Package: conStruct 1.0.6
conStruct: Models Spatially Continuous and Discrete Population Genetic Structure
A method for modeling genetic data as a combination of discrete layers, within each of which relatedness may decay continuously with geographic distance. This package contains code for running analyses (which are implemented in the modeling language 'rstan') and visualizing and interpreting output. See the paper for more details on the model and its utility.
Authors:
conStruct_1.0.6.tar.gz
conStruct_1.0.6.zip(r-4.5)conStruct_1.0.6.zip(r-4.4)conStruct_1.0.6.zip(r-4.3)
conStruct_1.0.6.tgz(r-4.4-x86_64)conStruct_1.0.6.tgz(r-4.4-arm64)conStruct_1.0.6.tgz(r-4.3-x86_64)conStruct_1.0.6.tgz(r-4.3-arm64)
conStruct_1.0.6.tar.gz(r-4.5-noble)conStruct_1.0.6.tar.gz(r-4.4-noble)
conStruct.pdf |conStruct.html✨
conStruct/json (API)
NEWS
| # Install 'conStruct' in R: |
| install.packages('conStruct', repos = c('https://gbradburd.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gbradburd/construct/issues
- conStruct.data - Example dataset used in a 'conStruct' analysis
- data.block - Example 'data.block' generated by a 'conStruct' analysis
Last updated 11 months agofrom:a41049e475. Checks:OK: 2 NOTE: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 26 2024 |
| R-4.5-win-x86_64 | NOTE | Oct 26 2024 |
| R-4.5-linux-x86_64 | OK | Oct 26 2024 |
| R-4.4-win-x86_64 | NOTE | Oct 26 2024 |
| R-4.4-mac-x86_64 | NOTE | Oct 26 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 26 2024 |
| R-4.3-win-x86_64 | NOTE | Oct 26 2024 |
| R-4.3-mac-x86_64 | NOTE | Oct 26 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 26 2024 |
Exports:calculate.layer.contributioncompare.two.runsconStructmake.admix.pie.plotmake.all.the.plotsmake.structure.plotmatch.layers.x.runsstructure2conStructx.validation
Dependencies:abindbackportsBHcallrcarolinecheckmateclicodetoolscolorspacedescdistributionaldoParallelfansifarverforeachgenericsggplot2gluegridExtragtablegtoolsinlineisobanditeratorslabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsscalesStanHeaderstensorAtibbleutf8vctrsviridisLitewithr
How to format data for a conStruct analysis
Rendered fromformat-data.Rmdusingknitr::rmarkdownon Oct 26 2024.Last update: 2023-12-21
Started: 2018-08-15
How to compare conStruct model runs
Rendered frommodel-comparison.Rmdusingknitr::rmarkdownon Oct 26 2024.Last update: 2018-09-05
Started: 2018-08-21
How to run a conStruct analysis
Rendered fromrun-conStruct.Rmdusingknitr::rmarkdownon Oct 26 2024.Last update: 2018-09-05
Started: 2018-08-15
How to visualize the results of a conStruct analysis
Rendered fromvisualize-results.Rmdusingknitr::rmarkdownon Oct 26 2024.Last update: 2019-01-02
Started: 2018-09-04
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The 'conStruct' package. | conStruct-package |
| Calculate layer contribution | calculate.layer.contribution |
| Compare two conStruct runs | compare.two.runs |
| Run a conStruct analysis. | conStruct |
| Example dataset used in a 'conStruct' analysis | conStruct.data |
| Example 'data.block' generated by a 'conStruct' analysis | data.block |
| Make admixture pie plot | make.admix.pie.plot |
| Make output plots | make.all.the.plots |
| Make STRUCTURE output plot | make.structure.plot |
| Match layers up across independent conStruct runs | match.layers.x.runs |
| An S3 print method for class conStruct.results | print.conStruct.results |
| An S3 print method for class data.block | print.data.block |
| An S3 print method for class freq.data | print.freq.data |
| An S3 print method for class layer.params | print.layer.params |
| Convert a dataset from STRUCTURE to conStruct format | structure2conStruct |
| Run a conStruct cross-validation analysis | x.validation |
