Changelog
surveillance 1.21.0 (20230314)
surveillance no longer relies on the maptools package:
unionSpatialPolygons()
withmethod = "gpclib"
is deprecated and now uses the default method with a warning.Long unused
scale.gpc.poly()
andinside.gpc.poly()
are deprecated; the unused and undocumenteddiameter.gpc.poly()
method has been removed.nbOrder()
has been reimplemented: it is now more efficient and no longer depends on spdep. Furthermore, it now defaults tomaxlag = Inf
; the historical defaultmaxlag = 1
was barely useful. It no longer messages (about the range of the detected orders).Accommodate the current evolution of sp: sf is suggested and some examples are now conditionalized on its availability.
Printing
"sts"
objects with a map now shows the first row of the attached data (if present) instead of the object summary.stsplot_spacetime()
is formally deprecated; it has long been superseded bystsplot_space()
and ananimate()
method for"sts"
objects.
surveillance 1.20.3 (20221114)

vignette("monitoringCounts")
now uses knitr as its engine to work around Bug 18318.
surveillance 1.20.2 (20221031)
NEW FEATURES

plotHHH4_fitted()
can now produce simple (unformatted) time indexes if argumentxaxis = NA
.
MINOR CHANGES
Various documentation improvements, including an example for
predict.hhh4()
.intensityplot.twinstim()
no longer depends on package maptools.
BUG FIXES
hhh4()
now warns about interaction terms in model formulae. These are not implemented and were silently ignored previously.Fixed a memory leak in
algo.twins()
; note that this old experimental MCMC implementation for a twocomponent epidemic model may be removed in future versions of the package.
surveillance 1.20.1 (20220713)
BUG FIXES
ks.plot.unif()
: accommodate toNO_S_TYPEDEFS
in R >= 4.3.0.boda()
withsamplingMethod="marginals"
gave allNA
upperbounds in INLA >= 21.07.10.boda()
now also works around a scoping issue (withE
) in recent versions of INLA that led to wrongly scaled upperbounds.
surveillance 1.20.0 (20220215)
NEW FEATURES
plotHHH4_season()
gained aperiod
argument to support harmonics with periods longer than the frequency of the"sts"
object.stsplot_space()
now supports passing acol
argument tospplot()
to change the colour of the polygon lines.plotHHH4_fitted()
can now handle time series with missing values.
MINOR CHANGES
If the NelderMead optimizer is used for the variance parameters in
hhh4()
, it is now limited to 500 (not 300) iterations by default (consistent with the default inoptim()
).Printing an
"sts"
object now omits theneighbourhood
component if that was not set (allNA
prototype).simulate.hhh4(..., simplify = TRUE)
now consistently returns a 3d array (nTime x nUnit x nsim), even fornsim = 1
(for which plotting now works).The default legend in
stsplot_time1()
now only includes plotted elements.wrap.algo()
no longer prints progress when there is only one area.summary.hhh4()
now prints the number of excluded observations (due to missingness), if any.
BUG FIXES
The
print
method forsummary.hhh4()
did not apply thedigits
argument to the coefficient matrix. Furthermore, printing of estimated variance parameters now adheres to significantdigits
as documented.The
[
method for the"hhh4sims"
class was not registered and thus only available internally. Arraylike subsetting of simulated counts now retains the class.farringtonFlexible()
with activatedpopulationOffset
(nondefault) always used the population data of the first time series in the fitting step while iterating over a multivariate"sts"
object.plotHHH4_ri(..., exp = TRUE)
failed to use a logscale color axis if furthercolorkey
options were passed in a list. The (default) color breaks could fail to span the range of the data without warning (resulting in unfilled polygons). This is now checked and the default breaks are now equally spaced on the logscale.stsplot_time1()
did not passlty
topolygon()
andlwd
tolegend()
.rps()
was wrong for distributions close to a point mass at zero, e.g., formu = 1e3
andx >= 4
. It is now also protected against wide (quasicontinuous) NegBin distributions that would consume too much memory with discrete RPS calculation (returning a missing value with a warning). [both issues spotted by F. Rousseu]Plots of legacy
"disProg"
and"survRes"
objects are now generated via internaldisProg2sts()
conversion andstsplot_time()
. This fixes their xaxis labels for the defaultxaxis.years=TRUE
. The obsolete argumentsstartyear
andfirstweek
are now ignored with a warning.The default legend of
stsplot_time1()
did not show the fill color in the nondefault case!is.na(col[1])
.Multivariate
hhh4()
with neighbourhood component treatedNA
counts as zero when calculating the weighted sum over units. A missing count at t1 in any unit now givesNA
values for the neighbourhood terms of all units at time t, thus reducingnobs()
.
DEPRECATED AND DEFUNCT
create.disProg()
is deprecated. Methods for legacy"disProg"
objects are kept for backwards compatibility, but new projects should usests()
.The longdeprecated
qlomax()
implementation has been removed.
surveillance 1.19.1 (20210330)
DOCUMENTATION
 The project website at https://surveillance.RForge.Rproject.org/ has been overhauled using pkgdown.
BUG FIXES
The
CRS
ofdata(imdepi)
anddata(measlesWeserEms)
have been updated viasp
’srebuild_CRS()
to avoid warnings when rgdal is loaded with new PROJ and GDAL libraries.simEpidataCS()
now internally resets the CRS (temporary), which avoids spurious warnings and also reduces its runtime by about 25%.Fix encoding error in
vignette("twinstim")
for CRAN’s nonUTF8 Linux test machine.This version of surveillance (formally) requires the new spatstat umbrella package to avoid collisions of old spatstat and its new subpackages (we only use spatstat.geom). The spatstat dependence will be dropped in the future.
The
epoch<
replacement method for"sts"
objects now accepts a"Date"
vector. The standard plots may give nicer xaxis annotation if indexed by dates. See thexaxis.*
arguments ofstsplot_time()
.tidy.sts()
(and thusautoplot.sts()
) failed for dateindexed"sts"
objects with nonstandard frequencies. [spotted by Junyi Lu]
surveillance 1.19.0 (20210129)
NEW FEATURES
The
nowcast()
function withmethod="bayes.trunc.ddcp"
now adds support for negative binomial response distribution instead of Poisson. Furthermore, additional components of the design matrix for the discrete time survival model can be provided, which allows the inclusion of, e.g., day of the week effects. Finally, the order of the polynomial created by the changepoints in the discrete time survival model can now be specified. For further details see the work of Guenther et al. (2020) about nowcasting the Covid19 outbreak in Bavaria, Germany.animate.sts()
can position thetimeplot
on other sides of the map.
MINOR CHANGES
The weighted sum in the
ne
ighbourhood component ofhhh4()
models is computed more efficiently.simEpidataCS()
(and thussimulate.twinstim()
) uses a slightly more efficient location sampler for models withsiaf = siaf.constant()
. Simulation results will differ from previous package versions even if the same randomseed
is used.The default
main
title forstsplot_space()
now uses the ISO yearweek format for weekly"sts"
data.
BUG FIXES
Bug fix in the
farringtonFlexible()
function, which for the argumentthresholdMethod=="nbPlugin"
andthresholdMethod=="muan"
unfortunately computed the limit as an(1alpha/2)
prediction interval instead of the documented(1alpha)
prediction interval. This affects four threshold values in Table 2 ofvignette("monitoringCounts")
. The default method"delta"
worked as expected.In
hhh4()
models without AR component, the matrix of fitted values could lack column names.Experimental timevarying neighbourhood weights in
hhh4()
were indexed differently in model fitting and in thesimulate()
method (undocumented behaviour). Both now use the latter variant, where the mean at time t uses products of weights at time t and observed counts at time t1. [reported by Johannes Bracher]For weekly
sts
indexed viastart
andfreq=52
,epoch(sts, as.Date=TRUE)
now interprets thestart
week according to ISO 8601. For example,start = c(2020, 5)
corresponds to 20200127, not 20200203. This affectsas.xts.sts()
and the time plot inanimate.sts()
.stsplot_space()
automatically extends manual color breaks (at
), if the intervals do not cover the data range.simEndemicEvents()
and thusepitest(..., method="simulate")
are no longer slowed down by intermediateCRS()
computations.
PACKAGE INFRASTRUCTURE
Removed unused rmapshaper from “Suggests” and moved xts to “Enhances” (used only for
as.xts.sts
).Switched testing framework from (nowadays heavy) testthat to tinytest. Together with moving ggplot2 to “Enhances” (used only for
autoplot.sts
) — and only then — this switch further reduces the total number of required packages for a complete check (i.e., installing withdependencies = TRUE
) in a factoryfresh R environment from 119 to 94.spatstat was split into several subpackages, of which we only need to import spatstat.geom. This new package requires
R >= 3.5.0
, though.surveillance now requires
R >= 3.6.0
.
surveillance 1.18.0 (20200318)
NEW FEATURES
New spatial interaction function for
twinstim()
:siaf.exponential()
implements the exponential kernel f(x) = exp(x/σ), which is a useful alternative if the twoparameter powerlaw kernel is not identifiable.The
plot
type"maps"
for"hhh4"
fits,plotHHH4_maps()
, now allows for mapspecific color keys viazmax = NA
(useful forprop = TRUE
).
BUG FIXES
The
nowcast()
function now also works formethod="bayes.trunc.ddcp"
method when the number of breakpoints is greater than 1.The
amplitudeShift
transformation for sinecosine coefficient pairs in thesummary
of multivariate"hhh4"
models was incorrect in the rare case that the model used unitspecific seasonal terms (addSeason2formula
withlength(S) > 1
).
DEPRECATED AND DEFUNCT
 The original
algo.hhh()
implementation of the HHH model has been removed from the package. The functionhhh4()
provides an improved and much extended implementation since 2012.
surveillance 1.17.3 (20191216)
BUG FIXES
The
head()
method for"epidataCS"
objects did not work with a negativen
argument.Fix for
"matrix"
changes in Rdevel.
surveillance 1.17.2 (20191111)
MINOR CHANGES
 For multivariate time series,
sts()
now checks for mismatches in column names of supplied matrices (observed
,population
,neighbourhood
, …). This is to catch input where the units (columns) are ordered differently in different slots, which would flaw subsequent analyses.
