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rprops / Phenoflow_package

R package offering functionality for the advanced analysis of microbial flow cytometry data
GNU General Public License v2.0
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Error in the wiki: some alpha-diversity components are not calculated #41

Closed FMKerckhof closed 6 years ago

FMKerckhof commented 6 years ago

In the wiki, at one point,

### Export ecological data to .csv file in the chosen directory
write.csv2(file="results.metrics.csv",
           cbind(Diversity.fbasis, Evenness.fbasis,
                                          Structural.organization.fbasis,
                 Coef.var.fbasis))

is called.

However, currently the objects Evenness.fbasis, Structural.organization.fbasis, Coef.var.fbasis are not generated in the alpha-diversity section. In the corresponding vignette, I will remove them from this chunck. However @rprops : how would you like to proceed here? Shall we keep them in the wiki? Should they be added to the vignette?

rprops commented 6 years ago

Removed those functions from the wiki. They haven't been properly validated/tested.

FMKerckhof commented 6 years ago

I'll add to the vignette that also the results of the diversity_rf get exported:

### Export ecological data to .csv file in the chosen directory
names(Diversity.clean) <- paste0(names(Diversity.clean),".clean")
write.csv2(file="results.metrics.csv",
           cbind(Diversity.fbasis,Diversity.clean))