hamster


  Point pattern of cell nuclei in hamster kidney, each nucleus classified as
  either `dividing' or `pyknotic'.
  A multitype point pattern.


datasets

spatial

Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.

Adrian Baddeley

spatstat

Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests

hamster function

An object of class <code>"ppp"</code>
  representing the point pattern of cell locations.
  Entries include
  <table><tr><td>
    <code>x</code> </td>
</tr><tr><td> Cartesian $x$-coordinate of cell </td>
</tr><tr><td>
    <code>y</code> </td>
</tr><tr><td> Cartesian $y$-coordinate of cell </td>
</tr></table>
  See <code><a rd-options="" href="/link/ppp.object?package=spatstat&version=1.48-0" data-mini-rdoc="spatstat::ppp.object">ppp.object</a></code> for details of the format.

Format

Dr W. A. Aherne, Department of Pathology, University of
  Newcastle-upon-Tyne, UK. Data supplied by Prof. Peter Diggle

Source

These data were presented and analysed by Diggle (1983, section 7.3). The data give the positions of the centres of the nuclei of certain
  cells in a histological
  section of tissue from a laboratory-induced metastasising lymphoma
  in the kidney of a hamster. The nuclei are classified as either
  "pyknotic" (corresponding to dying cells) or "dividing" (corresponding
  to cells arrested in metaphase, i.e. in the act of dividing). The
  background void is occupied by unrecorded, interphase cells in
  relatively large numbers. The sampling window is a square, originally about 0.25 mm square
  in real units, which has been rescaled to the unit square.

Notes

An object of class <code>"ppp"</code>
  representing the point pattern of cell locations.
  Entries include
  <table><tr><td>
    <code>x</code> </td>
</tr><tr><td> Cartesian $x$-coordinate of cell </td>
</tr><tr><td>
    <code>y</code> </td>
</tr><tr><td> Cartesian $y$-coordinate of cell </td>
</tr></table>
  See <code><a rd-options='' href='ppp.object'>ppp.object</a></code> for details of the format.

hamster: Aherne's hamster tumour data

Description

Usage

Arguments

Format

Source

Notes

References