BUG FIXES

simulate.twinSIR()
ignored theatRiskY
indicator of the underlying"epidata"
, so always assumed a completely susceptible population. Initially infectious individuals are now inherited. For the previous behaviour, adjust the supplieddata
viadata$atRiskY < 1
.
surveillance 1.17.1 (20190913)
NEW FEATURES
 New oneparameter powerlaw kernel
siaf.powerlaw1()
with fixedsigma = 1
. Useful ifsigma
is difficult to estimate withsiaf.powerlaw()
.
BUG FIXES
pit()
’s defaultylab
was wrong (default are densities not relative frequencies).R0()
for"twinstim"
fits with specifiednewevents
now handles levels of epidemic factor variables automatically via the newxlevels
attribute stored in the fitted model.Some S3 methods for the
"sts"
class are now formally registered and identical to the established S4 methods.Minor additions and fixes in the package documentation.
DEPRECATED AND DEFUNCT

hcl.colors()
, exported since 1.14.0, has been renamed.hcl.colors()
and is now internal again, to avoid a name clash with R’s own such function introduced in R 3.6.0.
surveillance 1.17.0 (20190222)
NEW FEATURES
W_powerlaw(..., from0 = TRUE)
enables more parsimonioushhh4
models in that the powerlaw weights are modified to include the autoregressive (0distance) case (seevignette("hhh4_spacetime")
). The unstructured distance weightsW_np()
gainedfrom0
support as well.sts()
creation can now handleepoch
arguments of classDate
directly.The
ranef()
method for"hhh4"
fits gained a logical argumentintercept
to extract the unitspecific intercepts of the loglinear predictors instead of the default zeromean deviations around the fixed intercepts. The correspondingplot
method (type="ri"
) gained an argumentexp
: if set toTRUE
random effects areexp
transformed and thus show multiplicative effects. [based on feedback by Tim Pollington]
MINOR CHANGES
W_np()
’s argumentto0
has been renamed totruncate
. The old name still works but is deprecated.plotHHH4_ri()
now usescm.colors(100)
ascol.regions
, and 0centered color breaks by default.The help pages of
twinSIR()
and related functions now give examples based ondata("hagelloch")
instead of using the toy datasetdata("fooepidata")
. The latter is now obsolete and will be removed in future versions of the package.The elements of the
control
list stored in the result ofalgo.farrington()
are now consistently ordered as in the defaultcontrol
argument.
BUG FIXES
Using negative indices to exclude time points from an
"sts"
object (e.g.,x[1,]
) is now supported and equivalent to the corresponding subset expression of retained indexes (x[2:nrow(x),]
) in resetting thestart
andepoch
slots. [reported by Johannes Bracher]For weekly
"sts"
data withepochAsDate=TRUE
, theas.data.frame()
method computedfreq
by"%Y"
year instead of by"%G"
year, which was inconsistent with theepochInPeriod
variable.For nonweekly
"sts"
data withepochAsDate=TRUE
,year()
as well as theyear
column of thetidy.sts()
output corresponded to the ISO weekbased year. It now gives the calendar year.sts_creation()
hardcodedstart = c(2006, 1)
.aggregate()
ing an"sts"
object over time now recomputes fractions from the cumulated population values if and only if this is nomultinomialTS
and already contains population fractions. The same rule holds when subsetting units of an"sts"
object. Theaggregate
method previously failed to recompute fractions in some cases.For
farringtonFlexible()
with multivariate time series, only the last unit had stored the additional control items (exceedence scores, pvalues, …), all others were 0. [reported by Johannes Bracher]The supplementary pvalues returned by
farringtonFlexible()
incontrol$pvalue
were wrong for the default approach, wherethresholdMethod="delta"
(the original Farrington method) and a power transformation was applied to the data (powertrans != "none"
). Similarly,algo.farrington()
returned wrong predictive probabilities incontrol$pd[,1]
if a power transformation was used. [reported by Lore Merdrignac]The
control
argument list ofalgo.farrington()
as stated in the formal function definition was incomplete (plot
was missing) and partially out of sync with the default values that were actually set inside the function (b=5
andalpha=0.05
). This has been fixed. Results ofalgo.farrington()
would only be affected if the function was called without anycontrol
options (which is hardly possible). So this can be regarded as a documentation error. The formalcontrol
list of thefarrington()
wrapper function has been adjusted accordingly.The
control
argument lists offarringtonFlexible()
andbodaDelay()
as stated in the formal function definitions were partially out of sync with respect to the following default values that were actually set inside these functions:b=5
(not 3),alpha=0.05
(not 0.01),pastWeeksNotIncluded=w
(not 26), and, forbodaDelay()
only,delay=FALSE
(notTRUE
). This has been fixed. Results would only be affected if the functions were called without anycontrol
options (which is hardly possible). So this can be regarded as a documentation error.pairedbinCUSUM()
did not properly subset thests
object if arange
was specified, and forgot to store thecontrol
arguments in the result.wrap.algo()
now aborts if the monitored range is not supplied as a numeric vector.In
vignette("monitoringCounts")
: several inconsistencies between code and output have been fixed.epidataCS2sts()
no longer transfers thestgrid$BLOCK
indices to theepoch
slot of the resulting"sts"
object (to avoidepoch[1] != 1
scenarios).The
ranef()
matrix extracted from fitted"hhh4"
models could have wrong column names.
DEPRECATED AND DEFUNCT
 Several ancient functions deprecated in 1.16.1 are now defunct:
compMatrix.writeTable()
,makePlot()
,test()
,testSim()
,readData()
(the raw txt files have been removed as well),correct53to52()
,enlargeData()
,toFileDisProg()
.
surveillance 1.16.2 (20180724)
MINOR CHANGES
autoplot.sts()
gained awidth
argument to adjust the bar width, which now defaults to 7 for weekly time series (previously was 90% of that so there were gaps between the bars)."epidataCS"
generation now (again) employs spatstat’sbdist.points()
, which has been accelerated in version 1.560. If you use thetwinstim()
related modelling part of surveillance, you are thus advised to update your spatstat installation.The
boda()
examples invignette("monitoringCounts")
have been updated to also work with recent versions of INLA.
BUG FIXES
Offsets in
hhh4
’s epidemic components were ignored bysimulate.hhh4()
[spotted by Johannes Bracher] as well as in dominant eigenvalues (“maxEV”).The color key in
fanplot()
is no longer distorted bylog="y"
.
surveillance 1.16.1 (20180528)
BUG FIXES
autoplot.sts()
now sets the calling environment as theplot_env
of the result.Several
twinstim
related functions finally allow for prehistory events (long supported bytwinstim()
itself):as.epidataCS()
,glm_epidataCS()
,as.epidata.epidataCS()
.The
summary()
for SI[R]Stype"epidata"
failed if there were initially infectious individuals.
DEPRECATED AND DEFUNCT
 Several ancient functions have been deprecated and may be removed in future versions of surveillance:
qlomax()
,readData()
,toFileDisProg()
,correct53to52()
,enlargeData()
,compMatrix.writeTable()
,test()
,testSim()
,makePlot()
.
surveillance 1.16.0 (20180124)
NEW FEATURES
The
as.data.frame()
method for"sts"
objects gained atidy
argument, which enables conversion to the long data format and is also available as functiontidy.sts()
.A ggplot2 variant of
stsplot_time()
is now available viaautoplot.sts()
.as.epidata.data.frame()
gained an argumentmax.time
to specify the end of the observation period (which by default coincides with the last observed event).The now exported function
fanplot()
wraps fanplot::fan()
. It is used byplot.oneStepAhead()
andplot.hhh4sims()
, which now have an option to add the point forecasts to the fan as well.plotHHH4_fitted()
(andplotHHH4_fitted1()
) gained an optiontotal
to sum the fitted components over all units.
SIGNIFICANT CHANGES
Package polyCub is no longer automatically attached (only imported).
scores.oneStepAhead()
no longer reverses the ordering of the time points by default, as announced in 1.15.0.
MINOR CHANGES
Some code in
vignette("monitoringCounts")
has been adjusted to work with the new version of MGLM (0.0.9).Added a
[
method for the"hhh4sims"
class to retain the attributes when subsetting simulations.
BUG FIXES
aggregate(stsObj, by = "unit")
no longer results in empty colnames (set to"overall"
). The obsolete map is dropped.
The
subset
argument oftwinSIR()
was partially ignored:If
nIntervals = 1
, the modelsummary()
reported the total number of events.Automatic
knots
, modelresiduals()
, as well as the rug inintensityplot()
were computed from the whole set of event times.
The
as.epidata.data.frame()
converter did not actually allow for latent periods (viatE.col
). This is now possible but considered experimental (methods for"epidata"
currently ignore latent periods).The
all.equal()
methods for"hhh4"
and"twinstim"
objects now first check for the correct classes.
surveillance 1.15.0 (20171006)
NEW FEATURES
siaf.gaussian()
now also employs apolyCub.iso()
integration routine by default (similar to the powerlawtype kernels), instead of adaptive midpoint cubature. This increases precision and considerably accelerates estimation oftwinstim()
models with a Gaussian spatial interaction function. Models fitted with the new default (F.adaptive=FALSE, F.method="iso"
) will likely differ from previous fits (F.adaptive=TRUE
), and the numerical difference depends on the adaptive bandwidth used before (the defaultadapt=0.1
yielded a rather rough approximation of the integral).Added
quantile()
,confint()
, andplot()
methods for"oneStepAhead"
predictions.Exported the function
simEndemicEvents()
to simulate a spatiotemporal point pattern from an endemiconly"twinstim"
; faster than via the generalsimulate.twinstim()
method.
MINOR CHANGES
twinstim(..., siaf = siaf.gaussian())
uses a larger default initial value for the kernel’s standard deviation (based on the size of the observation region).Nondefault parametrizations of
siaf.gaussian()
are deprecated, i.e., always uselogsd=TRUE
anddensity=FALSE
.twinstim()
uses a smaller default initial value for the epidemic intercept, which usually allows for faster convergence.update.hhh4()
now allowssubset.upper
values beyond the originally fitted time range (but still within the time range of the underlying"sts"
object).scores.oneStepAhead()
by default reverses the ordering of the time points. This awkward behaviour will change in the next version, so the method now warns if the defaultreverse=TRUE
is used without explicit specification.Minor improvements in the documentation and some vignettes: corrected typos, simplified example code, documented some methods.
