R: Tools for Working with Connectivity Data

# Tools for Working with Connectivity Data

## Documentation for package ‘ConnMatTools’ version 0.3.5

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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