Example Data for R Package 'vortexR'

Contains selected data from two publications, Campbell 'et' 'al'. (2016) and 'Pacioni' 'et' 'al'. (2017) . The data is provided both as raw outputs from the population viability analysis software 'Vortex' and packaged as R objects. The R package 'vortexR' uses the raw data provided here to illustrate its functionality of parsing raw 'Vortex' output into R objects.


vortexRdata is the auxiliary data package for vortexR.

vortexRdata provides data from two publications, Campbell et al (2016) and Pacioni et al. (2017) both as original output from the population viability analysis software Vortex and as R objects.

The R package vortexR uses the raw data provided here to illustrate its functionality of parsing raw Vortex output into R objects.

Install

The stable versions of vortexRdata and vortexR can be installed with:

install.packages("vortexR", dependencies = TRUE)

The latest development versions of vortexRdata and vortexR can be installed with:

# install.packages("devtools")
devtools::install_github("carlopacioni/vortexRdata")
devtools::install_github("carlopacioni/vortexR")

See the vortexR README for detailed help with the installation of Java-based packages.

Use

Compiled data

You can use the data provided by vortexRdata as binary R objects as follows:

require(vortexRdata)
data("pac.clas")
head(pac.clas)

The full list of provided compiled data can be found in the package's documentation: help(package = "vortexRdata").

Raw data

If you wish to test vortexR's data handling functions on actual Vortex output files, you can use the raw data here as a starting point that is guaranteed to work.

pac.dir <- system.file("extdata", "pacioni", package="vortexRdata")
cam.dir <- system.file("extdata", "campbell", package="vortexRdata")
f <- file.path(pac.dir, "Pacioni_et_al_ST_Classic(Base).stdat")
require(vortexR)
one.st.classic <- collate_one_dat(f, 3)
head(one.st.classic)

The two folders of raw data are named "campbell" and "pacioni", respectively.

Using example data allows users of vortexR to trouble-shoot and validate their workflow before using their own Vortex output.

Cite

If you use data provided by vortexRdata, please use the citation generated from citation("vortexRdata").

Contribute

We are happy to receive feedback and contributions through bug reports and pull requests through the main package vortexR.

Future development

We are in the process of releasing vortexR and vortexRdata to CRAN. In addition, a paper describing vortexR is in press. Once both packages are available through CRAN, installation, citation, and usage of vortexR and vortexRdata are likely to change.

News

vortexRdata 1.0.5

  • Update data format to reflect new output format of irr (0.84.1)

vortexRdata 1.0.4

  • Update the code examples in the docs to use raw data provided by vortexRdata rather than vortexR, where it originally was stored. Now the usage examples in the docs are correct and inline with the README.

vortexRdata 1.0.3

  • This version was accepted on CRAN and is imported by vortexR.

vortexRdata pre-1.0.3

Versions 1.0.0, 1.0.1 and 1.0.2 were submitted to CRAN and rejected with reviewer requests to fine-tune some formatting of DESCRIPTION and code docs.

The history of these changes is preserved in earlier revisions of cran-comments.md on GitHub, but removed in the current released version 1.0.3.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("vortexRdata")

1.0.5 by Carlo Pacioni, a year ago


https://github.com/carlopacioni/vortexRdata/


Report a bug at https://github.com/carlopacioni/vortexR/issues


Browse source code at https://github.com/cran/vortexRdata


Authors: Carlo Pacioni [aut, cre] , Florian W. Mayer [aut]


Documentation:   PDF Manual  


GPL-3 license



Imported by vortexR.


See at CRAN