ConnMatTools: Tools for Working with Connectivity Data

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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.

Author
David M. Kaplan <dmkaplan2000@gmail.com> [cre,aut], Marco Andrello <marco.andrello@gmail.com> [ctb]
Date of publication
2016-11-02 17:52:03
Maintainer
David M. Kaplan <dmkaplan2000@gmail.com>
License
GPL (>= 2)
Version
0.3.3
URLs

View on CRAN

Man pages

betasVectorDefault
Compute vector of beta values
BevertonHolt
Beverton-Holt settler-recruit relationship
chile.loco
Connectivity matrix for loco (Concholepas concholepas) from...
ConnMatTools
Tools for working with connectivity matrices
damselfish.lods
Sample LOD score data for simulated and real parent-child...
DispersalPerRecruitModel
Population dynamics model based on lifetime-egg-production
d.mix.dists.func
Returns probability density function (PDF) for a mix of...
DPRHomerangeGravity
Extended DPR population dynamics model to include homerange...
d.rel.conn.beta.prior
Estimate the probability distribution of relative...
d.rel.conn.dists.func
Functions for estimating the probability distribution for...
d.rel.conn.finite.settlement
Estimate the probability distribution for the number of...
d.rel.conn.multinomial.unnorm
Calculates unnormalized probability density for relative...
d.rel.conn.multiple
Functions for estimating the probability distribution of...
d.rel.conn.unif.prior
Estimate the probability distribution of relative...
dual.mark.transmission
Fraction of eggs marked for male and female mark transmission
eigs
Compute some eigenvalues of a matrix
gammaParamsConvert
Gamma distribution shape and scale parameters from mean and...
hockeyStick
Hockey-stick settler-recruit relationship
laplacianConnMat
Uniform Laplacian connectivity matrix
localRetention
Local retention of a connectivity matrix
mergeSubpops
Merge subpopulations
optimalSplitConnMat
Iteratively, optimally split a connectivity matrix
optim.rel.conn.dists
Maximum-likelihood estimate for relative connectivity given...
prob.marked
Returns probability a set of observations correspond to...
protectedAreaSelection
Function to select optimal network of protected areas based...
qualitySubpops
Quality measure for subpopulation division
recSplitConnMat
Recursively subdivides a set of subpoplations
reducedConnMat
Reduced connectivity matrix according to a set of...
relativeLocalRetention
Relative local retention of a connectivity matrix
r.marked.egg.fraction
Estimates of fraction of eggs marked accounting for...
selfRecruitment
Self recruitment of a connectivity matrix
settlerRecruitSlopeCorrection
Correction for slope of settler-recruit relationship
splitConnMat
Split connectivity matrix into subpopulations
stepfun.hist
Create a probability density step function from a histogram...
subpopsVectorToList
Convert subpopulation vector to a list of indices

Files in this package

ConnMatTools
ConnMatTools/inst
ConnMatTools/inst/CITATION
ConnMatTools/tests
ConnMatTools/tests/test.laplacianConnMat.R
ConnMatTools/tests/test.optimalSplitConnMat.R
ConnMatTools/tests/test.connectivity_estimation.multinomial.R
ConnMatTools/tests/test.connectivity_estimation.multiple.R
ConnMatTools/tests/test.connectivity_estimation.beta.prior.R
ConnMatTools/tests/test.marked.egg.fraction.R
ConnMatTools/tests/test.dpr_model.R
ConnMatTools/tests/test.connectivity_estimation.R
ConnMatTools/tests/test.retentionStats.R
ConnMatTools/tests/test.connectivity_estimation.distributions.R
ConnMatTools/NAMESPACE
ConnMatTools/NEWS
ConnMatTools/data
ConnMatTools/data/chile.loco.RData
ConnMatTools/data/damselfish.lods.RData
ConnMatTools/R
ConnMatTools/R/connectivity_estimation.multinomial.R
ConnMatTools/R/connectivity_estimation.distributions.R
ConnMatTools/R/connectivity_estimation.multiple.R
ConnMatTools/R/utils.R
ConnMatTools/R/connectivity_estimation.R
ConnMatTools/R/Jacobi_EPT_reserve_selection.R
ConnMatTools/R/connectivity_estimation.finite_settlement.R
ConnMatTools/R/eigs.R
ConnMatTools/R/dpr_model.R
ConnMatTools/R/estimating_marked_egg_fraction.R
ConnMatTools/R/retentionStats.R
ConnMatTools/R/ConnMatTools.R
ConnMatTools/R/jacobi_etal_2012.R
ConnMatTools/R/datasets.R
ConnMatTools/README.md
ConnMatTools/MD5
ConnMatTools/DESCRIPTION
ConnMatTools/man
ConnMatTools/man/dual.mark.transmission.Rd
ConnMatTools/man/BevertonHolt.Rd
ConnMatTools/man/damselfish.lods.Rd
ConnMatTools/man/recSplitConnMat.Rd
ConnMatTools/man/protectedAreaSelection.Rd
ConnMatTools/man/stepfun.hist.Rd
ConnMatTools/man/DPRHomerangeGravity.Rd
ConnMatTools/man/selfRecruitment.Rd
ConnMatTools/man/chile.loco.Rd
ConnMatTools/man/relativeLocalRetention.Rd
ConnMatTools/man/settlerRecruitSlopeCorrection.Rd
ConnMatTools/man/optim.rel.conn.dists.Rd
ConnMatTools/man/prob.marked.Rd
ConnMatTools/man/qualitySubpops.Rd
ConnMatTools/man/ConnMatTools.Rd
ConnMatTools/man/laplacianConnMat.Rd
ConnMatTools/man/d.mix.dists.func.Rd
ConnMatTools/man/d.rel.conn.finite.settlement.Rd
ConnMatTools/man/r.marked.egg.fraction.Rd
ConnMatTools/man/mergeSubpops.Rd
ConnMatTools/man/DispersalPerRecruitModel.Rd
ConnMatTools/man/d.rel.conn.unif.prior.Rd
ConnMatTools/man/d.rel.conn.beta.prior.Rd
ConnMatTools/man/reducedConnMat.Rd
ConnMatTools/man/d.rel.conn.dists.func.Rd
ConnMatTools/man/localRetention.Rd
ConnMatTools/man/gammaParamsConvert.Rd
ConnMatTools/man/subpopsVectorToList.Rd
ConnMatTools/man/betasVectorDefault.Rd
ConnMatTools/man/splitConnMat.Rd
ConnMatTools/man/d.rel.conn.multinomial.unnorm.Rd
ConnMatTools/man/hockeyStick.Rd
ConnMatTools/man/optimalSplitConnMat.Rd
ConnMatTools/man/eigs.Rd
ConnMatTools/man/d.rel.conn.multiple.Rd