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✨
DESCRIPTION
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 4 scripts 223 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	223
linux-release-x86_64	OK	127
macos-release-arm64	OK	123
macos-oldrel-arm64	OK	222
windows-devel	OK	84
windows-release	OK	69
windows-oldrel	OK	65
wasm-release	OK	144

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

Function chromato_env16.R | Example with simulated data: | Function opti_eury_niche2.R | Function combina_niche3.R

Rendered fromReadme.Rmdusingknitr::rmarkdown

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