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fix #27
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@Bisaloo
Bisaloo committed Jun 30, 2021
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1 change: 1 addition & 0 deletions README.Rmd
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Expand Up @@ -35,6 +35,7 @@ pkg_has_vignettes_and_test = function(pkg_name, pkg_dir = temp_dir) {
[![R build status](https://github.com/Bisaloo/fundiversity/workflows/R-CMD-check/badge.svg)](https://github.com/Bisaloo/fundiversity/actions)
[![Coverage Status](https://codecov.io/gh/Bisaloo/fundiversity/branch/master/graph/badge.svg?token=HR4YH118VT)](https://codecov.io/gh/Bisaloo/fundiversity)
[![CRAN status](https://www.r-pkg.org/badges/version-ago/fundiversity)](https://CRAN.R-project.org/package=fundiversity)
[![DOI](https://zenodo.org/badge/300231216.svg)](https://zenodo.org/badge/latestdoi/300231216)
<!-- badges: end -->

`fundiversity` provides a lightweight package to compute common functional
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39 changes: 20 additions & 19 deletions README.md
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Expand Up @@ -13,6 +13,7 @@ status](https://github.com/Bisaloo/fundiversity/workflows/R-CMD-check/badge.svg)
Status](https://codecov.io/gh/Bisaloo/fundiversity/branch/master/graph/badge.svg?token=HR4YH118VT)](https://codecov.io/gh/Bisaloo/fundiversity)
[![CRAN
status](https://www.r-pkg.org/badges/version-ago/fundiversity)](https://CRAN.R-project.org/package=fundiversity)
[![DOI](https://zenodo.org/badge/300231216.svg)](https://zenodo.org/badge/latestdoi/300231216)
<!-- badges: end -->

`fundiversity` provides a lightweight package to compute common
Expand Down Expand Up @@ -95,14 +96,14 @@ fd_raoq(traits = NULL, dist_matrix = dist_traits_birds)

## Function Summary

| Function Name | Index Name | Parallelizable\[1\] | Memoizable\[2\] |
| :-------------------- | :-------------- | :-----------------: | :-------------: |
| `fd_fric()` | FRic | ✅ | ✅ |
| `fd_fric_intersect()` | FRic\_intersect | ✅ | ✅ |
| `fd_fdiv()` | FDiv | ✅ | ✅ |
| `fd_feve()` | FEve | ✅ | ❌ |
| `fd_fdis()` | FDis | ✅ | ❌ |
| `fd_raoq()` | Rao’s Q | ❌ | ❌ |
| Function Name | Index Name | Parallelizable[1] | Memoizable[2] |
|:----------------------|:----------------|:-----------------:|:-------------:|
| `fd_fric()` | FRic | ✅ | ✅ |
| `fd_fric_intersect()` | FRic\_intersect | ✅ | ✅ |
| `fd_fdiv()` | FDiv | ✅ | ✅ |
| `fd_feve()` | FEve | ✅ | ❌ |
| `fd_fdis()` | FDis | ✅ | ❌ |
| `fd_raoq()` | Rao’s Q | ❌ | ❌ |

## Parallelization

Expand Down Expand Up @@ -131,7 +132,7 @@ regularity. `fundiversity` provides function to compute indices that
assess this three facets at the site scale:

| Scale | Richness | Divergence | Evenness |
| ---------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------- |
|------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------|
| α-diversity<br />(= among sites) | FRic with [`fd_fric()`](https://bisaloo.github.io/fundiversity/reference/fd_fric.html) | FDiv with [`fd_fdiv()`](https://bisaloo.github.io/fundiversity/reference/fd_fdiv.html)<br />Rao’s QE with [`fd_raoq()`](https://bisaloo.github.io/fundiversity/reference/fd_raoq.html)<br />FDis with [`fd_fdis()`](https://bisaloo.github.io/fundiversity/reference/fd_fdis.html) | FEve with [`fd_feve()`](https://bisaloo.github.io/fundiversity/reference/fd_feve.html) |
| β-diversity<br />(= between sites) | FRic pairwise intersection with [`fd_fric_intersect()`](https://bisaloo.github.io/fundiversity/reference/fd_fric_intersect.html)<br />alternatives available in `betapart` | available in `entropart`, `betapart` or `hillR` | available in `BAT` |

Expand All @@ -144,7 +145,7 @@ between packages. We here mention some of them (but do not mention the
wrappers around these packages):

| Package Name | Indices included | Has vignettes | Has tests | On GitHub | On CRAN (last updated) |
| ------------------------------------------------------ | ----------------------------------------------------------- | ------------- | --------- | --------- | ---------------------------------------------------------- |
|--------------------------------------------------------|-------------------------------------------------------------|---------------|-----------|-----------|------------------------------------------------------------|
| [`FD`](https://github.com/cran/FD) | FRic, FDiv, FDis, FEve, Rao’s QE, Functional Group Richness | ❌ | ❌ | :x: | ![](https://www.r-pkg.org/badges/last-release/FD) |
| [`adiv`](https://github.com/cran/adiv) | Functional Entropy, Functional Redundancy | ✅ | ❌ | :x: | ![](https://www.r-pkg.org/badges/last-release/adiv) |
| [`betapart`](https://github.com/cran/betapart) | Functional β-diversity | ❌ | ❌ | :x: | ![](https://www.r-pkg.org/badges/last-release/betapart) |
Expand All @@ -155,14 +156,14 @@ wrappers around these packages):
| [`hypervolume`](https://github.com/cran/hypervolume) | Hypervolume measure functional diversity (\~FRic) | ❌ | ❌ | ✅ | ![](https://www.r-pkg.org/badges/last-release/hypervolume) |
| [`BAT`](https://github.com/cardosopmb/BAT) | β-, Richness, divergence, and evenness with hypervolumes | ❌ | ❌ | ✅ | ![](https://www.r-pkg.org/badges/last-release/BAT) |

-----
------------------------------------------------------------------------

1. parallelization through the `future` backend please refer to the
[parallelization
vignette](https://bisaloo.github.io/fundiversity/articles/parallel.html)
for details.
[1] parallelization through the `future` backend please refer to the
[parallelization
vignette](https://bisaloo.github.io/fundiversity/articles/parallel.html)
for details.

2. memoization means that the results of the functions calls are cached
and not recomputed when recalled, to toggle it off see the
`fundiversity::fd_fric()` [Details
section](https://bisaloo.github.io/fundiversity/reference/fd_fric.html#details).
[2] memoization means that the results of the functions calls are cached
and not recomputed when recalled, to toggle it off see the
`fundiversity::fd_fric()` [Details
section](https://bisaloo.github.io/fundiversity/reference/fd_fric.html#details).
6 changes: 4 additions & 2 deletions inst/CITATION
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Expand Up @@ -10,7 +10,8 @@ bibentry(
year = year,
note = note,
header = "To cite this package in publications, please use:",
url = "https://CRAN.R-project.org/package=fundiversity")
url = "https://CRAN.R-project.org/package=fundiversity",
doi = "10.5281/zenodo.4761754")

bibentry(
bibtype = "manual",
Expand All @@ -20,4 +21,5 @@ bibentry(
year = year,
note = note,
header = "To cite the development version, please use:",
url = "https://github.com/Bisaloo/fundiversity")
url = "https://github.com/Bisaloo/fundiversity",
doi = "10.5281/zenodo.4761754")

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