The goal of fishcom is to get all the informations concerning the ECOSTAB postdoc project in one place including reproducible code, notes, eventually data and manuscripts.
### Get the repository
You can clone the repository with git by pasting in your terminal:
git clone https://github.com/alaindanet/fishcom.git dir_name_to_be_created
OR
just download the repository: alaindanet/fishcom
If you have Rstudio installed on your
computer, just open fishcom.Rproj
with Rstudio.
My notes are available in the introductory vignette
vignettes/intro.html
Raw datas are spreadsheets (xls, csv, etc…) shapefiles and others
cartographic data and reports (of the AFB, ONEMA, etc). The raw datas
come together with R
scripts which describe cleaning procedures. The
cleaning procedures end by saving datasets used for data analysis.
It is located in data-raw
.
The clean datasets live in data
directory and stored in rda
compressed format. Once the package is loaded, they can be call as
easily as load(objet_name)
.
devtools::load_all()
#> Loading fishcom
data(metaweb_analysis)
names(metaweb_analysis)
#> [1] "metaweb" "species" "resource" "nb_class"
#> [5] "size_class" "piscivory_index" "th_prey_size"
The cleaned and filtered objects used for data analysis are named with
the suffix _analysis
.
The analysis of data lives in the directory named analysis
.
This folder contains scripts in which various metrics are computed for two different aspects that have been more or less arbitrary separated.
The community data lives in the community_metrics
and contains the
following metrics:
- species abondances
- species biomass
- species richness
The following metrics are summarised by station:
- mean and cv of species richness
- mean and cv of species biomass
- temporal beta-diversity
The network data lives in the network_analysis
and contains the
following metrics:
- connectance
- number of nodes
- modularity and modules
- nestedness
- trophic length
The following metrics are summarised by station:
- mean and cv of all the above indices