spatial.pred.binomial.Bayes: Bayesian spatial predictions for the binomial logistic model

In barryrowlingson/PrevMap: Geostatistical Modelling of Spatially Referenced Prevalence Data

Description

This function performs Bayesian spatial prediction for the binomial logistic model.

Usage

spatial.pred.binomial.Bayes(object, grid.pred, predictors = NULL,
  type = "marginal", scale.predictions = c("logit", "prevalence", "odds"),
  quantiles = c(0.025, 0.975), standard.errors = FALSE, thresholds = NULL,
  scale.thresholds = NULL, messages = TRUE)

Arguments

object	an object of class "Bayes.PrevMap" obtained as result of a call to binomial.logistic.Bayes.
grid.pred	a matrix of prediction locations.
predictors	a data frame of the values of the explanatory variables at each of the locations in grid.pred; each column correspond to a variable and each row to a location. Warning: the names of the columns in the data frame must match those in the data used to fit the model. Default is predictors=NULL for models with only an intercept.
type	a character indicating the type of spatial predictions: type="marginal" for marginal predictions or type="joint" for joint predictions. Default is type="marginal". In the case of a low-rank approximation only joint predictions are available.
scale.predictions	a character vector of maximum length 3, indicating the required scale on which spatial prediction is carried out: "logit", "prevalence" and "odds". Default is scale.predictions=c("logit","prevalence","odds").
quantiles	a vector of quantiles used to summarise the spatial predictions.
standard.errors	logical; if standard.errors=TRUE, then standard errors for each scale.predictions are returned. Default is standard.errors=FALSE.
thresholds	a vector of exceedance thresholds; default is NULL.
scale.thresholds	a character value ("logit", "prevalence" or "odds") indicating the scale on which exceedance thresholds are provided.
messages	logical; if messages=TRUE then status messages are printed on the screen (or output device) while the function is running. Default is messages=TRUE.

Value

A "pred.PrevMap" object list with the following components: logit; prevalence; odds; exceedance.prob, corresponding to a matrix of the exceedance probabilities where each column corresponds to a specified value in thresholds; samples, corresponding to a matrix of the posterior samples at each prediction locations for the linear predictor of the linear model; grid.pred prediction locations. Each of the three components logit, prevalence and odds is also a list with the following components:

predictions: a vector of the predictive mean for the associated quantity (logit, odds or prevalence).

standard.errors: a vector of prediction standard errors (if standard.errors=TRUE).

quantiles: a matrix of quantiles of the resulting predictions with each column corresponding to a quantile specified through the argument quantiles.

Author(s)

Emanuele Giorgi [e-mail]

Peter J. Diggle [e-mail]

barryrowlingson/PrevMap documentation built on May 11, 2019, 6:24 p.m.