BUG FIXES
The Croutines introduced in version 1.14.0 used
==
comparisons on parameter values to choose among casespecific formulae (e.g., for d==2 insiaf.powerlaw()
). We now employ an absolute tolerance of 1e7 (which should fix the failing tests on Solaris).Interaction functions for
twinstim()
, such assiaf.powerlaw()
ortiaf.exponential()
, no longer live in the global environment as this risks using masked base functions.
surveillance 1.14.0 (20170629)
DOCUMENTATION
 The replication code from Meyer et al. (2017, JSS) is now included as
demo("v77i11")
. It exemplifies the spatiotemporal endemicepidemic modelling frameworkstwinstim
,twinSIR
, andhhh4
(see also the corresponding vignettes).
NEW FEATURES
Pure Cimplementations of integration routines for spatial interaction functions considerably accelerate the estimation of
twinstim()
models containingsiaf.powerlaw()
,siaf.powerlawL()
, orsiaf.student()
.The color palette generating function used by
sts
plots,hcl.colors
, is now exported.The utility function
clapply
(conditionallapply
) is now exported.Some utility functions for
hhh4
fits are now exported (update.hhh4
,getNEweights
,coefW
), as well as several internal functions for use byhhh4
addon packages (meanHHH
,sizeHHH
,decompose.hhh4
).The
"fan"
type plot function for"hhh4sims"
gained akey.args
argument for an automatic color key.New auxiliary function
makeControl()
, which may be used to specify ahhh4()
model.
MINOR CHANGES

twinstim()
now throws an informative error message when trying to fit a purely epidemic model to data containing endemic events (i.e., events without ancestors). Thehelp("twinstim")
exemplifies such a model.
BUG FIXES
siaf.powerlaw()$deriv
returnedNaN
for the partial derivative wrt the decay parameter d, if d was large enough for f to be numerically equal to 0. It will now return 0 in this case.twinstim()
could fail (with an error fromduplicated.default
) if the fitted time range was substantially reduced via theT
argument.The
"simEpidataCSlist"
generated bysimulate.twinstim(..., simplify = TRUE)
was missing the elementsbbox
andcontrol.siaf
.
surveillance 1.13.1 (20170428)
DOCUMENTATION
 The paper on “SpatioTemporal Analysis of Epidemic Phenomena Using the R Package surveillance” (by Sebastian Meyer, Leonhard Held, and Michael Höhle) will appear in the upcoming volume of the Journal of Statistical Software. The main sections 3 to 5 of the paper are contained in the package as
vignette("twinstim")
,vignette("twinSIR")
, andvignette("hhh4_spacetime")
, respectively.
NEW FEATURES
The
calibrationTest()
andpit()
methods for"oneStepAhead"
forecasts gained an argumentunits
to allow for unitspecific assessments.A default
scores
method is now available to compute a set of proper scoring rules for Poisson or NegBin predictions.New plot
type = "fan"
for simulations from"hhh4"
models to produce a fan chart using the fanplot package.
MINOR CHANGES

scores.hhh4()
sets rownames for consistency withscores.oneStepAhead()
.
BUG FIXES
 The
"Lambda.const"
matrix returned bygetMaxEV_season()
was wrong for models with asymmetric neighbourhood weights. [spotted by Johannes Bracher]
Dominant eigenvalues ("maxEV"
) were not affected by this bug.
surveillance 1.13.0 (20161220)
NEW FEATURES
earsC
now has two new arguments thanks to Howard Burkom: the number of past time units to be used in calculation is now not always 7, it can be chosen in thebaseline
parameter. Furthermore, theminSigma
parameter allows to get a threshold in the case of sparse data. When one doesn’t give any value for those two parameters, the algorithm works like it used to.animate.sts()
gained support for date labels in the bottomtimeplot
.stsplot_space()
andanimate.sts()
can now generate incidence maps based on the population information stored in the supplied"sts"
object. Furthermore,animate.sts()
now supports timevarying population numbers.
MINOR CHANGES

hhh4()
guards against the misuse offamily = factor("Poisson")
for univariate time series. Previously, this resulted in a negative binomial model by definition, but is now interpreted asfamily = "Poisson"
(with a warning).
BUG FIXES
animate.sts()
now supports objects with missing values (with a warning). Furthermore, the automatic color breaks have been improved for incidence maps, also instsplot_space()
.The
as.data.frame
method for the"sts"
class, applied to classical timeindexbased"sts"
objects (epochAsDate=FALSE
), ignored astart
epoch different from 1 when computing theepochInPeriod
indexes. Furthermore, the returnedepochInPeriod
now is a fraction offreq
, for consistency with the result for objects withepochAsDate=TRUE
.simulate.hhh4()
did not handle shared overdispersion parameters correctly. The different parameters were simply recycled to the number of units, ignoring the factor specification from the model’sfamily
. [spotted by Johannes Bracher]Simulations from endemiconly
"hhh4"
models with unitspecific overdispersion parameters used wrong variances. [spotted by Johannes Bracher]oneStepAhead()
predictions oftype
"rolling"
(or"first"
) were incorrect for time pointstp
(tp[1]
) beyond the originally fitted time range (in that they were based on the original time range only). This usage ofoneStepAhead()
was never really supported and is now catched when checking thetp
argument.plot.hhh4simslist()
ignored itspar.settings
argument ifgroups=NULL
(default).
surveillance 1.12.2 (20161114)
NEW FEATURES
The internal auxiliary function, which determines the sets of potential source events in
"epidataCS"
has been implemented in C++, which acceleratesas.epidataCS()
,permute.epidataCS()
, and thereforeepitest()
. This is only really relevant for"epidataCS"
with a large number of events (>1000, say).Negativebinomial
hhh4()
models may not converge for nonoverdispersed data (try, e.g.,set.seed(1); hhh4(sts(rpois(104, 10)), list(family="NegBin1"))
). The resulting nonconvergence warning message now mentions low overdispersion if this is detected. [suggested by Johannes Bracher]An additional
type="delay"
option was added to theplot
method ofstsNC
objects. Furthermore, ananimate_nowcasts
function allows one to animate a sequence of nowcasts.
MINOR CHANGES
 In the
animate
method for"sts"
objects, the default top padding of lattice plots is now disabled for the bottomtimeplot
to reduce the space between the panels. Furthermore, the new optionfill
can be used to make the panel of thetimeplot
as large as possible.
BUG FIXES
bodaDelay()
: fixed spurious warnings fromrnbinom()
.vignette("monitoringCounts")
: fixedboda
related code and cache to obtain same results as in corresponding JSS paper.
surveillance 1.12.1 (20160518)
DOCUMENTATION
 The new
vignette("monitoringCounts")
illustrates the monitoring of count time series in R with a particular focus on aberration detection in public health surveillance. This vignette corresponds to a recently accepted manuscript for the Journal of Statistical Software (Salmon, Schumacher, and Höhle, 2016).
BUG FIXES
The code of
boda()
(withsamplingMethod="joint"
) andbodaDelay()
(withinferenceMethod="INLA"
) has been adjusted to a change of arguments of INLA’sinla.posterior.sample
function. Accordingly, the minimum INLA version required to runboda()
andbodaDelay()
is 0.01458166556.The functions returned by
W_powerlaw()
now have the package namespace as their environment to support situations where the package is not attached.Attaching package nlme after surveillance no longer masks
"hhh4"
’sranef
method. (We now import thefixef
andranef
generics from nlme.)
surveillance 1.12.0 (20160402)
DOCUMENTATION

Several new vignettes illustrate endemicepidemic modeling frameworks for spatiotemporal surveillance data:
vignette("twinstim")

describes a spatiotemporal point process regression model.
vignette("twinSIR")

describes a multivariate temporal point process regression model.
vignette("hhh4_spacetime")

describes an areal timeseries model for infectious disease counts.
These vignettes are based on a recently accepted manuscript for the Journal of Statistical Software (Meyer, Held, and Höhle, 2016).
Improved the documentation on various help pages.
The
hhh4()
based analysis ofdata("fluBYBW")
has been moved to a separate demo script ‘fluBYBW.R’. Due to the abundance of models and the relatively long runtime, we recommend to open the script in an editor rather than running all the code at once usingdemo("fluBYBW")
.
NEW FEATURES
Overhaul of the
"sts"
implementation. This mostly affects packageinternal code, which is simpler, cleaner and better tested now, but requires R >= 3.2.0 (due tocallNextMethod()
bugs in older versions of R). Beyond that, the userlevel constructor functionsts()
now has explicit arguments for clarity and convenience. For instance, its first argument sets theobserved
slot and no longer needs to be named, i.e.,sts(mycounts, start=c(2016,3), frequency=12)
works just like for the classicalts()
function.stsplot_time(..., as.one=TRUE)
is now implemented (yielding a simplematplot
of multiple time series).
MINOR CHANGES
plotHHH4_season()
now by default draws a horizontal reference line at unity if the multiplicative effect of component seasonality is shown (i.e., ifintercept=FALSE
).Since surveillance 1.80,
hhh4()
results are of class"hhh4"
instead of"ah4"
(renamed). Legacy methods for the old class name"ah4"
have been removed.The internal model preparation in
twinstim()
is more efficient (the distance matrix of the events is only computed if event sources actually need to be updated).
BUG FIXES
stsplot_spacetime()
now recognizes itsopts.col
argument.Conversion from
"ts"
to"sts"
usingas(ts, "sts")
could set a wrong start time. For instance,as(ts(1:10, start=c(1959,2), frequency=4), "sts")@start
wasc(1959,1)
.algo.twins()
now also accepts"sts"
input and the automatic legend in the first plot ofplot.atwins()
works again.The experimental
profile
method for"twinstim"
objects did not work if embeddedtwinstim()
fits issued warnings.
surveillance 1.11.0 (20160208)
NEW FEATURES
update.epidata()
can now handle a distance matrixD
in the form of a classed"Matrix"
. [suggested by George Wood]glrnb()
can now handleret="cases"
for the generalized likelihood ratio detector based on the negative binomial distribution. It’s based on a bruteforce search and hence might be slow in some situations.boda()
andbodaDelay()
now support an alternative method (quantileMethod="MM"
) to compute quantiles based on the posterior distribution. The new method samples parameters from the posterior distribution and then computes the quantile of the mixture distribution using bisectionning, which is faster and yields similar results compared to the original method (quantileMethod="MC"
, still the default).
