metadata cleanup

  achubaty

  committed
  a90060d

• fix assertions during plotting (close #73)

  achubaty

  committed
  c535543

• need latest LandR (with prev and #73)

  achubaty

  committed
  f1556fd

• Re-build Biomass_core.Rmd

  actions-user

  committed
  8a57a37

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

  

  CeresBarros

  committed
  49f66c8

• Merge pull request #61 from CeresBarros/development

  Show description for 4cc5a8c
  achubaty

  authored
  4cc5a8c

• temporary: example trait/parameter tables for manual

  

  CeresBarros

  committed
  a3943aa

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

  

  CeresBarros

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  99423a1

Commits on Nov 3, 2022

• [skip-ci] GHActions: improved worfklow

  

  CeresBarros

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  0dfb09f

• metadata: pkg bumps and re-organisation

  

  CeresBarros

  committed
  0d05fa8

• metadata: .sslVerify needs to be integer

  

  CeresBarros

  committed
  28c742f

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

  

  CeresBarros

  committed
  403b621

• bump to v1.3.10

  

  CeresBarros

  committed
  12efc55

• manual changes: formatting and rendering updates

  

  CeresBarros

  committed
  c6a8701

• manual: clean up old code

  

  CeresBarros

  committed
  0f74d5d

• manual: fix conflict between master & development

  

  CeresBarros

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  ad9dd6c

• manual: revamp working example

  

  CeresBarros

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  50e97d7

• manual: minor textual change

  

  CeresBarros

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  c081e5b

• manual: render

  

  CeresBarros

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  9118542

Commits on Nov 4, 2022

• manual: fix table formatting

  

  CeresBarros

  committed
  8191b0b

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

  Show description for a82173e
  

  Ceres Barros

  authored
  a82173e

Commits on Nov 18, 2022

• Re-build Biomass_core.Rmd

  actions-user

  committed
  af0134d

Commits on Feb 22, 2023

• metadata cleanup

  achubaty

  committed
  0a6af17

• metadata formatting

  achubaty

  committed
  1353d41

• Re-build Biomass_core.Rmd

  actions-user

  committed
  94e6bf7

• fix typo (partial matching) in plotting

  achubaty

  committed
  d2334bf

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

  achubaty

  committed
  a7bd136

• Re-build Biomass_core.Rmd

  actions-user

  committed
  2bd6322

Commits on Mar 9, 2023

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

  

  CeresBarros

  committed
  4dec6c3

• metadata cleanup and improvement (minor)

  

  CeresBarros

  committed
  94e03ef

• Re-build Biomass_core.Rmd

  actions-user

  committed
  58e7a1e

• Re-build Biomass_core.Rmd

  actions-user

  committed
  19d6a95

Commits on Jul 24, 2023

• rm reproducible deprecated args

  

  CeresBarros

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  efca8c9

Commits on Jul 26, 2023

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

  

  CeresBarros

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  3583166

• metadata: RasterLayer -> SpatRaster

  

  CeresBarros

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• metadata: SPDF -> sfc

  

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  484ca7f

• compareRaster -> .compareRas

  

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  d8af514

• compareCRS -> .compareCRS

  

  CeresBarros

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  5db4cb8

• spTransform -> projectInputs

  

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  439c42a

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

  

  CeresBarros

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  e86aa15

• raster::mask/projection-> mask/crs

  

  CeresBarros

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  078726e

• use new methods flow to make RTM

  

  CeresBarros

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  3532a17

Commits on Jul 27, 2023

• do rawBiomassMap and RTM steps if needRTM==TRUE

  

  CeresBarros

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  6844e89

• rm unused object

  

  CeresBarros

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  4141496

Commits on Aug 1, 2023

• add Biomass_sspParameters to loadOrder

  

  CeresBarros

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  f41530c

Commits on Aug 4, 2023

• document functions

  

  CeresBarros

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  7bf8095

• minorissimo

  

  CeresBarros

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  c7092e4

• more documenting

  

  CeresBarros

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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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  6b2f0ce

• bugfix: .compareRas argument

  

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  8c46b62

Commits on Aug 21, 2023

• arg name changed in .compareRas

  

  CeresBarros

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  d7f2bd4

• add LANDIS ref

  

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  7f68ce2

• minor: metadata improvements

  

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  48869a0

Commits on Sep 14, 2023

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

  

  CeresBarros

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  9801c2b

• rm unused objs/args

  

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  0ca6628

• 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

  achubaty

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  6b1c57a

• use figurePath()

  achubaty

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  c0f69d3

Commits on Sep 26, 2023

• update SpaDES.core

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  CeresBarros

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  171f838

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

  

