# nst.panova: Permutational multivariate ANOVA test for ST and NST In NST: Normalized Stochasticity Ratio

 nst.panova R Documentation

## Permutational multivariate ANOVA test for ST and NST

### Description

Permutational multivariate ANOVA test for stochasticity ratio and normalized stochasticity ratio between treatments

### Usage

```nst.panova(nst.result, group=NULL, rand=999, trace=TRUE, SES=FALSE, RC=FALSE)
```

### Arguments

 `nst.result` list object, the output of nsto, must have "details" `group` nx1 matrix, if the grouping is different from the nst.result. default is NULL, means to use the grouping in nst.result. `rand` integer, randomization times for permuational test `trace` logic, whether to show message when randomizing. `SES` Logic, whether to perform the test for standardized effect size (SES). SES is (observed dissimilarity - mean of null dissimilarity)/standard deviation of null dissimilarity. default is FALSE. `RC` Logic, whether to perform the test for modified Raup-Crick metric (RC). RC is percentage of null dissimilarity lower than observed dissimilarity x 2 - 1. default is FALSE.

### Details

PERMANOVA for stochasticity ratio (ST or NST or MST) or SES or RC is based on the comparison of F values between observed pattern and the permutated patterns where samples are randomly shuffled regardless of treatments. However, it is a bit different from PERMANOVA for dissimilarity. The PERMANOVA of stochasticity ratio here is to ask whether the ST values within a group is higher than those within another group. But the PERMANOVA of dissimilarity is to ask whether the between-group dissimilarity is higher than within-group dissimilarity.

### Value

Output is a data.frame object.

 `index` name of index `group1` treatment/group name `group2` treatment/group name `Index.group1` index value in group1 `Index.group2` index value in group2 `Difference` index.group1 - index.group2 `F.obs` F value `P.anova` P value of parametric ANOVA test `P.panova` P value of permutational ANOVA test `P.perm` P value of permutational test of the difference

### Note

Version 7: 2021.10.29, add PERMANOVA test for SES and RC. Version 6: 2021.9.28, avoid error for special cases in permutation. Version 5: 2021.8.25, revised to avoid error for special cases in MST calculation. Version 4: 2020.10.14, debug some error when replecate number is low and edit details in help. Version 3: 2019.10.8, Update reference. Version 2: 2019.5.10 Version 1: 2017.12.30

Daliang Ning

### References

Ning D., Deng Y., Tiedje J.M. & Zhou J. (2019) A general framework for quantitatively assessing ecological stochasticity. Proceedings of the National Academy of Sciences 116, 16892-16898. doi:10.1073/pnas.1904623116.

`tNST`, `nst.boot`

### Examples

```data(tda)
comm=tda\$comm
group=tda\$group
tnst=tNST(comm=comm, group=group, rand=20,
output.rand=TRUE, nworker=1)
# rand is usually set as 1000, here set rand=20 to save test time.

nst.pova=nst.panova(nst.result=tnst, rand=99)
# rand is usually set as 999, here set rand=99 to save test time.
```

NST documentation built on June 7, 2022, 1:07 a.m.