observed.coexp.sumstat: Observed codemographic hippersummary statistics calculation
In gehara/PipeMaster: Building and Simulating Coalescent models.
View source: R/observed.coexp.sumstat.R
observed.coexp.sumstat R Documentation
Observed codemographic hippersummary statistics calculation
Description
This function calculates the hippersummary statistics for a collection of fasta files present in a particular folder. It is instended to be used for codemographic inference in conjunction with simulations generated by sim.coexp or sim.coexp2. Here the same stats are calculated.
Usage
observed.coexp.sumstat(path.to.fasta)
Arguments
path.to.fasta
The path to the directory containing the fasta files for all species/populations.
Value
A list of hippersummary statistics.
Author(s)
Marcelo Gehara
References
Gehara M., Garda A.A., Werneck F.P., Oliveira E.F., da Fonseca E.M., Camurugi F., Magalhães F. de M., Lanna F.M., Sites J.W., Marques R., Silveira-Filho R., São Pedro V.A., Colli G.R., Costa G.C., & Burbrink F.T. (2017) Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil. Molecular Ecology, 26, 4756–4771.
Chan Y.L., Schanzenbach D., & Hickerson M.J. (2014) Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation. Molecular Biology and Evolution, 31, 2501–2515.
gehara/PipeMaster documentation built on April 19, 2024, 8:14 a.m.
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View source: R/observed.coexp.sumstat.R
| observed.coexp.sumstat | R Documentation |
Observed codemographic hippersummary statistics calculation
Description
This function calculates the hippersummary statistics for a collection of fasta files present in a particular folder. It is instended to be used for codemographic inference in conjunction with simulations generated by sim.coexp or sim.coexp2. Here the same stats are calculated.
Usage
observed.coexp.sumstat(path.to.fasta)
Arguments
path.to.fasta |
The path to the directory containing the fasta files for all species/populations. |
Value
A list of hippersummary statistics.
Author(s)
Marcelo Gehara
References
Gehara M., Garda A.A., Werneck F.P., Oliveira E.F., da Fonseca E.M., Camurugi F., Magalhães F. de M., Lanna F.M., Sites J.W., Marques R., Silveira-Filho R., São Pedro V.A., Colli G.R., Costa G.C., & Burbrink F.T. (2017) Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil. Molecular Ecology, 26, 4756–4771.
Chan Y.L., Schanzenbach D., & Hickerson M.J. (2014) Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation. Molecular Biology and Evolution, 31, 2501–2515.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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