sim.eco: Simulate ecological data and samples of individual-level data

Description Usage Arguments Value Author(s) See Also Examples

View source: R/simul.R

Description

Simulate ecological data and samples of individual-level data from an individual-level logistic regression model, depending on given binary, categorical or normally-distributed covariates.

Usage

1
2
sim.eco(N, ctx, binary, m, data=NULL, S=0, cross=NULL, covnames, ncats,
mu, alpha.c=0, alpha=0, beta=0, sig=0, strata, pstrata, isam = 0)

Arguments

N

Vector of population sizes, one for each group.

ctx

A model formula containing names of group-level, or contextual, covariates on the right-hand side.

binary

A model formula containing names of individual-level binary covariates on the right-hand side.

data

Data frame containing the group-level variables given in ctx. It should also contain the variables given in binary, interpreted as proportions of individuals exposed to each of the binary covariates.

m

A data frame with length(N) rows, containing the within-area means of a set of normally-distributed continuous covariates.

S

A data frame with length(N) rows, containing the within-area standard deviations of a set of normally-distributed continuous covariates. For the moment they are assumed to be independent.

cross

A matrix of cross-classifications of individuals in the area between categories of multiple binary or categorical covariates, defined in the same way as in eco. If this is not supplied, the binary covariates are assumed to be independent, and the probability of an individual having a certain combination of covariates is calculated as the product of the relevant marginal probabilities.

covnames

Vector of names of the covariates, if cross is supplied. Otherwise the names are taken from binary.

ncats

Numeric vector of the number of levels of the covariates used in cross.

mu

Regression intercept on the logit scale.

alpha.c

Vector of coefficients for the group-level covariates in the underlying logistic regression, corresponding to the columns of ctx.

alpha

Vector of coefficients for the individual-level binary covariates, corresponding to the columns of phi. Interactions are not currently supported.

beta

Vector of coefficients for the individual-level continuous covariates, corresponding to the columns of m or S. Interactions are not currently supported.

sig

Random-effects standard deviation.

strata

A matrix with rows representing groups, and columns representing strata occupancy probabilities.

pstrata

A vector with one element for each stratum, giving the assumed baseline outcome probabilities for the strata. The logits of pstrata are used as offsets in the logistic regression.

isam

Number of individuals per group to retain in the individual-level data.

Value

A list with components:

y

The simulated aggregate-level response, one for each group.

idata

A data frame containing the retained individual-level samples. The grouping indicator (with values 1 to length(N)) is named group, the response variable is named y, the group-level covariates are copied from ctx, and the binary covariates, with values 1 or 0, are individual-level equivalents of the proportions given in phi.

Author(s)

C. H. Jackson chris.jackson@mrc-bsu.cam.ac.uk

See Also

eco

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
N <- rep(50, 20)
ctx <- cbind(deprivation = rnorm(20), mean.income = rnorm(20))
phi <- cbind(nonwhite = runif(20), smoke = runif(20))
sim.df <- as.data.frame(cbind(ctx, phi))
mu <- qlogis(0.05)  ## Disease with approximate 5% prevalence
## Odds ratios for group-level deprivation and mean imcome
alpha.c <- c(1.01, 1.02)
## Odds ratios for individual-level ethnicity and smoking
alpha <- c(1.5, 2) 
sim.eco(N, ctx = ~ deprivation + mean.income, binary = ~ nonwhite +
        smoke, data=sim.df, mu=mu, alpha.c=alpha.c, alpha=alpha)
sim.eco(N, ctx = ~ deprivation + mean.income, binary = ~ nonwhite +
        smoke, data=sim.df, mu=mu, alpha.c=alpha.c, alpha=alpha, isam=3)

ecoreg documentation built on March 26, 2020, 7:39 p.m.