I have to perform ANOVA test on my samples. I would like to know to analyse in qiime2. What are the commands and and how one can choose value for --p-formula.
Please see following Docstring in qiim2 tutorial.
Usage: qiime longitudinal anova [OPTIONS]

Perform an ANOVA test on any factors present in a metadata file and/or
metadata-transformable artifacts. This is followed by pairwise t-tests to
examine pairwise differences between categorical sample groups.

Parameters:
–m-metadata-file METADATA…
(multiple Sample metadata containing formula terms.
arguments will
be merged) [required]
–p-formula TEXT R-style formula specifying the model. All terms must
be present in the sample metadata or
metadata-transformable artifacts and can be continuous
or categorical metadata columns. Formulae will be in
the format “a ~ b + c”, where “a” is the metric
(dependent variable) and “b” and “c” are independent
covariates. Use “+” to add a variable; “+ a:b” to add
an interaction between variables a and b; “*” to
include a variable and all interactions; and “-” to
subtract a particular term (e.g., an interaction term).
See https://patsy.readthedocs.io/en/latest/formulas.html
for full documentation of valid formula operators.
Always enclose formulae in quotes to avoid unpleasant
surprises. [required]
–p-sstype TEXT Choices(‘I’, ‘II’, ‘III’)
Type of sum of squares calculation to perform (I, II,
or III). [default: ‘II’]
Outputs:
–o-visualization VISUALIZATION
[required]

How to construct above formula using R-style formula specifying the model. .
Please help.

The formula let’s you compare categories in your metadata file. So if you medata looked like this:

sample-id

barcode-sequence

body-site

year

month

day

subject

reported-antibiotic-usage

days-since-experiment-start

#q2:types

categorical

categorical

numeric

numeric

numeric

categorical

categorical

numeric

L1S8

AGCTGACTAGTC

gut

2008

10

28

subject-1

Yes

0

L1S57

ACACACTATGGC

gut

2009

1

20

subject-1

No

84

L1S76

ACTACGTGTGGT

gut

2009

2

17

subject-1

No

112

L1S105

AGTGCGATGCGT

gut

2009

3

17

subject-1

No

140

L2S155

ACGATGCGACCA

left palm

2009

1

20

subject-1

No

84

L2S175

AGCTATCCACGA

left palm

2009

2

17

subject-1

No

112

L2S204

ATGCAGCTCAGT

left palm

2009

3

17

subject-1

No

140

L2S222

CACGTGACATGT

left palm

2009

4

14

subject-1

No

168

Your formula might look like this --p-formula subject+body-site
This will use the ANOVA test to compare the effect of subject number and body site locations.

Dear Collin, Please have a look at metadata file and command.

SampleID

BarcodeSequence

LinkerprimerSequence

Area

Place

SampleType

Date

DepthInCM

TemperatureAtTheTimeofSampling

pH

SampleNumber

SampleNumber-1

DistancefromSeashoreInKMS

DistancefromStartingPointInKMS

SamplingPointParallelTo

SerialNumber

SerialNumber-1

Description

AEMK01

AAAAAAAAT

YATGCTGCCTCCCGTAGGAGT

AndhraPradeshCoast

Ethamukkala

Soil

22 Oct. 2017

10

30

7

AEMK01

AEMK_One

Within 1 km

0

GMDM06

One

1

Blackish white

AEMK02

AAAAAAAAC

YATGCTGCCTCCCGTAGGAGT

AndhraPradeshCoast

Ethamukkala

Soil

22 Oct. 2017

10

32

8

AEMK02

AEMK_Two

Within 1 km

0

GMDM05

Two

2

Black

AEMK03

AAAAAAATT

YATGCTGCCTCCCGTAGGAGT

AndhraPradeshCoast

Ethamukkala

Soil

22 Oct. 2017

10

32

8

AEMK03

AEMK_Three

Within 1 km

0

GMDM04

Three

3

Black

AEMK04

AAAAAAATC

YATGCTGCCTCCCGTAGGAGT

AndhraPradeshCoast

Ethamukkala

Soil

22 Oct. 2017

10

32

7

AEMK04

AEMK_Four

Within 1 km

0

GMDM03

Four

4

Black

AEMK05

AAAAAAAGT

YATGCTGCCTCCCGTAGGAGT

AndhraPradeshCoast

Ethamukkala

Soil

22 Oct. 2017

10

30

7

AEMK05

AEMK_Five

Within 1 km

0

GMDM02

Five

5

Black

AEMK06

AAAAAAAAG

YATGCTGCCTCCCGTAGGAGT

AndhraPradeshCoast

Ethamukkala

Soil

22 Oct. 2017

10

32

7.5

AEMK06

AEMK_Six

Within 1 km

0

GMDM01

Six

6

Black

AKPT01

AAAAAAAAT

YATGCTGCCTCCCGTAGGAGT

AndhraPradeshCoast

Kothapatnam

Soil

22 Oct. 2017

10

25

8

AKPT01

AKPT_One

Within 1 km

20

GCLG06

Seven

7

Black

I have above columns in metadata file.

I am trying to run command:
qiime longitudinal anova --m-metadata-file sample-metadata.tsv --p-formula SampleNumber+Area --p-sstype II --o-visualization anova.qzv

error is coming: (1/1) Got unexpected extra arguments (/Users/rekadwad Area)

Could you suggest formula and correct command, please?

This error is a little cryptic. Before we get into the statistical test and what ‘asymptotically non-normal’ means, let’s take a look at the formula.

Your formula is faith_pd ~ SampleNumber+Area
You could say, “How is faith_pd affected by changes in SampleNumber and Area?”

So… let’s take a look at your SampleNumber and Area categories:

SampleNumber: 7 different levels (all levels are different)

Area: 1 level (all levels are the same)

“How do changes in Area effect faith_pd?” We don’t know because Area never changes.
“How do changes in SampleNumber effect faith_pd?” SampleNumber is always changing, so I guess faith_pd is always changing too!

Take a look at this metadata table from a small project:

SampleID

Treatment

WeeksAfterInfection

s1

A

1

S2

A

2

s3

A

3

s4

A

4

s5

B

1

s6

B

2

s7

B

3

s8

B

4

Based on this table, we could ask “How do changes in Treatment and Time effect faith_pd” and write this formula: faith_pd ~ Treatment+WeeksAfterInfection
Because our values are not all the same or all different, we can answer this question.

Which metadata categories would you like to test with your samples?