R: sTiles utils: streaming spy plots and graph<->mtx I/O

stiles.utils {INLA}

R Documentation

sTiles utils: streaming spy plots and graph<->mtx I/O

Description

Streaming sparsity-pattern plots and conversions between INLA graph files and MatrixMarket .mtx files. The spy plots stream the input file (never loading the full matrix), bin entries into a ⁠GRID x GRID⁠ grid, and render a log-density image. This makes them usable on matrices that would otherwise exhaust memory if read into a Matrix.

INLA graph files are autodetected as 0-based or 1-based by inspecting the first data row; override with base = 0L or base = 1L. MatrixMarket files use the standard 1-based coordinate convention.

inla.stiles.graph2mtx writes a symmetric MatrixMarket file. By default the diagonal is set to the node degree (matches the typical precision-matrix convention where Q[i,i] equals the sum of weights of incident edges, giving a diagonally-dominant Q with unit off-diagonals). Use diagonal = "one" for unit diagonals, or diagonal = "none" to omit the diagonal entirely.

Usage

inla.stiles.spy.mtx(
  file,
  out = NULL,
  GRID = 1000L,
  text = FALSE,
  colorbar = FALSE,
  palette = "grey",
  CHUNK = 2000000L
)

inla.stiles.spy.graph(
  file,
  out = NULL,
  GRID = 1000L,
  text = FALSE,
  colorbar = FALSE,
  palette = "grey",
  CHUNK = 100000L,
  base = NULL
)

inla.stiles.graph2mtx(
  graph_file,
  mtx_file,
  diagonal = c("degree", "one", "none"),
  base = NULL
)

inla.stiles.mtx2graph(mtx_file, graph_file, base = 0L, CHUNK = 2000000L)

Arguments

file

For inla.stiles.spy.mtx: path to a .mtx file. For inla.stiles.spy.graph: path to an INLA graph file.

out

Output PNG path. Defaults to the input path with extension replaced by .png.

GRID

Bin grid resolution (default 1000).

text

If TRUE, draw title and axis labels (default FALSE).

colorbar

If TRUE, draw a colorbar to the right (default FALSE).

palette

Colour palette: "grey" (default), "gray", "binary", "viridis", or any name accepted by hcl.colors().

CHUNK

Lines read per streaming chunk. Tune for very large files.

base

Index base for INLA graph files. NULL (default) auto-detects by peeking at the first data row.

graph_file

Path to an INLA graph file (ASCII).

mtx_file

Path to a MatrixMarket .mtx file.

diagonal

Diagonal value for inla.stiles.graph2mtx: "degree" (default), "one", or "none".

Value

The output file path (invisibly).

Author(s)

Esmail Abdul Fattah esmail.abdulfattah@kaust.edu.sa

Examples

## Not run: 
## spy a large MTX file (streamed, never fully loaded)
inla.stiles.spy.mtx("Q.mtx", "Q.png")

## spy an INLA graph file directly
inla.stiles.spy.graph("inla_graph_animal1", "animal.png")

## convert between formats (round-trips bit-identical up to neighbour order)
inla.stiles.graph2mtx("inla_graph_animal1", "animal.mtx")
inla.stiles.mtx2graph("animal.mtx",         "animal.graph")

## End(Not run)

[Package INLA version 26.06.08 Index]