hhh4_validation: Predictive Model Assessment for 'hhh4' Models

In surveillance: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Predictive Model Assessment for hhh4 Models

Description

The function oneStepAhead computes successive one-step-ahead predictions for a (random effects) HHH model fitted by hhh4. These can be inspected using the quantile, confint or plot methods. The associated scores-method computes a number of (strictly) proper scoring rules based on such one-step-ahead predictions; see Paul and Held (2011) for details. There are also calibrationTest and pit methods for oneStepAhead predictions.

Scores, calibration tests and PIT histograms can also be computed for the fitted values of an hhh4 model (i.e., in-sample/training data evaluation).

Usage

oneStepAhead(result, tp, type = c("rolling", "first", "final"),
             which.start = c("current", "final"),
             keep.estimates = FALSE, verbose = type != "final",
             cores = 1)

## S3 method for class 'oneStepAhead'
quantile(x, probs = c(2.5, 10, 50, 90, 97.5)/100, ...)
## S3 method for class 'oneStepAhead'
confint(object, parm, level = 0.95, ...)
## S3 method for class 'oneStepAhead'
plot(x, unit = 1, probs = 1:99/100,
     start = NULL, means.args = NULL, ...)

## assessment of "oneStepAhead" predictions
## S3 method for class 'oneStepAhead'
scores(x, which = c("logs", "rps", "dss", "ses"),
       units = NULL, sign = FALSE, individual = FALSE, reverse = FALSE, ...)
## S3 method for class 'oneStepAhead'
calibrationTest(x, units = NULL, ...)
## S3 method for class 'oneStepAhead'
pit(x, units = NULL, ...)

## assessment of the "hhh4" model fit (in-sample predictions)
## S3 method for class 'hhh4'
scores(x, which = c("logs", "rps", "dss", "ses"),
       subset = x$control$subset, units = seq_len(x$nUnit), sign = FALSE, ...)
## S3 method for class 'hhh4'
calibrationTest(x,
                subset = x$control$subset, units = seq_len(x$nUnit), ...)
## S3 method for class 'hhh4'
pit(x, subset = x$control$subset, units = seq_len(x$nUnit), ...)

Arguments

result	fitted hhh4 model (class "hhh4").
tp	numeric vector of length 2 specifying the time range in which to compute one-step-ahead predictions (for the time points tp[1]+1, ..., tp[2]+1). If a single time index is specified, it is interpreted as tp[1], and tp[2] is set to the penultimate time point of result$control$subset.
type	The default "rolling" procedure sequentially refits the model up to each time point in tp and computes the one-step-ahead predictions for the respective next time point. The alternative types are no true one-step-ahead predictions but much faster: "first" will refit the model for the first time point tp[1] only and use this specific fit to calculate all subsequent predictions, whereas "final" will just use result to calculate these. The latter case thus gives nothing else than a subset of result$fitted.values if the tp's are part of the fitted subset result$control$subset.
which.start	Which initial parameter values should be used when successively refitting the model to subsets of the data (up to time point tp[1], up to tp[1]+1, ...) if type="rolling"? Default ("current") is to use the parameter estimates from the previous time point, and "final" means to always use the estimates from result as initial values. Alternatively, which.start can be a list of start values as expected by hhh4, which then replace the corresponding estimates from result as initial values. This argument is ignored for “non-rolling” types.
keep.estimates	logical indicating if parameter estimates and log-likelihoods from the successive fits should be returned.
verbose	non-negative integer (usually in the range 0:3) specifying the amount of tracing information to output. During hhh4 model updates, the following verbosity is used: 0 if cores > 1, otherwise verbose-1 if there is more than one time point to predict, otherwise verbose.
cores	the number of cores to use when computing the predictions for the set of time points tp in parallel (with mclapply). Note that parallelization is not possible in the default setting type="rolling" and which.start="current" (use which.start="final" for this to work).
object	an object of class "oneStepAhead".
parm	unused (argument of the generic).
level	required confidence level of the prediction interval.
probs	numeric vector of probabilities with values in [0,1].
unit	single integer or character selecting a unit for which to produce the plot.
start	x-coordinate of the first prediction. If start=NULL (default), this is derived from x.
means.args	if a list (of graphical parameters for lines), the point predictions (from x$pred) are added to the plot.
x	an object of class "oneStepAhead" or "hhh4".
which	character vector determining which scores to compute. The package surveillance implements the following proper scoring rules: logarithmic score ("logs"), ranked probability score ("rps"), Dawid-Sebastiani score ("dss"), and squared error score ("ses"). The normalized SES ("nses") is also available but it is improper and hence not computed by default. It is possible to name own scoring rules in which. These must be functions of (x, mu, size), vectorized in all arguments (time x unit matrices) except that size is NULL in case of a Poisson model. See the available scoring rules for guidance, e.g., dss.
subset	subset of time points for which to calculate the scores (or test calibration, or produce the PIT histogram, respectively). Defaults to the subset used for fitting the model.
units	integer or character vector indexing the units for which to compute the scores (or the calibration test or the PIT histogram, respectively). By default, all units are considered.
sign	logical indicating if the function should also return sign(x-mu), i.e., the sign of the difference between the observed counts and corresponding predictions. This does not really make sense when averaging over multiple units with individual=FALSE.
individual	logical indicating if the individual scores of the units should be returned. By default (FALSE), the individual scores are averaged over all units.
reverse	logical indicating if the rows (time points) should be reversed in the result. The long-standing but awkward default was to do so for the oneStepAhead-method. This has changed in version 1.16.0, so time points are no longer reversed by default.
...	Unused by the quantile, confint and scores methods. The plot-method passes further arguments to the fanplot function, e.g., fan.args, observed.args, and key.args can be used to modify the plotting style. For the calibrationTest-method, further arguments are passed to calibrationTest.default, e.g., which to select a scoring rule. For the pit-methods, further arguments are passed to pit.default.

