Comments (2)
Bisaloo
commented on May 31, 2024
More generally, other software, even if not implemented in R, is acceptable for comparison.
from fundiversity.
Rekyt
commented on May 31, 2024
There seems to be a factor two difference between fd_raoq() and other packages.
# Comparing Rao's Quadratic Entropy results
library("fundiversity")
data("traits_birds")
site_sp = matrix(1/nrow(traits_birds), ncol = nrow(traits_birds))
rownames(site_sp) = "s1"
colnames(site_sp) = rownames(traits_birds)
dist_traits_birds = dist(traits_birds)
mat_dist = as.matrix(dist_traits_birds)
# fundiversity results
fd_raoq(traits_birds)
#> site Q
#> 1 s1 85.02597
fd_raoq(traits_birds, site_sp)
#> site Q
#> 1 s1 85.02597
fd_raoq(traits = NULL, site_sp, mat_dist)
#> site Q
#> 1 s1 85.02597
# ade4
ade4::divc(as.data.frame(t(site_sp)), dis = dist_traits_birds, scale = FALSE)
#> diversity
#> s1 55849.24
# adiv
adiv::QE(site_sp, dis = dist_traits_birds)
#> Registered S3 method overwritten by 'spdep':
#> method from
#> plot.mst ape
#> Registered S3 methods overwritten by 'adegraphics':
#> method from
#> biplot.dudi ade4
#> kplot.foucart ade4
#> kplot.mcoa ade4
#> kplot.mfa ade4
#> kplot.pta ade4
#> kplot.sepan ade4
#> kplot.statis ade4
#> scatter.coa ade4
#> scatter.dudi ade4
#> scatter.nipals ade4
#> scatter.pco ade4
#> score.acm ade4
#> score.mix ade4
#> score.pca ade4
#> screeplot.dudi ade4
#> diversity
#> s1 170.0519
# hillR
hillR::hill_func(site_sp, dist_traits_birds, traits_as_is = TRUE)[1, ]
#> [1] 170.0519
# SYNCSA
SYNCSA::rao.diversity(site_sp, phylodist = mat_dist, standardize = FALSE)$PhyRao
#> s1
#> 170.0519Created on 2020-11-20 by the reprex package (v0.3.0)
Session info
devtools::session_info()
#> - Session info ---------------------------------------------------------------
#> setting value
#> version R version 4.0.2 (2020-06-22)
#> os Windows 10 x64
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate French_France.1252
#> ctype French_France.1252
#> tz Europe/Berlin
#> date 2020-11-20
#>
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#>
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Related Issues (20)
- Add a switch in `options()` to prevent use of memoised function?
- Add references that compute convex hulls intersections
- Hex logo
- Managing error from qhull transferred to geometry::convhulln() in fd_chull()
- Error when site contains no species in fd_fdiv() and fd_feve() HOT 2
- Errors when using non-quantitative traits in fd_fric()
- Release fundiversity 0.2.1
- Specific error obtained with Qhull HOT 3
- Investigate RCGAL as a replacement of geometry HOT 4
- Simplify CI matrix by using `_R_CHECK_DEPENDS_ONLY_TESTS_` HOT 2
- fd_fdiv() returns `NaN` on datasets without rownames
- FRic returns NA without warnings nor messages HOT 1
- Add tip in error message because of non-continuous traits HOT 1
- Renaming the vignettes to order them logically? HOT 2
- Change title of package in DESCRIPTION as it doesn't only computes "Alpha functional diversity indices"
- fd_fdis() bugs when site-species object is a data.frame() expects a matrix. HOT 2
- Using future and memoise together HOT 2
- Add link to published paper
- Should we write a vignette for non-continuous trait data? HOT 1
- fd_dis gives error if site x species matrix does not have row names HOT 4
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from fundiversity.