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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,112 +1,111 @@ | ||
| Package: dartR | ||
| Type: Package | ||
| Title: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by | ||
| Genome-Wide Restriction Fragment Analysis | ||
| Version: 2.9.7 | ||
| Date: 2023-06-07 | ||
| Authors@R: c( | ||
| person("Bernd", "Gruber", email="bernd.gruber@canberra.edu.au", role=c("aut","cre")), | ||
| person("Arthur", "Georges", email="georges@aerg.edu.au", role="aut"), | ||
| person("Jose L.", "Mijangos", email="Luis.MijangosAraujo@canberra.edu.au", role="aut"), | ||
| person("Carlo", "Pacioni",email="carlo.pacioni@delwp.vic.gov.au",role="aut"), | ||
| person("Peter J.", "Unmack", email="peter.mail2@unmack.net", role="ctb"), | ||
| person("Oliver", "Berry", email="oliver.berry@csiro.au", role="ctb" ), | ||
| person("Lindsay V.", "Clark", email="lvclark@illinois.edu", role="ctb"), | ||
| person("Floriaan", "Devloo-Delva",email="Floriaan.Devloo-Delva@csiro.au", role="ctb"), | ||
| person("Eric","Archer", email="eric.archer@noaa.gov", role="ctb") | ||
| ) | ||
| Description: Functions are provided that facilitate the import and analysis of | ||
| 'SNP' (single nucleotide polymorphism) and 'silicodart' (presence/absence) data. | ||
| The main focus is on data generated by 'DarT' (Diversity Arrays Technology), | ||
| however, data from other sequencing platforms can be used once 'SNP' or related | ||
| fragment presence/absence data from any source is imported. Genetic datasets | ||
| are stored in a derived 'genlight' format (package 'adegenet'), that allows for | ||
| a very compact storage of data and metadata. Functions are available for | ||
| importing and exporting of 'SNP' and 'silicodart' data, for reporting on and | ||
| filtering on various criteria (e.g. 'CallRate', heterozygosity, reproducibility, | ||
| maximum allele frequency). Additional functions are available for visualization | ||
| (e.g. Principle Coordinate Analysis) and creating a spatial representation | ||
| using maps. 'dartR' supports also the analysis of 3rd party software package | ||
| such as 'newhybrid', 'structure', 'NeEstimator' and 'blast'. Since version | ||
| 2.0.3 we also implemented simulation functions, that allow to forward simulate | ||
| 'SNP' dynamics under different population and evolutionary dynamics. | ||
| Comprehensive tutorials and support can be found at our 'github' repository: | ||
| github.com/green-striped-gecko/dartR/. If you want to cite 'dartR', you find | ||
| the information by typing citation('dartR') in the console. | ||
| VignetteBuilder: knitr | ||
| Encoding: UTF-8 | ||
| Depends: R (>= 3.5), adegenet (>= 2.0.0), ggplot2, dplyr, dartR.data | ||
| biocViews: | ||
| Imports: ape,crayon,data.table,fields,foreach,gridExtra,MASS,methods,patchwork,plyr,PopGenReport,raster,reshape2,shiny,SNPRelate,sp (>= 1.6.1),StAMPP,stats,stringr,tidyr,utils,vegan | ||
| Suggests: | ||
| boot, | ||
| devtools, | ||
| directlabels, | ||
| dismo, | ||
| doParallel, | ||
| expm, | ||
| gdistance, | ||
| ggtern, | ||
| gganimate, | ||
| ggrepel, | ||
| grid, | ||
| gtable, | ||
| ggthemes, | ||
| gplots, | ||
| HardyWeinberg, | ||
| hierfstat, | ||
| igraph, | ||
| iterpc, | ||
| knitr, | ||
| label.switching, | ||
| lattice, | ||
| leaflet, | ||
| leaflet.minicharts, | ||
| markdown, | ||
| mmod, | ||
| networkD3, | ||
| parallel, | ||
| pegas, | ||
| pheatmap, | ||
| plotly, | ||
| poppr, | ||
| proxy, | ||
| purrr, | ||
| qvalue, | ||
| RColorBrewer, | ||
| Rcpp, | ||
| rgl, | ||
| rmarkdown, | ||
| rrBLUP, | ||
| scales, | ||
| seqinr, | ||
| shinyBS, | ||
| shinyjs, | ||
| shinythemes, | ||
| shinyWidgets, | ||
| SIBER, | ||
| snpStats, | ||
| stringi, | ||
| terra, | ||
| tibble, | ||
| vcfR, | ||
| zoo, | ||
| viridis, | ||
| testthat (>= 3.0.0) | ||
| License: GPL (>= 3) | ||
| LazyData: true | ||
| RoxygenNote: 7.2.3 | ||
| NeedsCompilation: no | ||
| Packaged: 2023-06-02 23:28:46 UTC; Bernd Gruber | ||
| Author: Bernd Gruber [aut, cre], | ||
| Arthur Georges [aut], | ||
| Jose L. Mijangos [aut], | ||
| Carlo Pacioni [aut], | ||
| Peter J. Unmack [ctb], | ||
| Oliver Berry [ctb], | ||
| Lindsay V. Clark [ctb], | ||
| Floriaan Devloo-Delva [ctb], | ||
| Eric Archer [ctb] | ||
| Config/testthat/edition: 3 | ||
| URL: https://green-striped-gecko.github.io/dartR/ | ||