Value

oneStepAhead returns a list (of class "oneStepAhead") with the following components:

pred	one-step-ahead predictions in a matrix, where each row corresponds to one of the time points requested via the argument tp, and which has ncol(result$stsObj) unit-specific columns. The rownames indicate the predicted time points and the column names are identical to colnames(result$stsObj).
observed	matrix with observed counts at the predicted time points. It has the same dimensions and names as pred.
psi	in case of a negative-binomial model, a matrix of the estimated overdispersion parameter(s) at each time point on the internal -log-scale (1 column if "NegBin1", ncol(observed) columns if "NegBinM" or shared overdispersion). For a "Poisson" model, this component is NULL.
allConverged	logical indicating if all successive fits converged.

If keep.estimates=TRUE, there are the following additional elements:

coefficients	matrix of estimated regression parameters from the successive fits.
Sigma.orig	matrix of estimated variance parameters from the successive fits.
logliks	matrix with columns "loglikelihood" and "margll" with their obvious meanings.

The quantile-method computes quantiles of the one-step-ahead forecasts. If there is only one unit, it returns a tp x prob matrix, otherwise a tp x unit x prob array. The confint-method is a convenient wrapper with probs set according to the required confidence level.

The function scores computes the scoring rules specified in the argument which. If multiple units are selected and individual=TRUE, the result is an array of dimensions c(nrow(pred),length(units),5+sign) (up to surveillance 1.8-0, the first two dimensions were collapsed to give a matrix). Otherwise, the result is a matrix with nrow(pred) rows and 5+sign columns. If there is only one predicted time point, the first dimension is dropped in both cases.

The calibrationTest- and pit-methods are just convenient wrappers around the respective default methods.

Author(s)

Sebastian Meyer and Michaela Paul

References

Czado, C., Gneiting, T. and Held, L. (2009): Predictive model assessment for count data. Biometrics, 65 (4), 1254-1261. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/j.1541-0420.2009.01191.x")}

Paul, M. and Held, L. (2011): Predictive assessment of a non-linear random effects model for multivariate time series of infectious disease counts. Statistics in Medicine, 30 (10), 1118-1136. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/sim.4177")}

See Also

vignette("hhh4") and vignette("hhh4_spacetime")

Examples

### univariate salmonella agona count time series

data("salmonella.agona")
## convert from old "disProg" to new "sts" class
salmonella <- disProg2sts(salmonella.agona)

## generate formula for temporal and seasonal trends
f.end <- addSeason2formula(~1 + t, S=1, period=52)
model <- list(ar = list(f = ~1), end = list(f = f.end), family = "NegBin1")
## fit the model
result <- hhh4(salmonella, model)

## do sequential one-step-ahead predictions for the last 5 weeks
pred <- oneStepAhead(result, nrow(salmonella)-5, type="rolling",
                     which.start="final", verbose=FALSE)
pred
quantile(pred)
confint(pred)

## simple plot of the 80% one-week-ahead prediction interval
## and point forecasts
if (requireNamespace("fanplot"))
    plot(pred, probs = c(.1,.9), means.args = list())



## note: oneStepAhead(..., type="final") just means fitted values
stopifnot(identical(
    unname(oneStepAhead(result, nrow(salmonella)-5, type="final")$pred),
    unname(tail(fitted(result), 5))))


## compute scores of the one-step-ahead predictions
(sc <- scores(pred))

## the above uses the scores-method for "oneStepAhead" predictions,
## which is a simple wrapper around the default method:
scores(x = pred$observed, mu = pred$pred, size = exp(pred$psi))

## scores with respect to the fitted values are similar
(scFitted <- scores(result, subset = nrow(salmonella)-(4:0)))




## test if the one-step-ahead predictions are calibrated
calibrationTest(pred)  # p = 0.8746

## the above uses the calibrationTest-method for "oneStepAhead" predictions,
## which is a simple wrapper around the default method:
calibrationTest(x = pred$observed, mu = pred$pred, size = exp(pred$psi))

## we can also test calibration of the fitted values
## using the calibrationTest-method for "hhh4" fits
calibrationTest(result, subset = nrow(salmonella)-(4:0))


## plot a (non-randomized) PIT histogram for the predictions
pit(pred)

## the above uses the pit-method for "oneStepAhead" predictions,
## which is a simple wrapper around the default method:
pit(x = pred$observed, pdistr = "pnbinom", mu = pred$pred, size = exp(pred$psi))


### multivariate measles count time series
## (omitting oneStepAhead forecasts here to keep runtime low)

data("measlesWeserEms")

## simple hhh4 model with random effects in the endemic component
measlesModel <- list(
    end = list(f = addSeason2formula(~0 + ri(type="iid"))),
    ar = list(f = ~1),
    family = "NegBin1")
measlesFit <- hhh4(measlesWeserEms, control = measlesModel)

## assess overall (in-sample) calibration of the model, i.e.,
## if the observed counts are from the fitted NegBin distribution
calibrationTest(measlesFit) # default is DSS (not suitable for low counts)
calibrationTest(measlesFit, which = "logs") # p = 0.7238

## to assess calibration in the second year for a specific district
calibrationTest(measlesFit, subset = 53:104, units = "03452", which = "rps")
pit(measlesFit, subset = 53:104, units = "03452")


### For a more sophisticated multivariate analysis of
### areal time series of influenza counts - data("fluBYBW") -
### see the (computer-intensive) demo("fluBYBW") script:
demoscript <- system.file("demo", "fluBYBW.R", package = "surveillance")
#file.show(demoscript)

surveillance documentation built on Nov. 4, 2024, 3 a.m.