MINOR CHANGES
 Revised
vignette("hhh4")
, updated the package description as well as some references in the documentation. Also updated (the cache of) the slightly outdatedvignette("surveillance")
to account for the corrected version ofalgo.bayes()
implemented since surveillance 1.100.
BUG FIXES
Fixed bug in
categoricalCUSUM()
, which ignored alarms generated for the last time point inrange
. Furthermore, the exact computation in case of returns of the type"value"
for the binomial are now checked through an attribute.Fixed bug in the
estimateGLRNbHook
function ofalgo.glrnb
, which ignored potential fixedalpha
values. Ifalpha
is fixed this is now taken into consideration while fitting the negative binomial function. See revised help files for the details.Made a hotfix such that the
algo.quality
function now also works forsts
objects and if thestate
oralarm
slots consists of TRUE/FALSE instead of 0/1.intensity.twinstim()
did not work for nonendemic models.A parallelized
epitest()
could fail with a strange error message if some replications were left unassigned. This seems to happen if forking is used (mclapply
) with insufficient memory. Incomplete replications are now ignored with a warning.
surveillance 1.100 (20151104)
NEW FEATURES
Calibration tests for count data (Wei and Held, 2014, Test) are now implemented and available as
calibrationTest()
. In addition to a default method taking pure counts and predictive means and dispersion parameters, there are convenient methods for"hhh4"
and"oneStepAhead"
objects.Shared overdispersion across units in negative binomial
hhh4()
time series models (by specifying a factor variable as thefamily
argument).scores()
andpit()
are now generic and have convenient methods for"oneStepAhead"
predictions and"hhh4"
fits.The initial values used for model updates during the
oneStepAhead()
procedure can now be specified directly through thewhich.start
argument (as an alternative to the previous options"current"
and"final"
).plotHHH4_fitted()
(andplotHHH4_fitted1()
) gained an optiondecompose
to plot the contributions from each single unit (and the endemic part) instead of the default endemic + AR + neighbours decomposition. Furthermore, a formatted time axis similar tostsplot_time1()
can now be enabled via the new argumentxaxis
.The new
plot
type
"maps"
for"hhh4"
fits shows maps of the fitted mean components averaged over time.New
plot
method for simulations from"hhh4"
models (usingsimulate.hhh4(..., simplify = TRUE)
, which now has a dedicated class:"hhh4sims"
) to show the final size distribution or the simulated time series (possibly stratified by groups of units). There is also a newscores
method to compute proper scoring rules based on such simulations.The argument
idx2Exp
ofcoef.hhh4()
may now be conveniently set toTRUE
to exptransform all coefficients.Added a
coeflist()
method for"hhh4"
fits.The generator function
sts()
can now be used to initialize objects of class"sts"
(instead of writingnew("sts", ...)
).Additional arguments of
layout.scalebar()
now allow to change the style of the labels.A precomputed distance matrix
D
can now be used as input for theas.epidata()
converter – offering an alternative to the default Euclidean distance based on the individuals coordinates. (Request of George Wood to supporttwinSIR
models on networks.)
MINOR CHANGES
The first argument of
scores()
is now calledx
instead ofobject
(for consistency withcalibrationTest()
).The result of
oneStepAhead()
now has the dedicated class attribute"oneStepAhead"
(previously was just a list).Changed interpretation of the
col
argument ofplotHHH4_fitted()
andplotHHH4_fitted1()
(moved color of “observed” to separate argumentpt.col
and reversed remaining colors). The oldcol
specification as a vector of length 4 still works (catched internally) but is undocumented.The
epoch
slot of class"sts"
is now initialized to1:nrow(observed)
by default and thus no longer needs to be explicitly set when creating anew("sts", ...)
for this standard case.Initialization of
new("sts", ...)
now supports the argumentfrequency
(for consistency withts()
). Note thatfreq
still works (via partial argument matching) and that the corresponding"sts"
slot is still calledfreq
.If
missing(legend.opts)
instsplot_time1()
, the default legend will only be produced if the"sts"
object contains information on outbreaks, alarms, or upperbounds.The default
summary()
of a"twinstim"
fit is more concise since it no longer includes the number of loglikelihood and score function evaluations and the elapsed time during model fitting. Set the newruntime
argument ofsummary.twinstim()
toTRUE
to add this information to the summary as before.The
animate
method for"sts"
objects gained an argumentdraw
(to disable the default instantaneous plotting) and now invisibly returns the sequential plot objects (of class"gtable"
or"trellis"
) in a list for postprocessing.The flexible time axis configurations for
"sts"
plots introduced in version 1.80 now also work for classical"sts"
objects with integer epochs and standard frequencies (tryplot(..., epochsAsDate = TRUE)
).stsplot_time()
initiatespar
settings only if thepar.list
argument is a list.The new
all.equal()
method for class"hhh4"
compares two fits ignoring their"runtime"
and"call"
elements (at least).
BUG FIXES
Fixed a bug in
algo.bayes
, where an alarm was already sounded if the current observation was equal to the quantile of the predictive posterior. This was changed in order to get alarm_t = I(obs_t > quantile_t) which is consistent with the use inboda
andbodaDelay
.Fixed bug in
algo.outbreakP
causing a halt in the computations ofvalue="cases"
whencalc.outbreakP.statistic
returnedNaN
. Now, aNaN
is returned.wrap.algo
argumentcontrol.hook
usedcontrol
argument defined outside it’s scope (and not the one provided to the function). It is now added as additional 2nd argument to thecontrol.hook
function.stsplot_time()
did not account for the optionalunits
argument for multivariate"sts"
objects when choosing a suitable value forpar("mfrow")
.hhh4()
could have used a functiondpois()
ordnbinom()
from the global environment instead of the respective function from package stats.The default time variable
t
created as part of thedata
argument inhhh4()
was incompatible with"sts"
objects havingepochAsDate=TRUE
.A consistency check in
as.epidata.default()
failed for SItype data (and, more generally, for all data which ended with an Ievent in the last time block). [spotted by George Wood]
surveillance 1.91 (20150612)
This is a quick patch release to make the test suite run smoothly on CRAN’s Windows and Solaris Sparc systems.
The new
hhh4()
option to scale neighbourhood weights did not work for parametric weights with more than one parameter ifnormalize=FALSE
.
surveillance 1.90 (20150609)
NEW FEATURES
New functions and data for Bayesian outbreak detection in the presence of reporting delays (Salmon et al., 2015):
bodaDelay()
,sts_observation()
, andsts_creation()
.
New functions implementing tests for spacetime interaction:
knox()
supports both the Poisson approximation and a Monte Carlo permutation approach to determine the pvalue,stKtest()
wraps spacetime Kfunction methods from package splancs for use with"epidataCS"
,and
epitest()
fortwinstim
models (makes use of the new auxiliary functionsimpleR0()
).
New function
plapply()
: a parallel and verbose version oflapply()
wrapping around bothmclapply()
andparLapply()
of package parallel.New converter
as.xts.sts()
to transform"sts"
objects to the quasi standard"xts"
class, e.g., to make use of package dygraphs for interactive time series plots.New options for scaling and normalization of neighbourhood weights in
hhh4()
models.New auxiliary function
layout.scalebar()
for use as part ofsp.layout
inspplot()
or in the traditional graphics system.
New features for "epidataCS"
New argument
by
forplot.epidataCS()
, which defines a stratifying variable for the events (default is the event type as before). It can also be set toNULL
to make the plot not distinguish between event types.The spatial plot of
"epidataCS"
gained the argumentstiles
,pop
andsp.layout
, and can now produce anspplot()
with the tilespecific population levels behind the point pattern.New function
permute.epidataCS()
to randomly permute time points or locations of the events (holding other marks fixed).
New features for twinstim()
New S3generic
coeflist()
to list model coefficients by component. It currently has a default method and one for"twinstim"
and"simEpidataCS"
.New argument
newcoef
forsimulate.twinstim()
to customize the model parameters used for the simulation.New argument
epilink
fortwinstim()
, offering experimental support for an identity link for the epidemic predictor. The default remainsepilink = "log"
.Simulation from
"twinstim"
models and generation of"epidataCS"
is slightly faster now (faster spatstat functions are used to determine the distance of events to the border).New option
scaled = "standardized"
iniafplot()
to plot f(x) / f(0) or g(t) / g(0), respectively.
MINOR CHANGES
Initial data processing in
twinstim()
is faster since event sources are only redetermined if there is effective need for an update (due to subsetting or a change ofqmatrix
).formatPval()
disablesscientific
notation by default.The
"time"
plot for"epidataCS"
uses the temporal grid points as the default histogrambreaks
.The special
fe()
function which sets up fixed effects inhhh4()
models gained an argumentunitSpecific
as a convenient shortcut forwhich = rep(TRUE, nUnits)
.The convenient
plot
option ofpermutationTest()
uses MASS::truehist()
instead ofhist()
and accepts graphical parameters to customize the histogram.
BUG FIXES
The
bodaFit
function did not draw samples from the joint posterior. Instead draws were from the respective posterior marginals. A new argumentsamplingMethod
is now introduced defaulting to the proper ‘joint’. For backwards compatibility use the value ‘marginal’.The functions
as.epidataCS()
andsimEpidataCS()
could throw inappropriate warnings when checking polygon areas (only ifW
ortiles
, respectively, contained holes).Nonconvergent endemiconly
twinstim
models produced an error. [spotted by Bing Zhang]The
"owin"
method ofintersectPolyCircle
could have returned a rectangletype"owin"
instead of a polygon.An error occurred in
twinstim()
iffinetune=TRUE
or choosingoptim()
instead of the defaultnlminb()
optimizer without supplying acontrol
list inoptim.args
.The
"time"
plot for"epidataCS"
did not necessarily use the same histogrambreaks
for all strata.Specifying a step function of interaction via a numeric vector of knots did not work in
twinstim()
.plot.hhh4()
did not support an unnamedtype
argument such asplot(x, "season")
.simEpidataCS()
did not work ift0
was in the last block ofstgrid
(thus it did not work for singlecell grids), and mislabeled thestart
column copied toevents
if there were no covariates instgrid
.Evaluating
intensity.twinstim()$hFUN()
at time points beforet0
was an error. The function now returnsNA_real_
as for time points beyondT
.Truncated, normalized powerlaw weights for
hhh4()
models, i.e.,W_powerlaw(maxlag = M, normalize = TRUE)
withM < max(neighbourhood(stsObj))
, had wrong derivatives and thus failed to converge.update.hhh4(..., use.estimates = TRUE)
did not use the estimated weight function parameters as initial values for the new fit. It does so now iff the weight functionne$weights
is left unchanged.
surveillance 1.83 (20150105)
Accommodate a new note given by Rdevel checks, and set the new INLA additional repository in the ‘DESCRIPTION’ file.
