Package: specieschrom 1.0.0

specieschrom: The Species Chromatogram

A simple method to display and characterise the multidimensional ecological niche of a species. The method also estimates the optimums and amplitudes along each niche dimension. Give also an estimation of the degree of niche overlapping between species. See Kleparski and Beaugrand (2022) <doi:10.1002/ece3.8830> for further details.

Authors:Loick Kleparski [aut, cre], Gregory Beaugrand [aut], Universite Littoral Cote d'Opale [cph]

specieschrom_1.0.0.tar.gz
specieschrom_1.0.0.zip(r-4.7)specieschrom_1.0.0.zip(r-4.6)specieschrom_1.0.0.zip(r-4.5)
specieschrom_1.0.0.tgz(r-4.6-any)specieschrom_1.0.0.tgz(r-4.5-any)
specieschrom_1.0.0.tar.gz(r-4.7-any)specieschrom_1.0.0.tar.gz(r-4.6-any)
specieschrom_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
specieschrom/json (API)

# Install 'specieschrom' in R:

install.packages('specieschrom', repos = c('https://loick-klpr.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/loick-klpr/specieschrom/issues

Datasets:

data_abundance - Abundance of 14 pseudo-species. A dataset containing the abundance values of 14 pseudo-species in 100 samples. The environmental conditions associated with each samples are described in the environment dataset. Pseudo-species v1 and v2, v3 and v4, v5 and v6, v7 and v8, v9 and v10, v11 and v12, v13 and v14 have the same niche.
environment - Three fictive environmental variables A dataset containing the values of three fictive envionemental variables in 100 samples. The corresponding pseudo-species abundance in each sample are available in the data_abundance dataset.

On CRAN:

3.70 score 1 stars 3 scripts 166 downloads 3 exports 24 dependencies

Last updated from:80f57adc74. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	119
source / vignettes	OK	175
linux-release-x86_64	OK	116
macos-release-arm64	OK	150
macos-oldrel-arm64	OK	196
windows-devel	OK	91
windows-release	OK	135
windows-oldrel	OK	75
wasm-release	OK	103

Exports:chromato_env16 combina_niche3 opti_eury_niche2

Dependencies:cli colorRamps cpp11 farver ggplot2 glue gtable isoband labeling lifecycle magrittr plyr R6 RColorBrewer Rcpp reshape2 rlang S7 scales stringi stringr vctrs viridisLite withr

specieschrom

Loïck Kléparski and Grégory Beaugrand

Rendered fromReadme.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2022-10-14
Started: 2022-02-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Display the multidimensional ecological niche of a species with a species chromatogram.	chromato_env16
Estimate the degree of niche overlapping among species from their chromatograms.	combina_niche3
Abundance of 14 pseudo-species. A dataset containing the abundance values of 14 pseudo-species in 100 samples. The environmental conditions associated with each samples are described in the environment dataset. Pseudo-species v1 and v2, v3 and v4, v5 and v6, v7 and v8, v9 and v10, v11 and v12, v13 and v14 have the same niche.	data_abundance
Three fictive environmental variables A dataset containing the values of three fictive envionemental variables in 100 samples. The corresponding pseudo-species abundance in each sample are available in the data_abundance dataset.	environment
m order simple moving average.	moymob1
Mean of the n highest values of a vector.	nanmean4
Nested function for niche overlapping estimation with 'combina_niche3.R'.	niche_difer_sp
Nested function for niche overlapping estimation with 'combina_niche3.R' and 'niche_differ_sp.R'.	niche_difer2
Optimums and amplitudes estimations along each niche dimension.	opti_eury_niche2