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.

Install the latest version of this package by entering the following in R:
AuthorDavid M. Kaplan <> [cre,aut], Marco Andrello <> [ctb]
Date of publication2016-11-02 17:52:03
MaintainerDavid M. Kaplan <>
LicenseGPL (>= 2)

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


betasVectorDefault Man page
BevertonHolt Man page
chile.loco Man page
ConnMatTools Man page
ConnMatTools-package Man page
damselfish.lods Man page
DispersalPerRecruitModel Man page
d.mix.dists.func Man page
DPRHomerangeGravity Man page
d.rel.conn.beta.prior Man page
d.rel.conn.dists.func Man page
d.rel.conn.finite.settlement Man page
d.rel.conn.multinomial.unnorm Man page
d.rel.conn.multiple Man page
d.rel.conn.unif.prior Man page
dual.mark.transmission Man page
eigs Man page
gammaParamsConvert Man page
hockeyStick Man page
laplacianConnMat Man page
localRetention Man page
mergeSubpops Man page
optimalSplitConnMat Man page
optim.rel.conn.dists Man page
p.rel.conn.beta.prior Man page
p.rel.conn.dists.func Man page
p.rel.conn.finite.settlement Man page
p.rel.conn.multiple Man page
p.rel.conn.unif.prior Man page
prob.marked Man page
protectedAreaSelection Man page
q.rel.conn.beta.prior Man page
q.rel.conn.beta.prior.func Man page
q.rel.conn.dists.func Man page
q.rel.conn.finite.settlement Man page
q.rel.conn.multiple Man page
q.rel.conn.multiple.func Man page
q.rel.conn.unif.prior Man page
qualitySubpops Man page
recSplitConnMat Man page
reducedConnMat Man page
relativeLocalRetention Man page
r.marked.egg.fraction Man page
selfRecruitment Man page
settlerRecruitSlopeCorrection Man page
splitConnMat Man page
stepfun.hist Man page
subpopsVectorToList Man page


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

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