| Title: | Auxiliary Data Package for Our Main Package 'dartR' |
| Version: | 1.0.8 |
| Date: | 2024-05-24 |
| Description: | Data package for 'dartR'. Provides data sets to run examples in 'dartR'. This was necessary due to the size limit imposed by 'CRAN'. The data in 'dartR.data' is needed to run the examples provided in the 'dartR' functions. All available data sets are either based on actual data (but reduced in size) and/or simulated data sets to allow the fast execution of examples and demonstration of the functions. |
| Depends: | R (≥ 3.5), adegenet (≥ 2.0.0) |
| Imports: | methods, utils, crayon |
| License: | GPL (≥ 3) |
| LazyData: | true |
| LazyDataCompression: | xz |
| Encoding: | UTF-8 |
| NeedsCompilation: | no |
| RoxygenNote: | 7.3.1 |
| URL: | https://github.com/green-striped-gecko/dartR.data |
| BugReports: | https://groups.google.com/g/dartr?pli=1 |
| Packaged: | 2024-05-29 10:51:05 UTC; bernd |
| Author: | Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Oliver Berry [ctb] |
| Maintainer: | Bernd Gruber <bernd.gruber@canberra.edu.au> |
| Repository: | CRAN |
| Date/Publication: | 2024-05-30 00:10:03 UTC |
Eastern yellow robin (EYR) DArT data in a genlight object
Description
Genetic data from EYR collected in VIC, Australia by researchers at Monash University. The data comes in the form of a genlight object ready to be used by dartR. The file contains data for 782 individuals from 4 populations and 1,000 binary SNPs. The dataset contains a mix of autosomal and sex-linked loci.
Usage
EYR
Format
genlight object
Author(s)
Custodian: Diana Robledo-Ruiz – Post to https://groups.google.com/d/forum/dartr
References
Robledo-Ruiz et al. (2023) Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex assignment. Mol. Ecol. Res. (doi:10.1111/1755-0998.13844)
Laedbeater's possum (LBP) DArT data in a genlight object
Description
Genetic data from LBP collected in VIC, Australia by researchers at Monash University. The data comes in the form of a genlight object ready to be used by dartR. The file contains data for 376 individuals from 2 populations and 1,000 binary SNPs. The dataset contains a mix of autosomal and sex-linked loci.
Usage
LBP
Format
genlight object
Author(s)
Custodian: Diana Robledo-Ruiz – Post to https://groups.google.com/d/forum/dartr
References
Robledo-Ruiz et al. (2023) Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex assignment. Mol. Ecol. Res. doi:10.1111/1755-0998.13844
Yellow-tufted honeyeater (YTH) DArT data in a genlight object
Description
Genetic data from YTH collected in VIC, Australia by researchers at Monash University. The data comes in the form of a genlight object ready to be used by dartR. The file contains data for 641 individuals from 8 populations and 1,000 binary SNPs. The dataset contains a mix of autosomal and sex-linked loci.
Usage
YTH
Format
genlight object
Author(s)
Custodian: Diana Robledo-Ruiz – Post to https://groups.google.com/d/forum/dartr
References
Robledo-Ruiz et al. (2023) Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex assignment. Mol. Ecol. Res. (doi:10.1111/1755-0998.13844)
A genlight object created via the read.dart functions
Description
This a test data set to test the validity of functions within dartR and is based on a DArT SNP data set of simulated bandicoots across Australia. It contains 96 individuals and 1000 SNPs.
Usage
bandicoot.gl
Format
genlight object
Author(s)
Bernd Gruber (bugs? Post to https://groups.google.com/d/forum/dartr
Example data set as text file to be imported into a genlight object
Description
Check ?read.genetable in pacakge PopGenReport for details on the format.
Format
csv
Author(s)
Bernd Gruber (bugs? Post to https://groups.google.com/d/forum/dartr
Examples
## Not run:
library(PopGenReport)
fp <- file.path(system.file( package="dartR.data"),"extdata/platy.csv")
read.csv(fp)
platy <- read.genetable(fp, ind=1, pop=2, lat=3, long=4, other.min=5, other.max=6,
oneColPerAll=FALSE, sep='/')
platy.gl <- gi2gl(platy, parallel=FALSE)
df.loc <- data.frame(RepAvg = runif(nLoc(platy.gl)), CallRate = 1)
platy.gl@other$loc.metrics <- df.loc
gl.report.reproducibility(platy.gl)
## End(Not run)
A genlight object created via the gl.read.dart function
Description
This is a test data set on platypus with 81 individuals, 3 populations and 1,000 binary SNPs.
Usage
platypus.gl
Format
genlight object
Author(s)
Luis Mijangos (bugs? Post to https://groups.google.com/d/forum/dartr
A simulated genlight object created to run a landscape genetic example
Description
This a test data set to run a landscape genetics example. It contains 10 populations of 30 individuals each and each individual has 300 loci. There are no covariates for individuals or loci.
Usage
possums.gl
Format
genlight object
Author(s)
Bernd Gruber (bugs? Post to https://groups.google.com/d/forum/dartr
A genlight object created via the gl.read.dart function
Description
This is a test data set on turtles. 250 individuals, 255 loci in >30 populations.
Usage
testset.gl
Format
genlight object
Author(s)
Custodian: Arthur Georges (bugs? Post to https://groups.google.com/d/forum/dartr
A genlight object created via the gl.read.silicodart function
Description
This is a test data set on turtles. 218 individuals, 255 loci in >30 populations.
Usage
testset.gs
Format
genlight object
Author(s)
Custodian: Arthur Georges (bugs? Post to https://groups.google.com/d/forum/dartr
Testfile in DArT format (as provided by DArT)
Description
This test data set is provided to show a typical DArT file format. Can be used to create a genlight object using the read.dart function.
Format
csv
Author(s)
Custodian: Arthur Georges (bugs? Post to https://groups.google.com/d/forum/dartr
Metadata file. Can be integrated via the dart2genlight function.
Description
Metadata file. Can be integrated via the dart2genlight function.
Format
csv
Author(s)
Custodian: Arthur Georges (bugs? Post to https://groups.google.com/d/forum/dartr
Recode file to be used with the function.
Description
This test data set is provided to show a typical recode file format.
Format
csv
Author(s)
Custodian: Arthur Georges (bugs? Post to https://groups.google.com/d/forum/dartr
dartR.data Imports data for examples in dartR.base
Description
dartR.data Imports data for examples in dartR.base
Usage
zzz
Format
An object of class NULL of length 0.