Welcome to natto!
natto is an extreme
vegan package that contains experimental, specialized or
unfinished code that does not fit to the more general vegan
package. Some of these functions may be merged to vegan later, but
the package is not a code kindergarten with guaranteed tenure track to
vegan.
Currently natto contains
- Rao's quadratic entropy, phylogenetic dissimilarities and
phylogenetic data standardization, plus related Clarke's taxonomic
dissimilarity.
- Polar Ordination A.K.A. Bray-Curtis Ordination.
- Orlóci's Position Vector Ordination and a related method using
species as ordination axes.
- Implementation of Decorana in R: easier to study the algorithm
and develop the method than with Fortran code.
- Estimate residual species associations in CCA and RDA.
- Randomized clustering and ordination based on Bayesian Jaccard
dissimilarity with applications. Dissimilarities are random numbers
from Beta distribution and each evaluation yields a new set of
dissimilarities. For clustering, this can be used to assess the
support of clusters, and for ordination the confidence areas of
coordinates.
- Hierarchical clustering based on information analysis after Williams,
Lambert & Lance, J. Ecol. 54, 427-445 (1966).
- beta and gamma diversity clustering.
- Plotting cluster dendrograms (
hclust
results) so that terminal
leaves are fans with base proportional to weight (size): ginkgogram
.
- Humped no-interaction model for species richness vs. biomass
(transferred from the vegan package).
- IAP functions to find the indicator values for species and statistics
for sites in Index of Atmospheric Purity. The main focus is in indicator
values for species which are the number of companion species. These can
be used to find species that indicate high or low biodiversity, and
permutation test is provided to assess these values.
- Mean Rank Shift function of Collins et al., Ecology 89,
3534-3541 (2008).
- Testing differences of slopes in Mantel style regression between
dissimilarities.
- Casting unconstrained
vegan::rda()
result object to stats::prcomp
object.
- Casting Delaunay triangulation from
deldir::deldir
result object to
stats::dist
object.
Installation
There are no binary packages available at the moment, but if you install
Hadley Wickham's devtools package from CRAN
, you can install natto
directly from github
:
install.packages("devtools") # if you have not yet installed devtools
library(devtools)
install_github("jarioksa/natto")
Binary package can be installed via R-Universe:
install.packages("natto", repos = c("https://jarioksa.r-universe.dev",
"https://cloud.r-project.org"))