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_pkgdown.yml
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url: https://cmlmagneville.github.io/mFD
reference:
- title: Summarize data
desc: >
These two functions are used to summarize up the species-traits and
assemblage data.
contents:
- sp.tr.summary
- asb.sp.summary
- title: Functional distances and Functional spaces
desc: >
These functions compute the functional distances between species, build
functional spaces (if the data gather only continuous traits or not),
assess/plot the quality of functional spaces (and dendrogram if asked),
plot the chosen functional space and caracterize its functional axes based
on traits correlation with each functional axes.
contents:
- funct.dist
- tr.cont.scale
- tr.cont.fspace
- quality.fspaces
- quality.fspaces.plot
- funct.space.plot
- traits.faxes.cor
- title: Compute Functional Entities
desc: >
This function gathers species into Functional Entities (FEs)
contents:
- sp.to.fe
- title: Compute and Plot functional indices
- subtitle: Based on FEs
desc: >
These functions compute and plot functional indices based on FEs as in
`Mouillot et al. (2014)`. They compute/plot Functional Redundancy,
Functional Overredundancy and Functional Vulnerability. They also help to
work with FEs.
contents:
- alpha.fd.fe
- alpha.fd.fe.plot
- fe.sp.df.computation
- from.fecoord.to.spcoord
- from.spfe.to.feasb
- search.sp.nm
- subtitle: Based on Hill numbers
desc: >
These functions compute alpha and beta indices based on Hill numbers according
to the Chao et al. (2019) framework.
contents:
- alpha.fd.hill
- beta.fd.hill
- subtitle: FUSE index
desc: >
This function computes FUSE (Functionally Unique, Specialized, and
Endangered) index that combines functional uniqueness, specialisation and
global endangerment to identify threatened species of particular importance
for functional diversity based on `Pimiento et al. (2020)`.
contents:
- fuse
- subtitle: Based on multidimensional space
desc: >
These functions compute/plot alpha and beta indices based on a given
multidimensional functional space.
contents:
- alpha.fd.multidim
- beta.fd.multidim
- alpha.multidim.plot
- beta.multidim.plot
- subtitle: Based on multidimensinal space for more complex graphs
desc: >
These functions return `ggplot` layers for each index allowing users to draw
more complex graphs.
contents:
- background.plot
- fdiv.plot
- fdis.plot
- feve.plot
- fide.plot
- fnnd.plot
- fori.plot
- fric.plot
- fspe.plot
- panels.to.patchwork
- pool.plot
- title: Other functions
desc: >
Various functions that can be used by the user for diverse usage
contents:
- dist.nearneighb
- dist.point
- dist.to.df
- mst.computation
- sp.filter
- vertices
- title: Data sets
desc: >
The three data sets used for examples and tutorials in the `mFD` package.
contents:
- baskets_fruits_weights
- fruits_traits
- fruits_traits_cat
template:
bootstrap: 5
bootswatch: yeti
navbar:
structure:
left: [reference, articles, news]
right: [search, github, lightswitch]
articles:
- title: Tutorials
navbar: ~
contents:
- mFD_general_workflow
- Compute_and_interpret_quality_of_functional_spaces
- Continuous_traits_framework
- How_to_deal_with_Functional_Entities
- Compute_functional_hill_indices
- Customised_plots
- FAQ