Tools for Working with Connectivity Data

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Documentation for package ‘ConnMatTools’ version 0.3.5

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betasVectorDefault Compute vector of beta values
BevertonHolt Beverton-Holt settler-recruit relationship
chile.loco Connectivity matrix for loco (Concholepas concholepas) from Chile
ConnMatTools Tools for working with connectivity matrices
d.mix.dists.func Returns probability density function (PDF) for a mix of marked and unmarked individuals
d.rel.conn.beta.prior Estimate the probability distribution of relative connectivity values assuming a Beta-distributed prior
d.rel.conn.dists.func Functions for estimating the probability distribution for relative connectivity given a pair of distributions for scores for marked and unmarked individuals
d.rel.conn.finite.settlement Estimate the probability distribution for the number of settlers originating at a site given a sample from a finite settler pool
d.rel.conn.multinomial.unnorm Calculates unnormalized probability density for relative connectivity values from multiple distinct sites
d.rel.conn.multiple Functions for estimating the probability distribution of relative connectivity values as a weighted sum over possible input parameters
d.rel.conn.unif.prior Estimate the probability distribution of relative connectivity values assuming a uniform prior distribution
damselfish.lods Sample LOD score data for simulated and real parent-child pairs
DispersalPerRecruitModel Population dynamics model based on lifetime-egg-production
DPRHomerangeGravity Extended DPR population dynamics model to include homerange movement
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 standard deviation, or vice-versa
hockeyStick Hockey-stick settler-recruit relationship
laplacianConnMat Uniform Laplacian connectivity matrix
localRetention Local retention of a connectivity matrix
mergeSubpops Merge subpopulations
optim.rel.conn.dists Maximum-likelihood estimate for relative connectivity given two distributions for scores for marked and unmarked individuals
optimalSplitConnMat Iteratively, optimally split a connectivity matrix
p.rel.conn.beta.prior Estimate the probability distribution of relative connectivity values assuming a Beta-distributed prior
p.rel.conn.dists.func Functions for estimating the probability distribution for relative connectivity given a pair of distributions for scores for marked and unmarked individuals
p.rel.conn.finite.settlement Estimate the probability distribution for the number of settlers originating at a site given a sample from a finite settler pool
p.rel.conn.multiple Functions for estimating the probability distribution of relative connectivity values as a weighted sum over possible input parameters
p.rel.conn.unif.prior Estimate the probability distribution of relative connectivity values assuming a uniform prior distribution
prob.marked Returns probability a set of observations correspond to marked individuals
protectedAreaSelection Function to select optimal network of protected areas based on connectivity
q.rel.conn.beta.prior Estimate the probability distribution of relative connectivity values assuming a Beta-distributed prior
q.rel.conn.beta.prior.func Estimate the probability distribution of relative connectivity values assuming a Beta-distributed prior
q.rel.conn.dists.func Functions for estimating the probability distribution for relative connectivity given a pair of distributions for scores for marked and unmarked individuals
q.rel.conn.finite.settlement Estimate the probability distribution for the number of settlers originating at a site given a sample from a finite settler pool
q.rel.conn.multiple Functions for estimating the probability distribution of relative connectivity values as a weighted sum over possible input parameters
q.rel.conn.multiple.func Functions for estimating the probability distribution of relative connectivity values as a weighted sum over possible input parameters
q.rel.conn.unif.prior Estimate the probability distribution of relative connectivity values assuming a uniform prior distribution
qualitySubpops Quality measure for subpopulation division
r.marked.egg.fraction Estimates of fraction of eggs marked accounting for variability in reproductive output
recSplitConnMat Recursively subdivides a set of subpoplations
reducedConnMat Reduced connectivity matrix according to a set of subpopulations
relativeLocalRetention Relative local retention of a connectivity matrix
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 object
subpopsVectorToList Convert subpopulation vector to a list of indices