Package: CBMutils 0.0.7.9011

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'))

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

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

3.78 score 3 scripts 63 exports 71 dependencies

Last updated 8 days agofrom:994e0e20c4 (on development). Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 14 2024
R-4.5-win-x86_64	WARNING	Nov 14 2024
R-4.5-linux-x86_64	WARNING	Nov 14 2024
R-4.4-win-x86_64	WARNING	Nov 14 2024
R-4.4-mac-x86_64	WARNING	Nov 14 2024
R-4.4-mac-aarch64	WARNING	Nov 14 2024
R-4.3-win-x86_64	WARNING	Nov 14 2024
R-4.3-mac-x86_64	WARNING	Nov 14 2024
R-4.3-mac-aarch64	WARNING	Nov 14 2024

Exports:.pooldef .pooldefids .poolids .poolnames b_m barPlot biomassTurnoverMatrix biomProp calcC calcTurnoverRates carbonOutPlot checkProp checkTransactions computeBioTurnoverMatrices computeDomDecayMatrices computeDomTurnoverMatrices ComputeGrowthAndDeclineMatrices ComputeGrowthAndDeclineMatrices2 ComputeGrowthIncrements ComputeOvermatureDecline computeSlowDecayMatrices computeSlowMixingMatrix convertM3biom cumPoolsCreate cumPoolsSmooth decayRate domDecayMatrix domDecayMatrixItem domTurnOverMatrix gcidsCreate getDecayRates getIdentityCoordinateMatrix getTable hash histDist loadDisturbanceMatrixIds m3ToBiomIncOnlyPlots m3ToBiomPlots m3ToVolCheckPlots matrixDT matrixHash nmfac NPP NPPplot plotCarbonRasters prepInputsEcozones prepInputsVRI prepInputsVRIage query readSqlFile retrieveSpuRaster sapfac seeDist simDist slowDecayMatrix spatialPlot spatialRaster spatialUnitDecayRates Spinup spuDist StepPools StepPoolsRef ws3Build

Dependencies:bit bit64 blob cachem class classInt cli colorspace cpp11 crayon data.table DBI DEoptimR digest e1071 fansi farver fasterize fastmap filelock fpCompare fs ggforce ggplot2 glue gtable isoband KernSmooth labeling lattice lifecycle lobstr magrittr MASS Matrix memoise mgcv munsell nlme pillar pkgconfig plogr polyclip prettyunits proxy quickPlot R6 raster RColorBrewer Rcpp RcppArmadillo RcppEigen reproducible rlang robustbase RSQLite s2 scales sf sp systemfonts terra tibble tidyselect tweenr units utf8 vctrs viridisLite withr wk

i-overview

Rendered fromi-overview.Rmdusingknitr::rmarkdownon Nov 14 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
'CBMutils'	CBMutils-package CBMutils
Disturbance matrix pool names and ids	.pooldef .pooldefids .poolids .poolnames
Calculate stemwood biomass (per ha) of live merchantable trees	b_m
'barPlot'	barPlot
Biomass turnover matrix	biomassTurnoverMatrix
Proportions of total tree biomass in stemwood, bark, branches, and foliage	biomProp
Sum carbon for 'totalCarbon' or 'aboveGround' or 'belowGround'	calcC
Calculate turnover rates	calcTurnoverRates
'carbonOutPlot'	carbonOutPlot
check that the proportions add up to 1	checkProp
Verify and check transactions	checkTransactions
Compute Turnover Matrices	computeBioTurnoverMatrices
Compute all dom decay matrices in coordinate matrix format	computeDomDecayMatrices
Compute DOM turnover matrices	computeDomTurnoverMatrices
Compute growth and decline matrices	ComputeGrowthAndDeclineMatrices
Compute growth and decline matrices	ComputeGrowthAndDeclineMatrices2
Compute growth coordinate matrices	ComputeGrowthCoordinateMatrices
Compute growth increments	ComputeGrowthIncrements
Compute overmature decline	ComputeOvermatureDecline
Compute overmature decline coordinate matrices	ComputeOverMatureDeclineCoordinateMatrices
Compute slow decay matrices	computeSlowDecayMatrices
Compute slow mixing matrix	computeSlowMixingMatrix
Calculate biomass from gross merchantable volume	convertM3biom
Create 'cumPools' data.table	cumPoolsCreate
Smooth the 'cumPools' 'data.table'	cumPoolsSmooth
Dataset class	dataset-class
Calculate the decay rate based on mean annual temperature and other parameters	decayRate
Compute a single dom decay matrix based on the specified table of decay rates	domDecayMatrix
Calculate a portion of the DOM decay matrix	domDecayMatrixItem
DOM turnover matrix	domTurnOverMatrix
Standardized way to create gcids	gcidsCreate
Get decay rates	getDecayRates
getIdentityCoordinateMatrix	getIdentityCoordinateMatrix
getTable	getTable
Hashing functions	hash matrixHash
Historical disturbances	histDist
Load disturbance matrix IDs	loadDisturbanceMatrixIds
'm3ToBiomIncOnlyPlots'	m3ToBiomIncOnlyPlots
Plot all columns that are not id_col	m3ToBiomPlots
m3ToVolCheckPlots	m3ToVolCheckPlots
Make a 'data.table' out of the carbon transfer matrices	matrixDT
Expansion factor for non-merchantable live tree biomass	nmfac
Calculate post-simulation net primary productivity	NPP
'NPPplot'	NPPplot
Plotting pools	plotCarbonRasters
'prepInputsEcozones'	prepInputsEcozones
'prepInputsVRI'	prepInputsVRI
Read in the BC VRI, with growth curve information (from 'ws3'), and creates a raster stack of the age	prepInputsVRIage
query	query
readSqlFile	readSqlFile
Produce a raster with 'spUnits'	retrieveSpuRaster
Expansion factor for sapling-sized trees	sapfac
See disturbances	seeDist
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 matrix	slowDecayMatrix
'spatialPlot'	spatialPlot
Plot	spatialRaster
Spatial unit decay rates	spatialUnitDecayRates
Spinup	Spinup
Identify the ID number (CBM-CFS3 legacy) possible in the current spatial unit	spuDist
Step through pools, computing carbon transfers	StepPools
Step through pools, computing carbon transfers	StepPoolsRef
'ws3Build'	ws3Build