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phyloraster's Introduction

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phyloraster phyloraster website


phyloraster is an R package to calculate measures of endemism and evolutionary diversity using rasters of presence-absence as input, allowing to join the results derived from species distribution models (SDMs) with phylogenetic information.


Installation

The CRAN version of the package can be installed using:

install.packages("phyloraster") 

The development version of phyloraster can be downloaded from GitHub using the following code:

devtools::install_github("gabferreira/phyloraster")

phyloraster basics

Basic information about the package can be found at the package's webpage or in the vignette vignette("phyloraster-vignette")


Citation

  • Thank you for using phyloraster! Please remember to cite phyloraster in your publications:

Alves-Ferreira G., Heming N. M., Mota F. M. M. (2023). phyloraster: Evolutionary Diversity Metrics for Raster Data. R package version 2.0.

Alves-Ferreira G, Mota FMM, Talora DC, Oliveira, C, Solé, MK, Heming NM (2023). phyloraster: an R package to calculate measures of endemism and evolutionary diversity for rasters. Ecography. doi: 10.1111/ecog.06902.

  • For more information:
citation("phyloraster")

Issues

If you have any question or find any bug, let us know through the topic "Issues".


phyloraster's People

Contributors

gabferreira avatar hemingnm avatar

Stargazers

Guang-Fu Zhu avatar  avatar Ricardo I avatar Kostas Kougioumoutzis avatar Jeff Hanson avatar Cynthia Valéria Oliveira avatar

Watchers

 avatar  avatar Flávio Mota avatar

phyloraster's Issues

Submission checklist:

TO DOs:

  • reduce size of example files
  • reduce size of test files
  • remove vec.*() functions. No longer needed.
  • remove argument cores from functions that do not use terra::app() anymore. Probably all.
  • add #' @keywords internal to the documentation of all functions with names starting with "dot"
  • check all function examples (mostly update inv.range() arguments). Use devtools::run_examples()
  • epm tests should run using a raster instead of using dependency package. Create raster using epm, save script in "data-raw" folder and tiff in "inst/extdata" folder. See: SESraster
  • remove rnaturalearth dependency creating custom polygons. See terra::vect()
  • add option to compute tree metrics (branch.length, n.descen) from full tree or subset
  • organize README according to SESraster
  • CRAN like check: devtools::check(remote = TRUE, manual = TRUE)
  • organize vignettes and README
  • update "hexalogo"
  • set up pkgdown website

SES.pd

I tried to run an example of SES code that was feasible. But when I run large data SES, it always goes wrong. null.pd <-rast.pd.ses(data$x, tree, aleats = 3, random = "spat",overwrite=TRUE)
错误: [writeStart] file exists. You can use 'overwrite=TRUE' to overwrite i但是执行overwrite=TRUE后依然显示错误: [writeStart] file exists. You can use 'overwrite=TRUE' to overwrite

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