Made
linelist2sts()
work for quarters by adding extra"%q"
formatting informatDate()
.
surveillance 1.82 (20141216)
MINOR CHANGES related to hhh4
In the coefficient vector resulting from a
hhh4
fit, random intercepts are now named.Parameter
start
values inhhh4()
are now matched by name but need not be complete in that case (default initial values are used for unspecified parameters).The
update.hhh4()
method now by default doesuse.estimates
from the previous fit. This reduces the number of iterations during model fitting but may lead to slightly different parameter estimates (within a tolerance of1e5
). Settinguse.estimates = FALSE
means to reuse the previous start specification.
MINOR CHANGES related to the "sts"
class
For univariate
"sts"
objects, the (meaningless) “head of neighbourhood” is no longershow
n.The
"sts"
class now has adimnames
method instead of acolnames
method. Furthermore, the redundantnrow
andncol
methods have been removed (thedim
method is sufficient).If a
map
is provided wheninitialize()
ing an"sts"
object, it is now verified that allobserved
regions are part of themap
(matched byrow.names
).In
stsplot_space()
, extra (unobserved) regions of themap
are no longer dropped but shown with a dashed border by default.
surveillance 1.81 (20141029)
NEW FEATURES
The
R0
method for"twinstim"
gained an argumentnewcoef
to simplify computation of reproduction numbers with a different parameter vector (also used for Monte Carlo CI’s).New plot
type="neweights"
for"hhh4"
fits.The
scores()
function allows the selection of multipleunits
(by index or name) for which to compute (averaged) proper scores. Furthermore, one can now selectwhich
scores to compute.Added a
formula
method for"hhh4"
fits to extract thef
specifications of the three components from the control list.The
update()
method for fitted"hhh4"
models gained an argumentS
for convenient modification of component seasonality usingaddSeason2formula()
.The new auxiliary function
layout.labels()
generates ansp.layout
item forspplot()
in order to draw labels.When generating the
pit()
histogram with a single predictive CDFpdistr
, the...
arguments can now bex
specific and are recycled if necessary usingmapply()
. Ifpdistr
is a list of CDFs,pit()
no longer requires the functions to be vectorized.New method
as.epidata.data.frame()
, which constructs the start/stop SIR event history format from a simple individualbased data frame (e.g.,hagelloch.df
).New argument
w
inas.epidata.default()
to generate covariatebased weights for the force of infection intwinSIR
. Thef
argument is for distancebased weights.The result of
profile.twinSIR()
gained a class and an associatedplot
method.
MAJOR CHANGES
For multivariate
oneStepAhead()
predictions,scores(..., individual=TRUE)
now returns a 3d array instead of a collapsed matrix. Furthermore, the scores computed by default arec("logs","rps","dss","ses")
, excluding the normalized squared error score"nses"
which is improper.The plot
type="season"
for"hhh4"
fits now by default plots the multiplicative effect of seasonality on the respective component (new argumentintercept=FALSE
). The default set of components to plot has also changed.When
as.epidata()
andsimEpidata()
calculate distancebased epidemic weights from thef
functions, they no longer set the distance of an infectious individual to itself artificially toInf
. This changes the corresponding columns in the"epidata"
in rows of currently infectious individuals, but thetwinSIR
model itself is invariant, since only rows withatRiskY=1
contribute to the likelihood.Several modifications and corrections in
data("hagelloch")
.
MINOR CHANGES
Better plotting of
stsNC
objects by writing an own plot method for them. Prediction intervals are now shown jointly with the point estimate.Reduced package size by applying
tools::resaveRdaFiles
to some large datasets and by building the package withcompactvignettes=both
, i.e., using additional GhostScript compression with ebook quality, see?tools::compactPDF
.Added
units
argument tostsplot_time
to select only a subset of the multivariate time series for plotting.The
untie
method for class"epidataCS"
gained an argumentverbose
which is nowFALSE
by default."epidataCS"
objects store theclipper
used during generation as attribute of$events$.influenceRegion
.In
plotHHH4_fitted()
, the argumentlegend.observed
now defaults toFALSE
.The default weights for the spatiotemporal component in
hhh4
models now areneighbourhood(stsObj) == 1
. The previous defaultneighbourhood(stsObj)
does not make sense for the newly supportednbOrder
neighbourhood matrices (shortestpath distances). The new default makes no difference for (old) models with binary adjacency matrices in the neighbourhood slot of thestsObj
.The default for nonparametric weights
W_np()
inhhh4()
is now to assume zero weight for neighbourhood orders abovemaxlag
, i.e.,W_np()
’s argumentto0
now defaults toTRUE
.Added a
verbose
argument topermutationTest()
, which defaults toFALSE
. The previous behaviour corresponds toverbose=TRUE
.simulate.twinstim()
now by default uses the originaldata$W
as observation region.The
data("measlesWeserEms")
contain two additional variables in the@map@data
slot:"vaccdoc.2004"
and"vacc1.2004"
.The plotmethod for
"epidata"
objects now uses colored lines by default.The surveillance package now depends on R >= 3.0.2, which, effectively, is the minimum version required since surveillance 1.70 (see the corresponding NEWS below).
The two diagnostic plots of
checkResidualProcess()
are now by default plotted side by side (mfrow=c(1,2)
) instead of one below the other.
BUG FIXES
In
farringtonFlexible
alarms are now forobserved>upperbound
and not forobserved>=upperbound
which was not correct.Fixed duplicate
"functions"
element resulting fromupdate.twinstim(*,model=TRUE)
and ensured that"twinstim"
objects always have the same components (some may beNULL
).animate.epidata
works again with the animation package (ani.options("outdir")
was removed in version 2.3)For
hhh4
models with random effects,confint()
only worked if argumentparm
was specified.Computing onesided AIC weights by simulation for
twinSIR
models with more than 2 epidemic covariates now is more robust (by rescaling the objective function for the quadratic programming solver) and twice as fast (due to code optimization).simulate.twinstim(..., rmarks=NULL)
can now handle the case wheredata
has no events within the simulation period (by sampling marks from all ofdata$events
).The
lambda.h
values of simulated events in"simEpidataCS"
objects were wrong if the model contained an endemic intercept (which is usually the case).Automatic choice of color breaks in the
animate
method for class"sts"
now also works for incidence maps (i.e., with apopulation
argument).hhh4()
did not allow the use of nonparametric neighbourhood weightsW_np()
withmaxlag=2
.scores()
did not work for multivariateoneStepAhead()
predictions if bothindividual=TRUE
andsign=TRUE
, and it could not handle aoneStepAhead()
prediction of only one time point. Furthermore, the"sign"
column ofscores(..., sign=TRUE)
was wrong (reversed).For
"epidataCS"
with only one event,epidataCSplot_space()
did not draw the point.The trivial (identity) call
aggregate(stsObj, nfreq=stsObj@freq)
did not work.
surveillance 1.80 (20140616)
PACKAGE INFRASTRUCTURE
Package surveillance now depends on newer versions of packages sp (>= 1.015), polyCub (>= 0.42), and spatstat (>= 1.360). The R packages INLA and runjags are now suggested to support a new outbreak detection algorithm (
boda()
) and the newnowcast()
ing procedure, respectively. The R packages for lattice, grid, gridExtra, and scales are suggested for added visualization facilities.More tests have been implemented to ensure package integrity. We now use testthat instead of the outdated package RUnit.
hhh4()
fits now have class"hhh4"
instead of"ah4"
, for consistency withtwinstim()
,twinSIR()
, and to follow the common convention (cp.lm()
). Standard S3methods for the old"ah4"
name are still available for backwards compatibility but may be removed in the future.Plot variants for
"sts"
objects have been cleaned up: The functions implementing the various plot types (stsplot_*
, previously namedplot.sts.*
) are now exported and documented separately.
NEW FEATURES
The
nowcast
procedure has been completely rewritten to handle the inherit righttruncation of reporting data (best visualized as a reporting triangle). The new code implements the generalizedDirichlet and the hierarchical Bayesian approach described in Höhle and an der Heiden (2014). No backwards compatibility to the old nowcasting procedure is given.The package contains a new monitoring function
boda
. This is a first experimental surveillance implementation of the Bayesian Outbreak Detection Algorithm (BODA) proposed in Manitz and Höhle (2012). The function relies on the nonCRAN package INLA, which has to be installed first in order to use this function. Expect initial problems.New
toLatex
method for"sts"
objects.The new function
stsplot_space()
provides an improved map plot of disease incidence for"sts"
objects aggregated over time. It corresponds to the newtype = observed ~ unit
of thestsplot
method, and supersedestype = observed ~ 1unit
(except for alarm shading).An
animate()
method for the"sts"
class provides a new implementation for animated maps (superseding theplot
type=observed ~ 1  unit * time
) with an optional evolving time series plot below the map.The
plot()
method for"sts"
objects with epochs as dates is now made more flexible by introducing the argumentsxaxis.tickFreq
,xaxis.labelFreq
andxaxis.labelFormat
. These allow the specification of tickmarks and labelling based onstrftime
compatible conversion codes – independently if data are daily, weekly, monthly, etc. As a consequence, the old argumentxaxis.years
is removed. Seestsplot_time()
for more information.Inference for neighbourhood weights in
hhh4()
models:W_powerlaw()
andW_np()
both implement weights depending on the order of neighbourhood between regions, a powerlaw decay and nonparametric weights, i.e., unconstrained estimation of individual weights for each neighbourhood order.hhh4()
now allows the inclusion of multiplicative offsets also in the epidemic components"ar"
and"ne"
.hhh4()
now has support forlag != 1
in the autoregressive and neighbordriven components. The applied lags are stored as component"lags"
of the return value (previously there was an unused component"lag"
which was always 1 and has been removed now).
