Djeppschmidt/Model.Microbiome
Environment And Community Simulation Package

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Djeppschmidt/Model.Microbiome: Environment And Community Simulation Package
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Man pages for Djeppschmidt/Model.Microbiome
Environment And Community Simulation Package

BENCHMARK.MMshell script for benchmarking
competerun adjustment for species interactions / core function
ConnStatgenerate network analysis and network stats
data_summarysummarize data for plotting mean/ se
data_summary2summarize data for plotting media + min/max
Delta.sppcountstandardizes the taxon abundance by taking counts relative to...
deseqIndicsmake indicators from deseq
deseq.resp values of deseq indicator species
deseqVSTcreate transformed community to deseqVST
divCalculate diversity and skew metrics
DMIDelta Model index (DMI)
eRarecreate transformed community to even rarefaction
ext.DMIextract Overmodeling Index values from a benchmarked object
ext.LIIextract Lost Information Index values from a benchmarked...
ext.PERMANOVAextract PERMANOVA r2 values from a benchmarked object
ext.RIextract correlation values between LII and DMI
filter.limmado filter protocol for limma
getmodemode function
getNetPlotget network plot from networks that have been generated by...
getNetStatsget network stats from networks that have been generated by...
getTaxCor.Tabextract output from taxa correlation ratio in a table form
gm_meangeometric mean function for deseq functions
indicsppmake indicator species
indicsummaryextract summary from indicspp()
LIIextract Lost Information Index values from a benchmarked...
limma.Indicsmake limma indicators
limma.Indics3make limma indicators
limmaVSTcreate transformed community to limmaVST
lm.modelproduce linear model of each taxon against environmental...
lm.model2produce linear model of each taxon against experimental...
lm.testmake linear model for each taxon
make.commconstruct community (simple)
make.comm2construct community
make.deseqVSTnormalize routine using deseq
make.guildtabmake guild and keyestone species table for the interaction...
make.limmaVSTnormalize routine using limma
make.PERMANOVAconducts a PERMANOVA specific for this model
make.rarefy1subsample community
make.rarefy2subsample community
make.refcommconstruct reference community
make.scaled2normalize routine using scaling
make.tablesubsample community
make.table2do filter protocol for limma
model.rarefysubsample community
pRarecreate transformed community to proportional rarefaction
QSeqcreate transformed community to Quantitative Sequencing value
RAcreate transformed community to relative abundance
run.analysis2workhorse function for BENCHMARK.MM
run.analysis3workhorse function for simulate.MM
run.competewrapper for running adjustment for species interactions /...
run.LIIRun LII
run.PERMANOVARun Permanova, make PERMANVOA ratios
run.rarecurveRun rarecurve
set.seqDepthset "sequencing depth"
simulate.MMshell script for creating the simulation
spike1function for spike in species 1
spike2function for spike in species 2
spike3function for spike in species 3
spp1species function
spp10species function
spp100species function
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Summarize.Ftableoutput sum of F values to a table from PERMANOVA across all...
Summarize.LIISummarize the LII
Summarize.lmRatiotab.MeanSummarize output from lm ratio index for median (categorical)
Summarize.lmRatiotabModel.MeanSummarize output from lm ratio index for median (environment)
Summarize.lmRatiotabModel.VarSummarize output from lm ratio index for variance...
Summarize.lmRatiotab.VarSummarize output from lm ratio index for variance...
Summarize.PERMANOVA.Rratioextract and summarize PERMANOVA r-squared values
SVItest difference of linear model r2 values
SVI2test difference of linear model r2 values
Djeppschmidt/Model.Microbiome documentation built on Sept. 17, 2022, 9:15 p.m.

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