# epGPCA.inference.battery

##### epGPCA.inference.battery: Inference tests for Generalized Principal Component Analysis (PCA) via InPosition.

Generalized Principal Component Analysis (PCA) and a battery of inference tests via InPosition. The battery includes permutation and bootstrap tests.

- Keywords
- Bootstrap, multivariate, Permutation

##### Usage

```
epGPCA.inference.battery(DATA, scale = TRUE, center = TRUE, DESIGN = NULL,
make_design_nominal = TRUE, masses = NULL, weights = NULL,
graphs = TRUE, k = 0,
test.iters = 100, constrained = FALSE, critical.value = 2)
```

##### Arguments

- DATA
original data to perform a PCA on.

- scale
a boolean, vector, or string. See

`expo.scale`

for details.- center
a boolean, vector, or string. See

`expo.scale`

for details.- DESIGN
a design matrix to indicate if rows belong to groups.

- make_design_nominal
a boolean. If TRUE (default), DESIGN is a vector that indicates groups (and will be dummy-coded). If FALSE, DESIGN is a dummy-coded matrix.

- masses
a diagonal matrix or column-vector of masses for the row items.

- weights
a diagonal matrix or column-vector of weights for the column items.

- graphs
a boolean. If TRUE (default), graphs and plots are provided (via

`epGraphs`

)- k
number of components to return.

- test.iters
number of iterations

- constrained
a boolean. If a DESIGN matrix is used, this will constrain bootstrap resampling to be within groups.

- critical.value
numeric. A value, analogous to a z- or t-score to be used to determine significance (via bootstrap ratio).

##### Details

`epGPCA.inference.battery`

performs generalized principal components analysis and inference tests on a data matrix.
If the expected time to compute the results (based on `test.iters`

) exceeds 1 minute, you will be asked (via command line) if you want to continue.

##### Value

Returns two lists ($Fixed.Data and $Inference.Data). For $Fixed.Data, see `epGPCA`

, `corePCA`

for details on the descriptive (fixed-effects) results.

$Inference.Data returns:

Permutation tests of components. p-values ($p.vals) and distributions of eigenvalues ($eigs.perm) for each component

Bootstrap tests of measures (columns). See `boot.ratio.test`

output details.

##### See Also

##### Examples

```
# NOT RUN {
#this is for ExPosition's iris data
data(ep.iris)
data<-ep.iris$data
design<-ep.iris$design
gpca.iris.res <- epGPCA.inference.battery(data,DESIGN=design,make_design_nominal=FALSE)
# }
```

*Documentation reproduced from package InPosition, version 0.12.7.1, License: GPL-2*