  CeresBarros

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Commits on Sep 27, 2023

• add terra to module pkgDeps

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  3ef5e77

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

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  c474226

Commits on Oct 12, 2023

• add function prefix to allow building of manual

  achubaty

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  298b35e

• citation cleanup + add Scheller et al. 2007

  achubaty

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  00f0224

Commits on Oct 21, 2023

• more terra-izing

  eliotmcintire

  committed
  ba13500

Commits on Nov 10, 2023

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

  eliotmcintire

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  c7b8e53

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

  eliotmcintire

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  be53b67

• tags -- use OtherFunction instead of function

  eliotmcintire

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• Re-build Biomass_core.Rmd

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• otherFunctions

  eliotmcintire

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

  

  Eliot McIntire

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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

  eliotmcintire

  committed
  f6aef16

• Re-build Biomass_core.Rmd

  actions-user

  committed
  1225cfa

Commits on Jan 22, 2024

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

  eliotmcintire

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  1bc62f3

• Re-build Biomass_core.Rmd

  actions-user

  committed
  df983f2

Commits on Apr 19, 2024

• use inputPath instead of dataPath per latest best practices

  achubaty

  committed
  7c84846

• Re-build Biomass_core.Rmd

  actions-user

  committed
  3eaae18

Commits on May 7, 2024

• minor metadata formatting

  achubaty

  committed
  aedae8e

• Re-build Biomass_core.Rmd

  actions-user

  committed
  c8279f6

Commits on May 10, 2024

• [v1.4.0] use latest LandR with assertSpeciesTable

  Show description for 999c303
  achubaty

  committed
  999c303

• Re-build Biomass_core.Rmd

  actions-user

  committed
  4fb5969

Commits on May 17, 2024

• minor metadata formatting

  achubaty

  committed
  1005b40

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

  achubaty

  committed
  c3996de

• Re-build Biomass_core.Rmd

  actions-user

  committed
  a9ba455

Commits on May 29, 2024

• switch to stable versions of pkgs where possible

  CeresBarros

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  949dddf

• bump v1.4.1

  CeresBarros

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  1e90fc4

Commits on May 30, 2024

• bump reproducible

  CeresBarros

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• minor

  CeresBarros

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Commits on May 31, 2024

• bump SpaDES.core & rm figurePath()

  CeresBarros

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• Re-build Biomass_core.Rmd

  actions-user

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  ab6ffde

• speciesLayers may not yet exist during .inputObjects

  CeresBarros

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  3e5eac2

• one .compareRas needs stopOnError = FALSE

  CeresBarros

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  c7d5bc3

Commits on Jun 4, 2024

• bump v1.4.1.9001

  CeresBarros

  committed
  93803e3

Commits on Jun 5, 2024

• LandR@development -> LandR

  CeresBarros

  committed
  9d11977

• bump v1.4.1.9002

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• minor

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  0678d84

• assert spp vectors/sppEquiv/species earlier

  CeresBarros

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  2028f1c

• filter sppEquiv/sppColorV/sppNameVect to simulated species

  Show description for f9da844
  CeresBarros

  committed
  f9da844

• minor

  CeresBarros

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  4b9ee2a

• use mo$sppEquiv throughout

  CeresBarros

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  5adee0d

• bump v1.4.1.9003

  CeresBarros

  committed
  85a3716

• Re-build Biomass_core.Rmd

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  committed
  f821e2c

Commits on Jun 6, 2024

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

  CeresBarros

  committed
  e956b81

• Update Biomass_core.R LandR@development >=1.1.3

  eliotmcintire

  authored
  ec7ed03

• Re-build Biomass_core.Rmd

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  committed
  fe50711

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

  

  Eliot McIntire

  committed
  6f61feb

• Merge branch 'development' into bugfixes

  achubaty

  authored
  0325ab0

• Merge pull request #84 from CeresBarros/bugfixes

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  eliotmcintire

  authored
  ec1f66e

• Merge branch 'development' into LandRAssertionFix

  eliotmcintire

  authored
  29b1222

• Re-build Biomass_core.Rmd

  actions-user

  committed
  07c9664

• Merge pull request #85 from PredictiveEcology/LandRAssertionFix

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  eliotmcintire

  authored
  0c277e3

• Re-build Biomass_core.Rmd

  actions-user

  committed
  2ad1d2d

• allow mixedType = 0 with latest LandR

  achubaty

  committed
  0e9e68e

• Re-build Biomass_core.Rmd

  actions-user

  committed
  d3b3bb2

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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  CeresBarros

  committed
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