Added support for parallel computation of predictions using
mclapply()
from package parallel.New argument
type
with a newtype
"first"
to base all subsequent onestepahead predictions on a single initial fit.Nicer interpretation of
verbose
levels, andtxtProgressBar()
.
The
plot()
method for fittedhhh4()
objects now offers three additional types of plots: component seasonality, seasonal or time course of the dominant eigenvalue, and maps of estimated random intercepts. It is documented and more customizable. Note that argument order and some names have changed:i
>units
,title
>names
.(Deviance)
residuals()
method for fittedhhh4()
models.Added methods of
vcov()
andnobs()
for the"hhh4"
class. ForAIC()
andBIC()
, the default methods work smoothly now (due to changes tologLik.hhh4()
documented below).New predefined interaction functions for
twinstim()
:siaf.student()
implements a tkernel for the distance decay, andsiaf.step()
andtiaf.step()
provide step function kernels (which may also be invoked by specifying the vector of knots as thesiaf
ortiaf
argument intwinstim
).Numerical integration over polygonal domains in the
F
andDeriv
components ofsiaf.powerlaw()
andsiaf.powerlawL()
is much faster and more accurate now since we use the newpolyCub.iso()
instead ofpolyCub.SV()
from package polyCub.New
as.stepfun()
method for"epidataCS"
objects.
The spatial plot has new arguments to automatically add legends to the plot:
legend.types
andlegend.counts
. It also gained anadd
argument.The temporal plot now supports typespecific subhistograms, additional lines for the cumulative number of events, and an automatic legend.
The new function
glm_epidataCS()
can be used to fit an endemiconlytwinstim()
viaglm()
. This is mainly provided for testing purposes since wrapping intoglm
usually takes longer.
MAJOR CHANGES
Fitted
hhh4()
objects no longer contain the associated"sts"
data twice: it is now only stored as$stsObj
component, the hidden duplicate in$control$data$.sts
was dropped, which makes fitted objects substantially smaller.logLik.hhh4()
always returns an object of class"logLik"
now; for random effects models, its"df"
attribute isNA_real_
. Furthermore, for nonconvergent fits,logLik.hhh4()
gives a warning and returnsNA_real_
; previously, an error was thrown in this case.
Default of
tp[2]
is now the penultimate time point of the fitted subset (not of the wholestsObj
).+1
on rownames of$pred
(now the same as for$observed
).
The optional
"twinstim"
result componentsfisherinfo
,tau
, andfunctions
are always included. They are set toNULL
if they are not applicable instead of missing completely (as before), such that all"twinstim"
objects have the same list structure.
invisibly returns a matrix containing the plotted values of the (scaled) interaction function (and the confidence interval as an attribute). Previously, nothing (
NULL
) was returned.detects a typespecific interaction function and by default uses
types=1
if it is not typespecific.has better default axis ranges.
adapts to the new step function kernels (with new arguments
verticals
anddo.points
).supports logarithmic axes (via new
log
argument passed on toplot.default
).optionally respects
eps.s
andeps.t
, respectively (by the new argumenttruncated
).now uses
scaled=TRUE
by default.
The argument
colTypes
ofplot.epidataCS(,aggregate="space")
is deprecated (usepoints.args$col
instead).The events in an
"epidataCS"
object no longer have a reserved"ID"
column.
MINOR CHANGES
hhh4()
now stores the runtime just liketwinstim()
.Take
verbose=FALSE
inhhh4()
more seriously.The following components of a
hhh4()
fit now have names:"se"
,"cov"
,"Sigma"
.The new default for
pit()
is to produce the plot.The
twinstim()
argumentcumCIF
now defaults toFALSE
.update.twinstim()
no longer uses recursivemodifyList()
for thecontrol.siaf
argument. Instead, the supplied new list elements ("F"
,"Deriv"
) completely replace the respective elements from the originalcontrol.siaf
specification.siaf.lomax()
is now defunct (it has been deprecated since version 1.52); usesiaf.powerlaw()
instead.Allow the default
adapt
ive bandwidth to be specified via theF.adaptive
argument insiaf.gaussian()
.Unsupported options (
logpars=FALSE
,effRangeProb
) have been dropped fromsiaf.powerlaw()
andsiaf.powerlawL()
.More rigorous checking of
tiles
insimulate.twinstim()
andintensityplot.twinstim()
.as.epidataCS()
gained averbose
argument.animate.epidataCS()
now by default does not draw influence regions (col.influence=NULL
), isverbose
ifinteractive()
, and ignoressleep
on noninteractive devices.The
multiplicity
generic and its default method have been integrated into spatstat and are imported from there.
DATA
The polygon representation of Germany’s districts (
system.file("shapes", "districtsD.RData", package="surveillance")
) has been simplified further. The union ofdistrictsD
is used as observation windowW
indata("imdepi")
. The exemplarytwinstim()
fitdata("imdepifit")
has been updated as well. Furthermore,row.names(imdepi$events)
have been reset (chronological index), and numerical differences inimdepi$events$.influenceRegion
are due to changes in polyclip 1.30.The Campylobacteriosis data set
campyDE
, where absolute humidity is used as concurrent covariate to adjust the outbreak detection is added to the package to exemplifyboda()
.New
data("measlesWeserEms")
(of class"sts"
), a corrected version ofdata("measles.weser")
(of the old"disProg"
class).
BUG FIXES
Fixed a bug in
LRCUSUM.runlength
where computations were erroneously always done under the incontrol parametermu0
instead ofmu
.Fixed a bug during alarm plots (
stsplot_alarm()
), where the use ofalarm.symbol
was ignored.Fixed a bug in
algo.glrnb
where the overdispersion parameteralpha
from the automatically fittedglm.nb
model (fitted byestimateGLRNbHook
) was incorrectly taken asmod[[1]]$theta
instead of1/mod[[1]]$theta
. The error is due to a different parametrization of the negative binomial distribution compared to the parametrization in Höhle and Paul (2008).The score function of
hhh4()
was wrong when fitting endemiconly models to asubset
including the first time point. This led to “false convergence”.twinstim()
did not work without an endemic offset ifis.null(optim.args$par)
.
surveillance 1.70 (20131119)
SYNOPSIS
Package gpclib is no longer necessary for the construction of
"epidataCS"
objects. Instead, we make use of the new dedicated package polyclip (licensed under the BSL) for polygon clipping operations (viaspatstat::intersect.owin()
). This results in a slightly different$events$.influenceRegion
component of"epidataCS"
objects, one reason being that polyclip uses integer arithmetic. Change oftwinstim()
estimates for a newly created"epidataCS"
compared with the same data prepared in earlier versions should be very small (e.g., fordata("imdepifit")
the mean relative difference of coefficients is 3.7e08, while thelogLik()
isall.equal()
). As an alternative, rgeos can still be chosen to do the polygon operations.The surveillanceinternal code now depends on R >= 2.15.2 (for
nlminb()
NA
fix of PR#15052, consistentrownames(model.matrix)
of PR#14992,paste0()
,parallel::mcmapply()
). However, the required recent version of spatstat (1.340, for polyclip) actually needs R >= 3.0.2, which therefore also applies to surveillance.Some minor new features and changes are documented below.
NEW FEATURES
Functions
unionSpatialPolygons()
andintersectPolyCircle()
are now exported. Both are wrappers around functionality from different packages supporting polygon operations: for determining the union of all subpolygons of a"SpatialPolygons"
object, and the intersection of a polygonal and a circular domain, respectively.discpoly()
moved back from polyCub to surveillance.
MINOR CHANGES
surveillance now Depends on polyCub (>= 0.40) and not only Imports it (which avoids
::
references in .GlobalEnvmade functions).Nicer default axis labels for
iafplot()
.For
twinstim()
, the default is now totrace
every iteration instead of every fifth only.Slightly changed default arguments for
plot.epidata()
:lwd
(1>2),rug.opts
(col
is set according towhich.rug
)twinstim()
saves the vector offixed
coefficients as part of the returnedoptim.args
component, such that these will again be held fixed uponupdate()
.The
plot
method forhhh4()
fits allows for region selection by name.
surveillance 1.60 (20130903)
SYNOPSIS
The
polyCub
methods for cubature over polygonal domains have been moved to the new dedicated package polyCub, since they are of a rather general use. Thediscpoly()
function has also been moved to that package.As a replacement for the licenserestricted gpclib package, the rgeos package is now used by default (
surveillance.options(gpclib=FALSE)
) in generating"epidataCS"
(polygon intersections, slightly slower). Therefore, when installing surveillance version 1.60, the system requirements for rgeos have to be met, i.e., GEOS must be available on the system. On Linux variants this means installing ‘libgeos’ (‘libgeosdev’).The improved Farrington method described in Noufaily et al. (2012) is now available as function
farringtonFlexible()
.New handling of reference dates in
algo.farrington()
for"sts"
objects withepochAsDate=TRUE
. Instead of always going back in time to the next Date in the"epoch"
slot, the function now determines the closest Date. Note that this might lead to slightly different results for the upperbound compared to previously. Furthermore, the functionality is only tested for weekly data (monthly data are experimental). The same functionality applies tofarringtonFlexible()
.To make the different retrospective modelling frameworks of the surveillance package jointly applicable, it is now possible to convert (aggregate)
"epidataCS"
(continuoustime continuousspace data) into an"sts"
object (multivariate time series of counts) by the new functionepidataCS2sts
.Simulation from
hhh4
models has been reimplemented, which fixes a bug and makes it more flexible and compatible with a wider class of models.The
map
slot of the"sts"
class now requires"SpatialPolygons"
(only) instead of"SpatialPolygonsDataFrame"
.Reimplementation of
oneStepAhead()
forhhh4
models with a bug fix, some speedup and more options.Slight speedup for
hhh4()
fits, e.g., by more use of.rowSums()
and.colSums()
.Crucial speedup for
twinstim()
fits by more efficient code:mapply
, dropped clumsyfor
loop infisherinfo
, new argumentcores
for parallel computing via forking (not available on Windows).Some further new features, minor changes, and bug fixes are described in the following subsections.