| BugReports: https://groups.google.com/g/dartr?pli=1 | ||
| Package: dartR | ||
| Type: Package | ||
| Title: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by | ||
| Genome-Wide Restriction Fragment Analysis | ||
| Version: 2.9.7 | ||
| Date: 2023-06-07 | ||
| Authors@R: c( | ||
| person("Bernd", "Gruber", email="bernd.gruber@canberra.edu.au", role=c("aut","cre")), | ||
| person("Arthur", "Georges", email="georges@aerg.edu.au", role="aut"), | ||
| person("Jose L.", "Mijangos", email="Luis.MijangosAraujo@canberra.edu.au", role="aut"), | ||
| person("Carlo", "Pacioni",email="carlo.pacioni@delwp.vic.gov.au",role="aut"), | ||
| person("Peter J.", "Unmack", email="peter.mail2@unmack.net", role="ctb"), | ||
| person("Oliver", "Berry", email="oliver.berry@csiro.au", role="ctb" ), | ||
| person("Lindsay V.", "Clark", email="lvclark@illinois.edu", role="ctb"), | ||
| person("Floriaan", "Devloo-Delva",email="Floriaan.Devloo-Delva@csiro.au", role="ctb"), | ||
| person("Eric","Archer", email="eric.archer@noaa.gov", role="ctb") | ||
| ) | ||
| Description: Functions are provided that facilitate the import and analysis of | ||
| 'SNP' (single nucleotide polymorphism) and 'silicodart' (presence/absence) data. | ||
| The main focus is on data generated by 'DarT' (Diversity Arrays Technology), | ||
| however, data from other sequencing platforms can be used once 'SNP' or related | ||
| fragment presence/absence data from any source is imported. Genetic datasets | ||
| are stored in a derived 'genlight' format (package 'adegenet'), that allows for | ||
| a very compact storage of data and metadata. Functions are available for | ||
| importing and exporting of 'SNP' and 'silicodart' data, for reporting on and | ||
| filtering on various criteria (e.g. 'CallRate', heterozygosity, reproducibility, | ||
| maximum allele frequency). Additional functions are available for visualization | ||
| (e.g. Principle Coordinate Analysis) and creating a spatial representation | ||
| using maps. 'dartR' supports also the analysis of 3rd party software package | ||
| such as 'newhybrid', 'structure', 'NeEstimator' and 'blast'. Since version | ||
| 2.0.3 we also implemented simulation functions, that allow to forward simulate | ||
| 'SNP' dynamics under different population and evolutionary dynamics. | ||
| Comprehensive tutorials and support can be found at our 'github' repository: | ||
| github.com/green-striped-gecko/dartR/. If you want to cite 'dartR', you find | ||
| the information by typing citation('dartR') in the console. | ||
| VignetteBuilder: knitr | ||
| Encoding: UTF-8 | ||
| Depends: R (>= 3.5), adegenet (>= 2.0.0), ggplot2, dplyr, dartR.data | ||
| biocViews: | ||
| Imports: ape,crayon,data.table,fields,foreach,gridExtra,MASS,methods,patchwork,plyr,PopGenReport,raster,reshape2,shiny,SNPRelate,sp (>= 1.6.1),StAMPP,stats,stringr,tidyr,utils,vegan | ||
| Suggests: | ||
| boot, | ||
| devtools, | ||
| directlabels, | ||
| dismo, | ||
| doParallel, | ||
| expm, | ||
| gdistance, | ||
| ggtern, | ||
| gganimate, | ||
| ggrepel, | ||
| grid, | ||
| gtable, | ||
| ggthemes, | ||
| gplots, | ||
| HardyWeinberg, | ||
| hierfstat, | ||
| igraph, | ||
| iterpc, | ||
| knitr, | ||
| label.switching, | ||
| lattice, | ||
| leaflet, | ||
| leaflet.minicharts, | ||
| markdown, | ||
| mmod, | ||
| networkD3, | ||
| parallel, | ||
| pegas, | ||
| pheatmap, | ||
| plotly, | ||
| poppr, | ||
| proxy, | ||
| purrr, | ||
| qvalue, | ||
| RColorBrewer, | ||
| Rcpp, | ||
| rgl, | ||
| rmarkdown, | ||
| rrBLUP, | ||
| scales, | ||
| seqinr, | ||
| shinyBS, | ||
| shinyjs, | ||
| shinythemes, | ||
| shinyWidgets, | ||
| SIBER, | ||
| snpStats, | ||
| stringi, | ||
| terra, | ||
| tibble, | ||
| vcfR, | ||
| zoo, | ||
| viridis | ||
| License: GPL (>= 3) | ||
| LazyData: true | ||
| RoxygenNote: 7.2.3 | ||
| NeedsCompilation: no | ||
| Packaged: 2023-06-02 23:28:46 UTC; Bernd Gruber | ||
| Author: Bernd Gruber [aut, cre], | ||
| Arthur Georges [aut], | ||
| Jose L. Mijangos [aut], | ||
| Carlo Pacioni [aut], | ||
| Peter J. Unmack [ctb], | ||
| Oliver Berry [ctb], | ||
| Lindsay V. Clark [ctb], | ||
| Floriaan Devloo-Delva [ctb], | ||
| Eric Archer [ctb] | ||
| Config/testthat/edition: 3 | ||
| URL: https://green-striped-gecko.github.io/dartR/ | ||
| BugReports: https://groups.google.com/g/dartr?pli=1 |
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