Package: ConnMatTools 0.3.5

ConnMatTools: Tools for Working with Connectivity Data

Collects several different methods for analyzing and working with connectivity data in R. Though primarily oriented towards marine larval dispersal, many of the methods are general and useful for terrestrial systems as well.

Authors:David M. Kaplan <[email protected]> [cre,aut], Marco Andrello <[email protected]> [ctb]

ConnMatTools_0.3.5.tar.gz
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ConnMatTools.pdf |ConnMatTools.html✨
ConnMatTools/json (API)
NEWS

# Install 'ConnMatTools' in R:
install.packages('ConnMatTools', repos = c('https://dmkaplan2000.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/dmkaplan2000/connmattools/issues

Datasets:
  • chile.loco - Connectivity matrix for loco (Concholepas concholepas) from Chile
  • damselfish.lods - Sample LOD score data for simulated and real parent-child pairs

On CRAN:

3.48 score 60 scripts 515 downloads 44 exports 0 dependencies

Last updated 5 years agofrom:8c6627ad97. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-winOKNov 05 2024
R-4.5-linuxOKNov 05 2024
R-4.4-winOKNov 05 2024
R-4.4-macOKNov 05 2024
R-4.3-winOKNov 05 2024
R-4.3-macOKNov 05 2024

Exports:betasVectorDefaultBevertonHoltd.mix.dists.funcd.rel.conn.beta.priord.rel.conn.dists.funcd.rel.conn.finite.settlementd.rel.conn.multinomial.unnormd.rel.conn.multipled.rel.conn.unif.priorDispersalPerRecruitModelDPRHomerangeGravitydual.mark.transmissioneigsgammaParamsConverthockeySticklaplacianConnMatlocalRetentionmergeSubpopsoptim.rel.conn.distsoptimalSplitConnMatp.rel.conn.beta.priorp.rel.conn.dists.funcp.rel.conn.finite.settlementp.rel.conn.multiplep.rel.conn.unif.priorprob.markedprotectedAreaSelectionq.rel.conn.beta.priorq.rel.conn.beta.prior.funcq.rel.conn.dists.funcq.rel.conn.finite.settlementq.rel.conn.multipleq.rel.conn.multiple.funcq.rel.conn.unif.priorqualitySubpopsr.marked.egg.fractionrecSplitConnMatreducedConnMatrelativeLocalRetentionselfRecruitmentsettlerRecruitSlopeCorrectionsplitConnMatstepfun.histsubpopsVectorToList

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Compute vector of beta valuesbetasVectorDefault
Beverton-Holt settler-recruit relationshipBevertonHolt
Connectivity matrix for loco (Concholepas concholepas) from Chilechile.loco
Tools for working with connectivity matricesConnMatTools
Returns probability density function (PDF) for a mix of marked and unmarked individualsd.mix.dists.func
Estimate the probability distribution of relative connectivity values assuming a Beta-distributed priord.rel.conn.beta.prior p.rel.conn.beta.prior q.rel.conn.beta.prior q.rel.conn.beta.prior.func
Functions for estimating the probability distribution for relative connectivity given a pair of distributions for scores for marked and unmarked individualsd.rel.conn.dists.func p.rel.conn.dists.func q.rel.conn.dists.func
Estimate the probability distribution for the number of settlers originating at a site given a sample from a finite settler poold.rel.conn.finite.settlement p.rel.conn.finite.settlement q.rel.conn.finite.settlement
Calculates unnormalized probability density for relative connectivity values from multiple distinct sitesd.rel.conn.multinomial.unnorm
Functions for estimating the probability distribution of relative connectivity values as a weighted sum over possible input parametersd.rel.conn.multiple p.rel.conn.multiple q.rel.conn.multiple q.rel.conn.multiple.func
Estimate the probability distribution of relative connectivity values assuming a uniform prior distributiond.rel.conn.unif.prior p.rel.conn.unif.prior q.rel.conn.unif.prior
Sample LOD score data for simulated and real parent-child pairsdamselfish.lods
Population dynamics model based on lifetime-egg-productionDispersalPerRecruitModel
Extended DPR population dynamics model to include homerange movementDPRHomerangeGravity
Fraction of eggs marked for male and female mark transmissiondual.mark.transmission
Compute some eigenvalues of a matrixeigs
Gamma distribution shape and scale parameters from mean and standard deviation, or vice-versagammaParamsConvert
Hockey-stick settler-recruit relationshiphockeyStick
Uniform Laplacian connectivity matrixlaplacianConnMat
Local retention of a connectivity matrixlocalRetention
Merge subpopulationsmergeSubpops
Maximum-likelihood estimate for relative connectivity given two distributions for scores for marked and unmarked individualsoptim.rel.conn.dists
Iteratively, optimally split a connectivity matrixoptimalSplitConnMat
Returns probability a set of observations correspond to marked individualsprob.marked
Function to select optimal network of protected areas based on connectivityprotectedAreaSelection
Quality measure for subpopulation divisionqualitySubpops
Estimates of fraction of eggs marked accounting for variability in reproductive outputr.marked.egg.fraction
Recursively subdivides a set of subpoplationsrecSplitConnMat
Reduced connectivity matrix according to a set of subpopulationsreducedConnMat
Relative local retention of a connectivity matrixrelativeLocalRetention
Self recruitment of a connectivity matrixselfRecruitment
Correction for slope of settler-recruit relationshipsettlerRecruitSlopeCorrection
Split connectivity matrix into subpopulationssplitConnMat
Create a probability density step function from a histogram objectstepfun.hist
Convert subpopulation vector to a list of indicessubpopsVectorToList