Built site for ModelArray@0.1.5: 8527406

Author: araikes

llms.txt

@@ -121,49 +121,41 @@ If you use ModelArray, please cite:
 
 # Package index
 
-## ModelArray Class
+## Package overview
 
-Create, load, and combine ModelArray objects backed by HDF5 files.
+- [`ModelArray-package`](https://pennlinc.github.io/ModelArray/reference/ModelArray-package.md)
+  : ModelArray: Statistical Analysis of Element-Wise Neuroimaging Data
+
+## ModelArray class and constructor
 
 - [`ModelArray()`](https://pennlinc.github.io/ModelArray/reference/ModelArray-class.md)
   [`show(`*`<ModelArray>`*`)`](https://pennlinc.github.io/ModelArray/reference/ModelArray-class.md)
   : ModelArray class
 - [`ModelArray()`](https://pennlinc.github.io/ModelArray/reference/ModelArray.md)
   : Load element-wise data from an HDF5 file
-- [`h5summary()`](https://pennlinc.github.io/ModelArray/reference/h5summary.md)
-  [`print(`*`<h5summary>`*`)`](https://pennlinc.github.io/ModelArray/reference/h5summary.md)
-  : Summarize an HDF5 file without loading a full ModelArray
-- [`mergeModelArrays()`](https://pennlinc.github.io/ModelArray/reference/mergeModelArrays.md)
-  : Merge multiple ModelArrays from different HDF5 files
 
 ## Accessors
 
-Extract scalar data, source filenames, results, and metadata from a
-ModelArray object.
-
-- [`scalars()`](https://pennlinc.github.io/ModelArray/reference/scalars.md)
-  : Element-wise scalar data of a ModelArray object
 - [`sources()`](https://pennlinc.github.io/ModelArray/reference/sources.md)
   : Source filenames of a ModelArray object
+- [`scalars()`](https://pennlinc.github.io/ModelArray/reference/scalars.md)
+  : Element-wise scalar data of a ModelArray object
 - [`results()`](https://pennlinc.github.io/ModelArray/reference/results.md)
   : Statistical results of a ModelArray object
-- [`scalarNames()`](https://pennlinc.github.io/ModelArray/reference/scalarNames.md)
-  : Names of scalars in a ModelArray
-- [`analysisNames()`](https://pennlinc.github.io/ModelArray/reference/analysisNames.md)
-  : Names of analyses in a ModelArray
 - [`nElements()`](https://pennlinc.github.io/ModelArray/reference/nElements.md)
   : Number of elements in a ModelArray
 - [`nInputFiles()`](https://pennlinc.github.io/ModelArray/reference/nInputFiles.md)
   : Number of input files in a ModelArray
-- [`numElementsTotal()`](https://pennlinc.github.io/ModelArray/reference/numElementsTotal.md)
-  : Number of elements in ModelArray
+- [`scalarNames()`](https://pennlinc.github.io/ModelArray/reference/scalarNames.md)
+  : Names of scalars in a ModelArray
+- [`analysisNames()`](https://pennlinc.github.io/ModelArray/reference/analysisNames.md)
+  : Names of analyses in a ModelArray
 - [`elementMetadata()`](https://pennlinc.github.io/ModelArray/reference/elementMetadata.md)
   : Element metadata from a ModelArray
+- [`exampleElementData()`](https://pennlinc.github.io/ModelArray/reference/exampleElementData.md)
+  : Example per-element data.frame for user functions
 
-## Element-wise Analysis
-
-Fit statistical models at every element (fixel, voxel, or vertex) in a
-ModelArray and write results back to HDF5.
+## Analysis functions
 
 - [`ModelArray.lm()`](https://pennlinc.github.io/ModelArray/reference/ModelArray.lm.md)
   : Fit element-wise linear models
@@ -177,31 +169,10 @@ ModelArray and write results back to HDF5.
 - [`ModelArray.wrap()`](https://pennlinc.github.io/ModelArray/reference/ModelArray.wrap.md)
   : Run a user-supplied function for element-wise data
 
