-
Notifications
You must be signed in to change notification settings - Fork 3
/
README.Rmd
148 lines (106 loc) · 11.5 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
temp_dir = tempdir(check = TRUE)
pkg_has_vignettes_and_test = function(pkg_name, pkg_dir = temp_dir) {
pkg_archive = download.packages(pkg_name, destdir = pkg_dir,
repos = "https://cran.r-project.org")
files_list = untar(pkg_archive[1, 2], list = TRUE)
has_vignette = paste0(pkg_archive[1, 1], "/vignettes/") %in% files_list
has_tests = paste0(pkg_archive[1, 1], "/tests/") %in% files_list
c(ifelse(has_vignette, "✅", "❌"), ifelse(has_tests, "✅", "❌"))
}
```
# fundiversity <img src="man/figures/logo.png" align="right" alt="fundiversity logo" width="120" />
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://github.com/funecology/fundiversity/actions)
[](https://app.codecov.io/gh/funecology/fundiversity)
[](https://CRAN.R-project.org/package=fundiversity)
[](https://zenodo.org/badge/latestdoi/300231216)
<!-- badges: end -->
`fundiversity` provides a lightweight package to compute common functional
diversity indices. To a get a glimpse of what `fundiversity` can do refer to the
[introductory vignette](https://funecology.github.io/fundiversity/articles/fundiversity.html).
The package is built using clear, public
[design principles](https://funecology.github.io/fundiversity/articles/fundiversity_4-design-principles.html)
inspired from our own experience and user feedback.
## Installation
You can install the stable version from CRAN with:
```{r, eval = FALSE}
install.packages("fundiversity")
```
Alternatively, you can install the development version with:
```{r eval = FALSE}
install.packages("fundiversity", repos = "https://bisaloo.r-universe.dev")
```
## Examples
`fundiversity` lets you compute six functional diversity indices: Functional Richness with `fd_fric()`, intersection with between convex hulls with `fd_fric_intersect()`, Functional Divergence with
`fd_fdiv()`, Rao's Quadratic Entropy with `fd_raoq()`, Functional Dispersion with `fd_fdis()` and Functional Evenness with `fd_feve()`. You can have a brief overview of the indices in the [introductory vignette](https://funecology.github.io/fundiversity/articles/fundiversity.html).
All indices can be computed either using global trait data or at the site-level:
```{r example}
library("fundiversity")
# If only the trait dataset is specified, considers all species together
# by default
fd_fric(traits_birds)
# We can also compute diversity across sites
fd_fric(traits_birds, site_sp_birds)
```
To compute Rao's Quadratic Entropy, the user can also provide a distance matrix between species directly:
```{r rao-distance-matrix}
dist_traits_birds = as.matrix(dist(traits_birds))
fd_raoq(traits = NULL, dist_matrix = dist_traits_birds)
```
## Function Summary
```{r child="man/rmdchunks/_fundiversity_functions.Rmd"}
```
## Parallelization
Thanks to the `future.apply` package, all functions (except `fd_raoq()`) within `fundiversity` support parallelization through the `future` backend. To toggle parallelization follow the [`future` syntax](https://cran.r-project.org/package=future):
```{r future-syntax, render=FALSE}
future::plan(future::multisession)
fd_fdiv(traits_birds)
```
For more details please refer to the [parallelization vignette](https://funecology.github.io/fundiversity/articles/fundiversity_1-parallel.html) or use `vignette("fundiversity_1-parallel", package = "fundiversity")` within R. **Note**: parallelization and memoization are **mutually exclusive**, when doing computation in parallel, fundiversity falls back on **unmemoised** versions of function.
## Available functional diversity indices
According to Pavoine & Bonsall (2011) classification, functional diversity indices can be classified in three "domains" that assess different properties of the functional space: richness, divergence, and regularity. We made sure that the computations in the package are correct in our [correctness vignette](https://funecology.github.io/fundiversity/articles/fundiversity_3-correctness.html).
`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://funecology.github.io/fundiversity/reference/fd_fric.html) | FDiv with [`fd_fdiv()`](https://funecology.github.io/fundiversity/reference/fd_fdiv.html)<br />Rao's QE with [`fd_raoq()`](https://funecology.github.io/fundiversity/reference/fd_raoq.html)<br />FDis with [`fd_fdis()`](https://funecology.github.io/fundiversity/reference/fd_fdis.html) | FEve with [`fd_feve()`](https://funecology.github.io/fundiversity/reference/fd_feve.html) |
| β-diversity<br />(= between sites) | FRic pairwise intersection with [`fd_fric_intersect()`](https://funecology.github.io/fundiversity/reference/fd_fric_intersect.html)<br />alternatives available in `betapart` | available in `entropart`, `betapart` or `hillR` | available in `BAT` |
## Related Packages
```{r pkg-vign-tests, include = FALSE}
adiv = pkg_has_vignettes_and_test("adiv")
bat = pkg_has_vignettes_and_test("BAT")
betapart = pkg_has_vignettes_and_test("betapart")
entropart = pkg_has_vignettes_and_test("entropart")
fd = pkg_has_vignettes_and_test("FD")
hilldiv = pkg_has_vignettes_and_test("hilldiv")
hillr = pkg_has_vignettes_and_test("hillR")
hypervolume = pkg_has_vignettes_and_test("hypervolume")
tpd = pkg_has_vignettes_and_test("TPD")
vegan = pkg_has_vignettes_and_test("vegan")
```
Several other packages exist that compute functional diversity indices. We did a [performance comparison](https://funecology.github.io/fundiversity/articles/fundiversity_2-performance.html) between related packages. We here mention some of them (but do not mention the numerous wrappers around these packages):
| Package Name | Indices included | Has vignettes | Has tests | On GitHub | On CRAN (last updated) |
|-------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------|--------------------|--------------------|-----------|-----------------------------------------------------------|
| [`adiv`](https://github.com/cran/adiv) | Functional Entropy, Functional Redundancy |`r adiv[[1]]` |`r adiv[[2]]` | ❌ |  |
| [`BAT`](https://github.com/cardosopmb/BAT) | β-diversity indices, Richness, divergence, and evenness with hypervolumes |`r bat[[1]]` |`r bat[[2]]` | ✅ |  |
| [`betapart`](https://github.com/cran/betapart) | Functional β-diversity |`r betapart[[1]]` |`r betapart[[2]]` | ❌ |  |
| [`entropart`](https://github.com/EricMarcon/entropart)| Functional Entropy |`r entropart[[1]]` |`r entropart[[2]]` | ✅ |  |
| [`FD`](https://github.com/cran/FD) | FRic, FDiv, FDis, FEve, Rao's QE, Functional Group Richness |`r fd[[1]]` |`r fd[[2]]` | ❌ |  |
| [`hilldiv`](https://github.com/anttonalberdi/hilldiv) | Dendrogram-based Hill numbers for functional diversity |`r hilldiv[[1]]` |`r hilldiv[[2]]` | ✅ |  |
| [`hillR`](https://github.com/daijiang/hillR) | Functional Diversity Hill Numbers |`r hillr[[1]]` |`r hillr[[2]]` | ✅ |  |
| [`hypervolume`](https://github.com/cran/hypervolume) | Hypervolume measure of functional diversity (~FRic) |`r hypervolume[[1]]`|`r hypervolume[[2]]`| ✅ | |
| [`mFD`](https://github.com/CmlMagneville/mFD) | Functional α- and β-diversity indices, including FRic, FDiv, FDis, FEve, FIde, FMPD, FNND, FOri, FSpe, Hill Numbers | ✅ | ❌ | ✅ |  |
| [`TPD`](https://github.com/cran/TPD) | FRic, FDiv, FEve but for probability distributions |`r tpd[[1]]` |`r tpd[[2]]` | ❌ |  |
| [`vegan`](https://github.com/vegandevs/vegan) | Only dendrogram-based FD (`treedive()`) |`r vegan[[1]]` |`r vegan[[2]]` | ✅ |  |
---