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EcologyR / Bloomers

Detect and identify potential bloomers in microbial communities
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TODO: - fix folde /data. Is needes? (now in buildignore) - Remove get_anomalies_season, Nacho_workflow_demo.R, data-raw and work_flow.R (now in buildignore) - tests are failing (both get and evenness) - examples fail, recheck - Datasets (if any) need documentation. - generar web con packege down -

Bloomers

R-CMD-check Codecov test coverage Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.

The main objective of Bloomers package is to detect sharp changes in abundances for individual taxa in microbial communities.

Installation

# install.packages("devtools")
devtools::install_github("EcologyR/Bloomers")

The code to create this package is available here.

##The workflow of the bloomers package is summarized in the following graph

Example

This is a basic example which shows you how to solve a common problem:

# library(templateRpackage)
## basic example code

What is special about using README.Rmd instead of just README.md? You can include R chunks like so:

summary(cars)
#>      speed           dist       
#>  Min.   : 4.0   Min.   :  2.00  
#>  1st Qu.:12.0   1st Qu.: 26.00  
#>  Median :15.0   Median : 36.00  
#>  Mean   :15.4   Mean   : 42.98  
#>  3rd Qu.:19.0   3rd Qu.: 56.00  
#>  Max.   :25.0   Max.   :120.00

You’ll still need to render README.Rmd regularly, to keep README.md up-to-date. devtools::build_readme() is handy for this. You could also use GitHub Actions to re-render README.Rmd every time you push. An example workflow can be found here: https://github.com/r-lib/actions/tree/v1/examples.

Put here a plot representing blooming species and how we do detect anomalies


#plot(bloomersdata$pseudoabundance) #improve this example 
#load("./data/bloomersdata.rda")
plot(pressure)

In that case, don’t forget to commit and push the resulting figure files, so they display on GitHub and CRAN.

Citation

If using this package, please cite it:

#citation("Bloomers")

Funding

The development of this software has been funded by Fondo Europeo de Desarrollo Regional (FEDER) and Consejería de Transformación Económica, Industria, Conocimiento y Universidades of Junta de Andalucía (proyecto US-1381388 led by Francisco Rodríguez Sánchez, Universidad de Sevilla).