-- [`writeResults()`](https://pennlinc.github.io/ModelArray/reference/writeResults.md)
-  : Write outputs from element-wise statistical analysis to an HDF5 file
-
-## Testing and Debugging
-
-Build per-element test data and inspect your setup before committing to
-a full analysis run.
+## Per-element internals
 
-- [`exampleElementData()`](https://pennlinc.github.io/ModelArray/reference/exampleElementData.md)
-  : Example per-element data.frame for user functions
-
-## Formula Helpers
-
-Generate GAM formulas for common interaction structures used with
-ModelArray.gam.
-
-- [`gen_gamFormula_fxSmooth()`](https://pennlinc.github.io/ModelArray/reference/gen_gamFormula_fxSmooth.md)
-  : Generate GAM formula with factor-smooth interaction
-- [`gen_gamFormula_contIx()`](https://pennlinc.github.io/ModelArray/reference/gen_gamFormula_contIx.md)
-  : Generate GAM formula with continuous-by-continuous interaction
-
-## Internal
-
-Per-element workhorse functions called by the analysis functions. Most
-users should not need to call these directly.
+These functions are called internally by the analysis functions. Most
+users should not call them directly.
 
 - [`analyseOneElement.lm()`](https://pennlinc.github.io/ModelArray/reference/analyseOneElement.lm.md)
   :
@@ -223,6 +194,25 @@ users should not need to call these directly.
 - [`analyseOneElement.wrap()`](https://pennlinc.github.io/ModelArray/reference/analyseOneElement.wrap.md)
   : Run a user-supplied function for a single element
 
+## Merging
+
+- [`mergeModelArrays()`](https://pennlinc.github.io/ModelArray/reference/mergeModelArrays.md)
+  : Merge multiple ModelArrays from different HDF5 files
+
+## Utilities
+
+- [`writeResults()`](https://pennlinc.github.io/ModelArray/reference/writeResults.md)
+  : Write outputs from element-wise statistical analysis to an HDF5 file
+- [`h5summary()`](https://pennlinc.github.io/ModelArray/reference/h5summary.md)
+  [`print(`*`<h5summary>`*`)`](https://pennlinc.github.io/ModelArray/reference/h5summary.md)
+  : Summarize an HDF5 file without loading a full ModelArray
+- [`numElementsTotal()`](https://pennlinc.github.io/ModelArray/reference/numElementsTotal.md)
+  : Number of elements in ModelArray
+- [`gen_gamFormula_fxSmooth()`](https://pennlinc.github.io/ModelArray/reference/gen_gamFormula_fxSmooth.md)
+  : Generate GAM formula with factor-smooth interaction
+- [`gen_gamFormula_contIx()`](https://pennlinc.github.io/ModelArray/reference/gen_gamFormula_contIx.md)
+  : Generate GAM formula with continuous-by-continuous interaction
+
 # Articles
 
 ### All vignettes

pkgdown.yml

@@ -12,7 +12,7 @@ articles:
   installations: installations.html
   modelling: modelling.html
   walkthrough: walkthrough.html
-last_built: 2026-04-01T18:52Z
+last_built: 2026-04-02T23:39Z
 urls:
   reference: https://pennlinc.github.io/ModelArray/reference
   article: https://pennlinc.github.io/ModelArray/articles

reference/ModelArray-class.html

@@ -55,13 +55,16 @@ or
 
 - `scalars`:
 
-  A named list of DelayedArray matrices. Each matrix has elements as
-  rows and source files as columns.
+  A named list of
+  [DelayedArray::DelayedArray](https://rdrr.io/pkg/DelayedArray/man/DelayedArray-class.html)
+  matrices. Each matrix has elements as rows and source files as
+  columns.
 
 - `results`:
 
   A named list of analysis results. Each element is itself a list
-  containing at minimum `results_matrix` (a DelayedArray).
+  containing at minimum `results_matrix` (a
+  [DelayedArray::DelayedArray](https://rdrr.io/pkg/DelayedArray/man/DelayedArray-class.html)).
 
 - `path`: