inst/examples/bcar_examples_no_inla.R

In sujit-sahu/bmstdr: Bayesian Modeling of Spatio-Temporal Data with R

# Set the validation row numbers 
vs <- sample(nrow(engtotals), 5)
# Total number of iterations 
N <- 60
# Number of burn in iterations 
burn.in <- 10
# Number of thinning iterations
thin <- 1

# Set the model formula for binomial distribution based modeling 
f1 <- noofhighweeks ~ jsa + log10(houseprice) + log(popdensity) + sqrt(no2)
## Independent error logistic regression
M1 <- Bcartime(formula = f1, data = engtotals, family = "binomial",
    trials = engtotals$nweek, N = N, burn.in = burn.in, thin = thin,
    verbose = TRUE)
summary(M1)
# Leroux model
M1.leroux <- Bcartime(formula = f1, data = engtotals, scol = "spaceid",
    model = "leroux", W = Weng, family = "binomial", trials = engtotals$nweek,
    N = N, burn.in = burn.in, thin = thin)
summary(M1.leroux)
# BYM model
M1.bym <- Bcartime(formula = f1, data = engtotals, scol = "spaceid",
    model = "bym", W = Weng, family = "binomial", trials = engtotals$nweek,
    N = N, burn.in = burn.in, thin = thin, verbose = FALSE)
summary(M1.bym)

# Validation for the Leroux model
M1.leroux.v <- Bcartime(formula = f1, data = engtotals, scol = "spaceid",
    model = "leroux", W = Weng, family = "binomial", trials = engtotals$nweek,
    validrows = vs, N = N, burn.in = burn.in, thin = thin, verbose = FALSE)
summary(M1.leroux.v)


## Poisson Distribution based models ####################################
# Model formula
f2 <- covid ~ offset(logEdeaths) + jsa + log10(houseprice) + log(popdensity) +
    sqrt(no2)

# Independent error Poisson regression
M2 <- Bcartime(formula = f2, data = engtotals, family = "poisson", N = N,
    burn.in = burn.in, thin = thin, verbose = FALSE)
summary(M2)
## Poisson regression with Leroux Model
M2.leroux <- Bcartime(formula = f2, data = engtotals, scol = "spaceid",
    model = "leroux", family = "poisson", W = Weng, N = N, burn.in = burn.in,
    thin = thin, verbose = FALSE)
summary(M2.leroux)
# Poisson regression with BYM Model
M2.bym <- Bcartime(formula = f2, data = engtotals, scol = "spaceid",
    model = "bym", family = "poisson", W = Weng, N = N, burn.in = burn.in,
    thin = thin)
summary(M2.bym)


## Gaussian distribution based models  ###############
f3 <- sqrt(no2) ~ jsa + log10(houseprice) + log(popdensity)

# Independent error model 
M3 <- Bcartime(formula = f3, data = engtotals, family = "gaussian", N = N,
    burn.in = burn.in, thin = thin, verbose = FALSE)
summary(M3)
# Leroux model 
M3.leroux <- Bcartime(formula = f3, data = engtotals, scol = "spaceid",
    model = "leroux", family = "gaussian", W = Weng, N = N, burn.in = burn.in,
    thin = thin, verbose = FALSE)
summary(M3.leroux)

## Validation
M3.leroux.v <- Bcartime(formula = f3, data = engtotals, scol = "spaceid",
    model = "leroux", family = "gaussian", W = Weng, N = N, burn.in = burn.in,
    thin = thin, validrows = vs, verbose = FALSE)
summary(M3.leroux.v)

\donttest{
## Spatio-temporal modeling ##################################################
head(engdeaths)
dim(engdeaths)
colnames(engdeaths)
vs <- sample(nrow(engdeaths), 5)