NEW FEATURES
Using
tiaf.exponential()
in atwinstim()
now works withnTypes=1
for multitype data.A legend can be added automatically in
iafplot()
.The
untie
methods are now able to produce jittered points with a required minimum separation (minsep
).simulate.ah4
gained asimplify
argument.New
update
method for fittedhhh4
models (class"ah4"
).oneStepAhead()
has more options: specify time range (not only start), choose type of start values,verbose
argument.pit()
allows for a list of predictive distributions (pdistr
), one for each observationx
.New spatial auxiliary function
polyAtBorder()
indicating polygons at the border (for a"SpatialPolygons"
object).animate.epidataCS()
allows for amain
title and can show a progress bar.
MINOR CHANGES
Changed parametrization of
zetaweights()
and completed its documentation (now no longer marked as experimental).twinstim(...)$converged
isTRUE
if the optimization routine converged (as before) but contains the failure message otherwise.Increased default
maxit
for the NelderMead optimizer inhhh4
from 50 to 300, and removed default artificial lower bound (20) on intercepts of epidemic components.Renamed returned list from
oneStepAhead
(mean>pred, x>observed, params>coefficients, variances>Sigma.orig) for consistency, andoneStepAhead()$psi
is only nonNULL
if we have a NegBin model.Argument order of
pit()
has changed, which is also faster now and got additional argumentsrelative
andplot
.twinstim(...)$runtime
now contains the complete information fromproc.time()
.
BUG FIXES
Fixed a bug in function
refvalIdxByDate()
which produced empty reference values (i.e.NA
s) in case the Date entries ofepoch
were not mondays. Note: The function works by subtracting1:b
years from the date of the range value and then takes the spanw:w
around this value. For each value in this set it is determined whether the closest date in the epoch slot is obtained by going forward or backward. Note that this behaviour is now slightly changed compared to previously, where we always went back in time.algo.farrington()
: Reference values too far back in time and hence not being in the"epoch"
slot of the"sts"
object are now ignored (previously the resultingNA
s caused the function to halt). A warning is displayed in this case.hhh4
: The entry (5,6) of the marginal Fisher information matrix in models with random intercepts in all three components was incorrect. Ifnlminb
was used as optimizer for the variance parameters (using the negative marginal Fisher information as Hessian), this could have caused false convergence (with warning) or minimally biased convergence (without warning). As a consequence, the"Sigma.cov"
component of thehhh4()
result, which is the inverse of the marginal Fisher information matrix at the MLE, was also wrong.untie.matrix()
could have produced jittering greater than the specifiedamount
.hhh4
: if there are no random intercepts, the redundantupdateVariance
steps are no longer evaluated.update.twinstim()
did not work withoptim.args=..1
(e.g., if updating a list of models with lapply). Furthermore, if adding themodel
component only, thecontrol.siaf
andoptim.args
components were lost.earsC
should now also work with multivariatests
timeseries objects.The last week in
data(fluBYBW)
(row index 417) has been removed. It corresponded to week 1 in year 2009 and was wrong (an artifact, filled with zero counts only). Furthermore, the regions in@map
are now ordered the same as in@observed
.Fixed start value of the overdispersion parameter in
oneStepAhead
(must be on internal logscale, not reparametrized as returned bycoef()
by default).When subsetting
"sts"
objects in time,@start
was updated but not@epoch
.pit
gaveNA
results if anyx[1]==0
.The returned
optim.args$par
vector intwinstim()
was missing any fixed parameters.hhh4()
did not work with timevarying neighbourhood weights due to an error in the internalcheckWeightsArray()
function.
surveillance 1.54 (20130421)
SYNOPSIS
Fixed obsolete
.path.package()
calls.Small corrections in the documentation.
update.twinstim()
performs better in preserving the original initial values of the parameters.New predefined spatial interaction function
siaf.powerlawL()
, which implements a _L_agged powerlaw kernel, i.e. accounts for uniform shortrange dispersal.
surveillance 1.52 (20130315)
SYNOPSIS
New method for outbreak detection:
earsC
(CUSUMmethod described in the CDC Early Aberration Reporting System, see Hutwagner et al, 2003).New features and minor bug fixes for the “
twinstim
” part of the package (see below).Yet another pvalue formatting function
formatPval()
is now also part of the surveillance package.polyCub.SV()
now also accepts objects of classes"Polygon"
and"Polygons"
for convenience.siaf.lomax
is deprecated and replaced bysiaf.powerlaw
(reparametrization).
NEW FEATURES (twinstim()
related)
The temporal
plot
method for class"epidataCS"
now understands theadd
parameter to add the histogram to an existing plot window, and autotransforms thet0.Date
argument usingas.Date()
if necessary.nobs()
methods for classes"epidataCS"
and"twinstim"
.New argument
verbose
fortwinstim()
which, if set toFALSE
, disables the printing of information messages during execution.New argument
start
fortwinstim()
, where (some) initial parameter values may be provided, which overwrite those inoptim.args$par
, which is no longer required (as a naive default, a crude estimate for the endemic intercept and zeroes for the other parameters are used).Implemented a wrapper
stepComponent()
forstep()
to perform algorithmic componentspecific model selection in"twinstim"
models. This also required the implementation of suitableterms()
andextractAIC()
methods. The singlestep methodsadd1()
anddrop1()
are also available.The
update.twinstim()
method now by default uses the parameter estimates from the previous model as initial values for the new fit (new argumentuse.estimates = TRUE
).as.epidataCS()
checks for consistency of the area ofW
and the (now really obligatory) area column instgrid
.simulate.twinstim()
now by default uses the previousnCircle2Poly
from thedata
argument.direction
argument foruntie.epidataCS()
.The
toLatex
method for"summary.twinstim"
got different defaults and a new argumenteps.Pvalue
.New
xtable
method for"summary.twinstim"
for printing the covariate effects as risk ratios (with CI’s and pvalues).
NEW FEATURES (hhh4()
related)
New argument
hide0s
in theplot
method for class"ah4"
.New argument
timevar
foraddSeason2formula()
, which now also works for long formulae.
surveillance 1.50 (20121212)
SYNOPSIS
This new version mainly improves upon the
twinstim()
andhhh4()
implementations (see below).As requested by the CRAN team, examples now run faster. Some are conditioned on the value of the new package option
"allExamples"
, which usually defaults toTRUE
(but is set toFALSE
for CRAN checking, if timings are active).Moved some rarely used package dependencies to “Suggests:”, and also removed some unused packages from there.
Dropped strict dependence on gpclib, which has a restricted license, for the surveillance package to be clearly GPL2. Generation of
"epidataCS"
objects, which makes use of gpclib’s polygon intersection capabilities, now requires prior explicit acceptance of the gpclib license via settingsurveillance.options(gpclib = TRUE)
. Otherwise,as.epidataCS()
andsimEpidataCS()
may not be used.
NEW FEATURES (twinstim()
related)
Speedup by memoisation of the
siaf
cubature (using the memoise package).Allow for
nlm
optimizer (really not recommended).Allow for
nlminb
specific control arguments.Use of the expected Fisher information matrix can be disabled for
nlminb
optimization.Use of the
effRange
trick can be disabled insiaf.gaussian()
andsiaf.lomax()
. The defaulteffRangeProb
argument for the latter has been changed from 0.99 to 0.999.The
twinstim()
argumentnCub
has been replaced by the newcontrol.siaf
argument list. The oldnCub.adaptive
indicator became a feature of thesiaf.gaussian()
generator (namedF.adaptive
there) and does no longer depend on theeffRange
specification, but uses the bandwidthadapt*sd
, where theadapt
parameter may be specified in thecontrol.siaf
list in thetwinstim()
call. Accordingly, the components"nCub"
and"nCub.adaptive"
have been removed from the result oftwinstim()
, and are replaced by"control.siaf"
.The
"method"
component of thetwinstim()
result has been replaced by the whole"optim.args"
.The new
"Deriv"
component ofsiaf
specifications integrates the “siaf$deriv” function over a polygonal domain.siaf.gaussian()
andsiaf.lomax()
usepolyCub.SV()
(with intelligentalpha
parameters) for this task (previously: midpointrule with naive bandwidth)scaled
iafplot()
(defaultFALSE
). Thengrid
parameter has been renamed toxgrid
and is more general.The
"simulate"
component ofsiaf
’s takes an argumentub
(upperbound for distance from the source).Numerical integration of spatial interaction functions with an
Fcircle
trick is more precise now; this slightly changes previous results.New S3generic
untie()
with a method for the"epidataCS"
class (to randomly break tied event times and/or locations).Renamed
N
argument ofpolyCub.SV()
tonGQ
, anda
toalpha
, which both have new default values. The optional polygon rotation proposed by Sommariva & Vianello is now also implemented (based on the corresponding MATLAB code) and available as the newrotation
argument.The
scale.poly()
method for"gpc.poly"
is now available asscale.gpc.poly()
. The default return class ofdiscpoly()
was changed from"gpc.poly"
to"Polygon"
.An
intensityplot()
method is now also implemented for"simEpidataCS"
.
NEW FEATURES (hhh4()
related)
Significant speedup (runs about 6 times faster now, amongst others by many code optimizations and by using sparse Matrix operations).
hhh4()
optimization routines can now be customized for the updates of regression and variance parameters seperately, which for instance enables the use of NelderMead for the variance updates, which seems to be more stable/robust as it does not depend on the inverse Fisher info and is usually faster.The
ranef()
extraction function for"ah4"
objects gained a usefultomatrix
argument, which rearranges random effects in a unit x effect matrix (also transforming CAR effects appropriately).Generalized
hhh4()
to also capture parametric neighbourhood weights (like a powerlaw decay). The new functionnbOrder()
determines the neighbourhood order matrix from a binary adjacency matrix (depends on package spdep).New argument
check.analyticals
(defaultFALSE
) mainly for development purposes.
BUG FIXES
Fixed sign of observed Fisher information matrix in
twinstim
.Simulation from the Lomax kernel is now correct (via polar coordinates).
Fixed wrong Fisher information entry for the overdispersion parameter in
hhh4
models.Fixed wrong entries in penalized Fisher information wrt the combination fixed effects x CAR intercept.
Fixed indexing bug in penalized Fisher calculation in the case of multiple overdispersion parameters and random intercepts.
Fixed bug in Fisher matrix calculation concerning the relation of unitspecific and random effects (did not work previously).
