Package: CBMutils 0.0.7.9015

Alex M Chubaty

CBMutils: Utilities for modelling carbon based on CBM-CFS3

Implementation of several components of the Carbon Budget Model of the Canadian Forest Service (v3).

Authors:Céline Boisvenue [aut], Alex M Chubaty [aut, cre], Ian Eddy [ctb], Eliot McIntire [aut]

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CBMutils.pdf |CBMutils.html✨
CBMutils/json (API)

# Install 'CBMutils' in R:
install.packages('CBMutils', repos = c('https://predictiveecology.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/predictiveecology/cbmutils/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

cpp

4.00 score 3 scripts 64 exports 77 dependencies

Last updated 17 hours agofrom:e0885ffc7d (on development). Checks:1 OK, 10 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 03 2025
R-4.5-win-x86_64NOTEFeb 03 2025
R-4.5-mac-x86_64NOTEFeb 03 2025
R-4.5-mac-aarch64NOTEFeb 03 2025
R-4.5-linux-x86_64NOTEFeb 03 2025
R-4.4-win-x86_64NOTEFeb 03 2025
R-4.4-mac-x86_64NOTEFeb 03 2025
R-4.4-mac-aarch64NOTEFeb 03 2025
R-4.3-win-x86_64NOTEFeb 03 2025
R-4.3-mac-x86_64NOTEFeb 03 2025
R-4.3-mac-aarch64NOTEFeb 03 2025

Exports:.pooldef.pooldefids.poolids.poolnamesb_mbarPlotbiomassTurnoverMatrixbiomPropcalcCcalcTurnoverRatescarbonOutPlotcheckPropcheckTransactionscomputeBioTurnoverMatricescomputeDomDecayMatricescomputeDomTurnoverMatricesComputeGrowthAndDeclineMatricesComputeGrowthAndDeclineMatrices2ComputeGrowthIncrementsComputeOvermatureDeclinecomputeSlowDecayMatricescomputeSlowMixingMatrixconvertM3biomcumPoolsCreatecumPoolsSmoothdecayRatedomDecayMatrixdomDecayMatrixItemdomTurnOverMatrixgcidsCreategetDecayRatesgetIdentityCoordinateMatrixgetTablehashhistDistloadDisturbanceMatrixIdsm3ToBiomIncOnlyPlotsm3ToBiomPlotsm3ToVolCheckPlotsmatrixDTmatrixHashnmfacNPPNPPplotplotCarbonRastersprepInputsEcozonesprepInputsVRIprepInputsVRIagequeryreadSqlFileretrieveSpuRastersapfacseeDistsimDistslowDecayMatrixspatialPlotspatialRasterspatialUnitDecayRatesSpinupspuDistspuDistMatchStepPoolsStepPoolsRefws3Build

Dependencies:bitbit64blobcachemclassclassIntclicolorspacecpp11crayondata.tableDBIDEoptimRdigeste1071evaluatefansifarverfasterizefastmapfilelockfpComparefsggforceggplot2gluegtablehighrisobandjsonliteKernSmoothknitrlabelinglatticelifecyclelobstrmagrittrMASSMatrixmemoisemgcvmunsellnlmepillarpkgconfigplogrpolyclipprettyunitsproxyquickPlotR6rasterRColorBrewerRcppRcppArmadilloRcppEigenreproduciblerlangrobustbaseRSQLites2scalessfspsystemfontsterratibbletidyselecttweenrunitsutf8vctrsviridisLitewithrwkxfunyaml

i-overview

Rendered fromi-overview.Rmdusingknitr::rmarkdownon Feb 03 2025.

Last update: 2020-10-02
Started: 2020-07-29

Readme and manuals

Help Manual

Help pageTopics
'CBMutils'CBMutils-package CBMutils
Disturbance matrix pool names and ids.pooldef .pooldefids .poolids .poolnames
Calculate stemwood biomass (per ha) of live merchantable treesb_m
'barPlot'barPlot
Biomass turnover matrixbiomassTurnoverMatrix
Proportions of total tree biomass in stemwood, bark, branches, and foliagebiomProp
Sum carbon for 'totalCarbon' or 'aboveGround' or 'belowGround'calcC
Calculate turnover ratescalcTurnoverRates
'carbonOutPlot'carbonOutPlot
check that the proportions add up to 1checkProp
Verify and check transactionscheckTransactions
Compute Turnover MatricescomputeBioTurnoverMatrices
Compute all dom decay matrices in coordinate matrix formatcomputeDomDecayMatrices
Compute DOM turnover matricescomputeDomTurnoverMatrices
Compute growth and decline matricesComputeGrowthAndDeclineMatrices
Compute growth and decline matricesComputeGrowthAndDeclineMatrices2
Compute growth coordinate matricesComputeGrowthCoordinateMatrices
Compute growth incrementsComputeGrowthIncrements
Compute overmature declineComputeOvermatureDecline
Compute overmature decline coordinate matricesComputeOverMatureDeclineCoordinateMatrices
Compute slow decay matricescomputeSlowDecayMatrices
Compute slow mixing matrixcomputeSlowMixingMatrix
Calculate biomass from gross merchantable volumeconvertM3biom
Create 'cumPools' data.tablecumPoolsCreate
Smooth the 'cumPools' 'data.table'cumPoolsSmooth
Dataset classdataset-class
Calculate the decay rate based on mean annual temperature and other parametersdecayRate
Compute a single dom decay matrix based on the specified table of decay ratesdomDecayMatrix
Calculate a portion of the DOM decay matrixdomDecayMatrixItem
DOM turnover matrixdomTurnOverMatrix
Standardized way to create gcidsgcidsCreate
Get decay ratesgetDecayRates
getIdentityCoordinateMatrixgetIdentityCoordinateMatrix
getTablegetTable
Hashing functionshash matrixHash
CBM-CFS3 Historical DisturbanceshistDist
Load disturbance matrix IDsloadDisturbanceMatrixIds
'm3ToBiomIncOnlyPlots'm3ToBiomIncOnlyPlots
Plot all columns that are not id_colm3ToBiomPlots
m3ToVolCheckPlotsm3ToVolCheckPlots
Make a 'data.table' out of the carbon transfer matricesmatrixDT
Expansion factor for non-merchantable live tree biomassnmfac
Calculate post-simulation net primary productivityNPP
'NPPplot'NPPplot
Plotting poolsplotCarbonRasters
'prepInputsEcozones'prepInputsEcozones
'prepInputsVRI'prepInputsVRI
Read in the BC VRI, with growth curve information (from 'ws3'), and creates a raster stack of the ageprepInputsVRIage
queryquery
readSqlFilereadSqlFile
Produce a raster with 'spUnits'retrieveSpuRaster
Expansion factor for sapling-sized treessapfac
See disturbancesseeDist
get the descriptive name and proportions transferred for disturbances in a simulation requires a simulation list post simulations (from spades()) and returns a list of data.frames. Each data had the descriptive name of a disturbance used in the simulations, the disturbance matrix identification number from cbm_defaults, the pool from which carbon is taken (source pools) in this specific disturbance, the pools into which carbon goes, and the proportion in which the carbon-transfers are completed.simDist
Slow decay matrixslowDecayMatrix
'spatialPlot'spatialPlot
PlotspatialRaster
Spatial unit decay ratesspatialUnitDecayRates
SpinupSpinup
CBM-CFS3 Spatial Unit DisturbancesspuDist
CBM-CFS3 Disturbances MatchspuDistMatch
Step through pools, computing carbon transfersStepPools
Step through pools, computing carbon transfersStepPoolsRef
'ws3Build'ws3Build