assist.ordination: Perform CCA and RDA Analysis for OTU Tables
In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description Usage Arguments Value Author(s) See Also Examples

This function simplifies CCA and RDA analysis by abstracting away some of the complexity and returning a list of useful measures.

assist.cca(otu1, otu2 = NULL, meta, full = TRUE, exclude = NULL,
           rank, na.action=na.exclude)
assist.rda(otu1, otu2 = NULL, meta, full = TRUE, exclude = NULL,
           rank, na.action=na.exclude)

`otu1`	the first OTU table to be used.
`otu2`	the second OTU table to be used.
`meta`	the metadata table to be used (must have same samples as `otu1`/`otu2`).
`full`	logical. Should a full model be considered? (If not, a restricted model is used).
`exclude`	A vector, either numeric or logical, specifying the columns to be removed from meta. If a character vector, columns with those names will be removed; if a numeric vector, columns with those indices will be removed.
`rank`	a character vector representing a rank. Must be in one of three specific formats (see ?RAM.rank.formatting for help).
`na.action`	choice of one of the following: "na.fail", "na.omit" or "na.exclude", see `na.action` in `cca` for detail.

If both otu1 and otu2 are given, a list of length 2 will be returned with the following items (if only otu1 is given, a list of length 1 will be returned with these items):

`$GOF`	the goodness of fit scores for the model.
`$VIF`	the VIF scores for the model.
`$percent_variation`	the percent variation explained by each axis
`$CCA_eig`	Eigenvalues for CCA axes.
`$CA_eig`	Eigenvalues for CA axes.
`$anova`	the ANOVA results for the model.

Wen Chen and Joshua Simpson.

cca, anova.cca

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data(ITS1, meta)
cca.help <- assist.cca(ITS1, meta=meta, rank="p")
cca.help$anova

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-3
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
[1] "A total of  1  columns are removed:  Harvestdate"
[1] "columns in exclude list: "
[1] "column# with missing data: "
[1] "columns# with one level: "
[1] "column# that are not numeric or factor: 6"
Warning messages:
1: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
2: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
3: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
Permutation test for cca under reduced model
Permutation: free
Number of permutations: 999

Model: cca(formula = tax ~ Sample + City + Crop + Plots + Harvestmethod + Ergosterol_ppm + Province + Latitude + Longitude, data = meta.remain, na.action = na.action)
         Df ChiSquare      F Pr(>F)    
Model     9   0.38230 12.149  0.001 ***
Residual  6   0.02098                  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1