The function smoothDirect replaces the previous function name fitINLA (before version 1.0.0).
Usage
smoothDirect(
data,
Amat,
formula = NULL,
time.model = c("rw1", "rw2", "ar1")[2],
st.time.model = NULL,
year_label,
year_range = c(1980, 2014),
is.yearly = TRUE,
m = 5,
type.st = 1,
survey.effect = FALSE,
hyper = c("pc", "gamma")[1],
pc.u = 1,
pc.alpha = 0.01,
pc.u.phi = 0.5,
pc.alpha.phi = 2/3,
pc.u.cor = 0.7,
pc.alpha.cor = 0.9,
pc.st.u = NA,
pc.st.alpha = NA,
control.compute = list(dic = TRUE, mlik = TRUE, cpo = TRUE, openmp.strategy =
"default", config = TRUE),
control.inla = list(strategy = "adaptive", int.strategy = "auto"),
control.fixed = list(),
verbose = FALSE,
geo = NULL,
rw = NULL,
ar = NULL,
options = NULL
)
fitINLA(
data,
Amat,
formula = NULL,
time.model = c("rw1", "rw2", "ar1")[2],
st.time.model = NULL,
year_label,
year_range = c(1980, 2014),
is.yearly = TRUE,
m = 5,
type.st = 1,
survey.effect = FALSE,
hyper = c("pc", "gamma")[1],
pc.u = 1,
pc.alpha = 0.01,
pc.u.phi = 0.5,
pc.alpha.phi = 2/3,
pc.u.cor = 0.7,
pc.alpha.cor = 0.9,
pc.st.u = NA,
pc.st.alpha = NA,
control.compute = list(dic = TRUE, mlik = TRUE, cpo = TRUE, openmp.strategy =
"default", config = TRUE),
control.inla = list(strategy = "adaptive", int.strategy = "auto"),
control.fixed = list(),
verbose = FALSE,
geo = NULL,
rw = NULL,
ar = NULL,
options = NULL
)Arguments
- data
Combined dataset
- Amat
Adjacency matrix for the regions
- formula
INLA formula. See vignette for example of using customized formula.
- time.model
Model for the main temporal trend, can be rw1, rw2, or ar1. ar1 is not implemented for yearly model with period data input. Default to be rw2. For ar1 main effect, a linear slope is also added with time scaled to be between -0.5 to 0.5, i.e., the slope coefficient represents the total change between the first year and the last year in the projection period on the logit scale.
- st.time.model
Temporal component model for the interaction term, can be rw1, rw2, or ar1. ar1 is not implemented for yearly model with period data input. Default to be the same as time.model unless specified otherwise. For ar1 interaction model, region-specific random slopes are currently not implemented.
- year_label
string vector of year names
- year_range
Entire range of the years (inclusive) defined in year_label.
- is.yearly
Logical indicator for fitting yearly or period model.
- m
Number of years in each period.
- type.st
type for space-time interaction
- survey.effect
logical indicator whether to include a survey iid random effect. If this is set to TRUE, there needs to be a column named 'survey' in the input data frame. In prediction, this random effect term will be set to 0. Notice this survey effect is implemented according to the Merter et al. (2015) model, and differently compared to the smoothCluster() function.
- hyper
which hyperpriors to use. Default to be using the PC prior ("pc").
- pc.u
hyperparameter U for the PC prior on precisions.
- pc.alpha
hyperparameter alpha for the PC prior on precisions.
- pc.u.phi
hyperparameter U for the PC prior on the mixture probability phi in BYM2 model.
- pc.alpha.phi
hyperparameter alpha for the PC prior on the mixture probability phi in BYM2 model.
- pc.u.cor
hyperparameter U for the PC prior on the autocorrelation parameter in the AR prior, i.e. Prob(cor > pc.u.cor) = pc.alpha.cor.
- pc.alpha.cor
hyperparameter alpha for the PC prior on the autocorrelation parameter in the AR prior.
- pc.st.u
hyperparameter U for the PC prior on precisions for the interaction term.
- pc.st.alpha
hyperparameter alpha for the PC prior on precisions for the interaction term.
- control.compute
list of options to be passed to control.compute() in the inla() function. The default argument saves the internal objects created by INLA for posterior sampling later. If the fitted object is too large in size and there is no need to perform joint posterior sampling from the model (only used in benchmarking), this argument can be set to
control.compute = list(config = FALSE)to reduce the size of the fitted object.- control.inla
list of options to be passed to control.inla() in the inla() function. Default to the "adaptive" integration strategy.
- control.fixed
list of options to be passed to control.fixed() in the inla() function.
- verbose
logical indicator to print out detailed inla() intermediate steps.
- geo
Deprecated.
- rw
Deprecated.
- ar
Deprecated.
- options
Deprecated.
References
Li, Z., Hsiao, Y., Godwin, J., Martin, B. D., Wakefield, J., Clark, S. J., & with support from the United Nations Inter-agency Group for Child Mortality Estimation and its technical advisory group. (2019). Changes in the spatial distribution of the under-five mortality rate: Small-area analysis of 122 DHS surveys in 262 subregions of 35 countries in Africa. PloS one, 14(1), e0210645.
Mercer, L. D., Wakefield, J., Pantazis, A., Lutambi, A. M., Masanja, H., & Clark, S. (2015). Space-time smoothing of complex survey data: small area estimation for child mortality. The annals of applied statistics, 9(4), 1889.
Examples
if (FALSE) { # \dontrun{
years <- levels(DemoData[[1]]$time)
# obtain direct estimates
data_multi <- getDirectList(births = DemoData, years = years,
regionVar = "region", timeVar = "time", clusterVar = "~clustid+id",
ageVar = "age", weightsVar = "weights", geo.recode = NULL)
data <- aggregateSurvey(data_multi)
# national model
years.all <- c(years, "15-19")
fit1 <- smoothDirect(data = data, Amat = NULL,
year_label = years.all, year_range = c(1985, 2019),
time.model = 'rw2', m = 5, control.compute = list(config =TRUE))
out1 <- getSmoothed(fit1)
plot(out1)
# subnational model
fit2 <- smoothDirect(data = data, Amat = DemoMap$Amat,
year_label = years.all, year_range = c(1985, 2019),
time.model = 'rw2', m = 5, type.st = 4)
out2 <- getSmoothed(fit2)
plot(out2)
# subnational space-only model for one period
fit3 <- smoothDirect(data = subset(data, years == "10-14"),
time.model = NULL, Amat = DemoMap$Amat)
out3 <- getSmoothed(fit3)
plot(out3, plot.CI = TRUE)
} # }