## Binomial distribution
nweek <- rep(1, nrow(engdeaths))
f1 <- highdeathsmr ~ jsa + log10(houseprice) + log(popdensity)

M1st_linear <- Bcartime(formula = f1, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", trials = nweek, W = Weng, model = "linear",
    family = "binomial", package = "CARBayesST", N = N, burn.in = burn.in,
    thin = thin, verbose = TRUE)
summary(M1st_linear)
M1st_sepspat <- Bcartime(formula = f1, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", trials = nweek, W = Weng, model = "sepspatial",
    family = "binomial", package = "CARBayesST", N = N, burn.in = burn.in,
    thin = thin, verbose = FALSE)
summary(M1st_sepspat)
M1st_ar <- Bcartime(formula = f1, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", trials = nweek, W = Weng, model = "ar", AR = 1,
    family = "binomial", package = "CARBayesST", N = N, burn.in = burn.in,
    thin = thin, verbose = FALSE)
summary(M1st_ar)
# Model validation
M1st_ar.v <- Bcartime(formula = f1, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", trials = nweek, W = Weng, model = "ar", AR = 1,
    family = "binomial", package = "CARBayesST", N = N, burn.in = burn.in,
    thin = thin, validrows = vs, verbose = FALSE)
summary(M1st_ar.v)


## Spatio temporal Poisson models###################################
colnames(engdeaths)
f2 <- covid ~ offset(logEdeaths) + jsa + log10(houseprice) + log(popdensity) +
    n0

M2st_linear <- Bcartime(formula = f2, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", W = Weng, model = "linear", family = "poisson",
    package = "CARBayesST", N = N, burn.in = burn.in, thin = thin,
    verbose = FALSE)
summary(M2st_linear)
M2st_anova <- Bcartime(formula = f2, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", W = Weng, model = "anova", family = "poisson",
    package = "CARBayesST", N = N, burn.in = burn.in, thin = thin,
    verbose = FALSE)
summary(M2st_anova)
M2st_anova_nointer <- Bcartime(formula = f2, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", W = Weng, model = "anova", interaction = FALSE,
    family = "poisson", package = "CARBayesST", N = N, burn.in = burn.in,
    thin = thin, verbose = FALSE)
summary(M2st_anova_nointer)
M2st_sepspat <- Bcartime(formula = f2, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", W = Weng, model = "sepspatial", family = "poisson",
    package = "CARBayesST", N = N, burn.in = burn.in, thin = thin,
    verbose = FALSE)
summary(M2st_sepspat)
M2st_ar <- Bcartime(formula = f2, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", W = Weng, model = "ar", AR = 1, family = "poisson",
    package = "CARBayesST", N = N, burn.in = burn.in, thin = thin,
    verbose = FALSE)
summary(M2st_ar)
M2st_ar.v <- Bcartime(formula = f2, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", W = Weng, model = "ar", family = "poisson",
    package = "CARBayesST", N = N, burn.in = burn.in, thin = thin,
    validrows = vs, verbose = FALSE)
M2st_anova.v <- Bcartime(formula = f2, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", W = Weng, model = "anova", family = "poisson",
    package = "CARBayesST", N = N, burn.in = burn.in, thin = thin,
    validrows = vs, verbose = FALSE)
summary(M2st_ar.v)
summary(M2st_anova.v)


## Spatio-temporal Normal models ###############################
colnames(engdeaths)
f3 <- sqrt(no2) ~ jsa + log10(houseprice) + log(popdensity)

M3st_linear <- Bcartime(formula = f3, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", W = Weng, model = "linear", family = "gaussian",
    package = "CARBayesST", N = N, burn.in = burn.in, thin = thin,
    verbose = FALSE)
summary(M3st_linear)
M3st_anova <- Bcartime(formula = f3, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", W = Weng, model = "anova", family = "gaussian",
    package = "CARBayesST", N = N, burn.in = burn.in, thin = thin,
    verbose = FALSE)
summary(M3st_anova)
M3st_anova_nointer <- Bcartime(formula = f3, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", W = Weng, model = "anova", interaction = FALSE,
    family = "gaussian", package = "CARBayesST", N = N, burn.in = burn.in,
    thin = thin, verbose = FALSE)
summary(M3st_anova_nointer)
M3st_ar <- Bcartime(formula = f3, data = engdeaths, scol = "spaceid",
    tcol = "Weeknumber", W = Weng, model = "ar", AR = 2, family = "gaussian",
    package = "CARBayesST", N = N, burn.in = burn.in, thin = thin,
    verbose = FALSE)
summary(M3st_ar)

}