Improved handling of nonconvergent / degenerate solutions during
hhh4
optimization. This involves usingginv()
from package MASS, if the penalized Fisher info is singular.Correct labeling of overdispersion parameter in
"ah4"
objects.Some control arguments of
hhh4()
have more clear defaults.The result of
algo.farrington.fitGLM.fast()
now additionally inherits from the"lm"
class to avoid warnings frompredict.lm()
about fake object.Improved ‘NAMESPACE’ imports.
Some additional tiny bug fixes, see the subversion log on RForge for details.
surveillance 1.42 (20120817)
SYNOPSIS
This is mainly a patch release for the
twinstim
related functionality of the package.Apart from that, the package is now again compatible with older releases of R (< 2.15.0) as intended (by defining
paste0()
in the package namespace if it is not found in R base at installation of the surveillance package).
NEW FEATURES
Important new
twinstim()
feature: fix parameters during optimization.Useful
update
method for"twinstim"
objects.New
[[
 andplot
methods for"simEpidataCSlist"
objects.simEpidataCS()
received tiny bug fixes and is now able to simulate from epidemiconly models.R0
method for"simEpidataCS"
objects (actually a wrapper forR0.twinstim()
).Removed
dimyx
andeps
arguments fromR0.twinstim()
; now usesnCub
andnCub.adaptive
from the fitted model and applies the same (numerical) integration method.animate.epidata
is now compatible with the animation package.More thorough documentation of
"twinstim"
related functions including many examples.
BUG FIXES ("twinstim"
related)
nlminb
(instead ofoptim
’s"BFGS"
) is now the default optimizer (as already documented).The
twinstim
argumentnCub
can now be omitted when usingsiaf.constant()
(as documented) and is internally set toNA_real_
in this case. Furthermore,nCub
andnCub.adaptive
are set toNULL
if there is no epidemic component in the model.toLatex.summary.twinstim
now again works forsummary(*, test.iaf=FALSE)
.print
 andsummary
methods for"epidataCS"
no longer assume that theBLOCK
index starts at 1, which may not be the case when using a subset insimulate.twinstim()
.The
"counter"
step function returned bysummary.epidataCS()
does no longer produce false numbers of infectives (they were lagged by one timepoint).plot.epidataCS()
now resolves … correctly and the argumentcolTypes
takes care of a possiblesubset
.simEpidataCS()
now also works for endemiconly models and is synchronised withtwinstim()
regarding the way howsiaf
is numerically integrated (including the argumentnCub.adaptive
).Fixed problem with
simEpidataCS()
related to missing ‘NAMESPACE’ imports (and reexports) ofmarks.ppp
andmarkformat.default
from spatstat, which are required forspatstat::runifpoint()
to work, probably because spatstat currently does not register its S3methods.Improved error handling in
simEpidataCS()
. Removed abrowser()
call and avoid potentially infinite loop.
BUG FIXES ("twinSIR"
related)
The
.allocate
argument ofsimEpidata()
has now a failsave default.Simulation without endemic
cox()
terms now works.
MINOR CHANGES
Simplified
imdepi
data to monthly instead of weekly intervals instgrid
for faster examples and reduced package size.The environment of all predefined interaction functions for
twinstim()
is now set to the.GlobalEnv
. The previous behaviour of defining them in theparent.frame()
could have led to hugesave()
’s of"twinstim"
objects even withmodel=FALSE
.simulate.twinSIR
only returns a list of epidemics ifnsim > 1
.simulate.twinstim
usesnCub
andnCub.adaptive
from fitted object as defaults.Removed the …argument from
simEpidataCS()
.The coefficients returned by
simEpidataCS()
are now stored in a vector rather than a list for compatibility with"twinstim"
methods.Argument
cex.fun
ofintensityplot.twinstim()
now defaults to thesqrt
function (as inplot.epidataCS()
.
surveillance 1.4 (20120726)
SYNOPSIS
 Besides minor bug fixes, additional functionality has entered the package and a new attempt is made to finally release a new version on CRAN (version 1.3 has not appeared on CRAN), including a proper ‘NAMESPACE’.
NEW FEATURES
Support for nonparametric backprojection using the function
backprojNP()
which returns an object of the new"stsBP"
class which inherits from"sts"
.Bayesian nowcasting for discrete time count data is implemented in the function
nowcast()
.Methods for cubature over polygonal domains can now also visualize what they do. There is also a new quasiexact method for cubature of the bivariate normal density over polygonal domains. The function
polyCub()
is a wrapper for the different methods.residuals.twinstim()
andresiduals.twinSIR()
: extract the “residual process”, see Ogata (1988). The residuals of"twinSIR"
and"twinstim"
models may be checked graphically by the new functioncheckResidualProcess()
.Many new features for the
"twinstim"
class of selfexciting spatiotemporal point process models (see below).
NEW FEATURES AND SIGNIFICANT CHANGES FOR "twinstim"
Modified arguments of
twinstim()
: new ordering, new argumentnCub.adaptive
, removed argumenttypeSpecificEndemicIntercept
(which is now specified as part of theendemic
formula as(1type)
).Completely rewrote the
R0
method (calculate “trimmed” and “untrimmed” R_0 values)The “trimmed”
R0
values are now part of the result of the model fit, as well asbbox(W)
. The model evaluation environment is now set as attribute of the result ifmodel=TRUE
.New predefined spatial kernel: the Lomax power law kernel
siaf.lomax()
plot
methods for"twinstim"
(intensityplot()
andiafplot()
)as.epidataCS()
now autogenerates the stopcolumn if this is missingprint
method for class"summary.epidataCS"
[
 and subsetmethod for"epidataCS"
(subsetting...$events
)plot
method for"epidataCS"
surveillance 1.3 (20110425)
SYNOPSIS
 This is a major realease integrating plenty of new code (unfortunately not all documented as good as it could be). This includes code for the
"twinstim"
and the"hhh4"
model. The"twinSIR"
class of models has been migrated from package RLadyBug to surveillance. It may take a while before this version will become available from CRAN. For further details see below.
SIGNIFICANT CHANGES
Renamed the
"week"
slot of the"sts"
S4 class to"epoch"
. All saved data objects have accordingly be renamed, but some hazzle is to be expected if one you have old"sts"
objects stored in binary form. The functionconvertSTS()
can be used to convert such “old school”"sts"
objects.Removed the functions
algo.cdc()
andalgo.rki()
.
NEW FEATURES
Support for
"twinSIR"
models (with associated"epidata"
objects) as described in Höhle (2009) has been moved from package RLadyBug to surveillance. That means continuoustime discretespace SIR models.Support for
"twinstim"
models as described in Meyer et al (2012). That means continuoustime continuousspace infectious disease models.Added functionality for nonparametric back projection (
backprojNP()
) and nowcasting (nowcast()
) based on"sts"
objects.
surveillance 1.22
Replaced the deprecated getSpPPolygonsLabptSlots method with calls to the coordinates method when plotting the map slot.
Minor proofreading of the documentation.
Added an argument
"extraMSMargs"
to the algo.hmm function.Fixed bug in
outbreakP()
when having observations equal to zero in the beginning. Here, μ̂^{C1} in (5) of Frisen et al (2008) is zero and hence the logbased summation in the code failed. Changed to product as in the original code, which however might be less numerically stable.Fixed bug in stcd which added one to the calculated index of idxFA and idxCC. Thanks to Thais Rotsen Correa for pointing this out.
surveillance 1.21 (20100610)
Added
algo.outbreakP()
(Frisen & Andersson, 2009) providing a semiparametric approach for outbreak detection for Poisson distributed variables.Added a pure R function for extracting ISO week and year from Date objects. This function (isoWeekYear) is only called if
"%G"
and"%V"
format strings are used on Windows (sessionInfo()[[1]]$os == "mingw32"
) as this is not implemented for"format.Date"
on Windows. Thanks to Ashley Ford, University of Warwick, UK for identifying this Windows specific bug.For
algo.farrington()
a faster fit routine"algo.farrington.fitGLM.fast"
has been provided by Mikko Virtanen, National Institute for Health and Welfare, Finland. The new function callsglm.fit()
directly, which gives a doubling of speed for long series. However, if one wants to process the fitted model output some of the GLM routines might not work on this output. For backwards compability the argumentcontrol$fitFun = "algo.farrington.fitGLM"
provides the old (and slow) behaviour.
surveillance 1.16 (20100525)
A few minor bug fixes
Small improvements in the Cimplementation of the
twins()
function by Daniel Sabanés Bové fixing the segmentation fault issue on 64bit architectures.
surveillance 1.12 (20091015)
Added the functions categoricalCUSUM and LRCUSUM.runlength for the CUSUM monitoring of general categorical time series (binomial, betabinomial, multinomial, ordered response, BradleyTerry models).
Added the functions pairedbinCUSUM and pairedbinCUSUM.runlength implementing the CUSUM monitoring and runlength computations for a paired binary outcome as described in Steiner et al. (1999).
Experimental implementation of the prospective spacetime cluster detection described in Assuncao and Correa (2009).
Added a
demo("biosurvbook")
containing the code of an upcoming book chapter on how to use the surveillance package. This contains the description of ISO date use, negative binomial CUSUM, runlength computation, etc. From an applicational point of view the methods are illustrated by Danish mortality monitoring.Fixed a small bug in algo.cdc found by Marian Talbert Allen which resulted in the control$m argument being ignored.
The constructor of the sts class now uses the argument
"epoch"
instead of weeks to make clearer that also daily, monthly or other data can be handled.Added additional epochAsDate slot to sts class. Modified plot functions so they can handle ISO weeks.
algo.farrington now also computes quantile and median of the predictive distribution. Furthermore has the computation of reference values been modified so its a) a little bit faster and b) it is also able to handle ISO weeks now. The reference values for date t0 are calculated as follows: For i, i=1,…, b look at date t0  i*year. From this date on move w months/weeks/days to the left and right. In case of weeks: For each of these determined time points go back in time to the closest Monday
Renamed the functions obsinyear to epochInYear, which now also handles objects of class Date.
surveillance 1.02 (20090306)
Negative Binomial CUSUM or the more general NegBin likelihood ratio detector is now implemented as part of algo.glrnb. This includes the back calculation of the required number of cases before an alarm.
Time varying proportion binomial CUSUM.
surveillance 0.910
Current status: Development version available from http://surveillance.rforge.rproject.org/
Rewriting of the plot.sts.time.one function to use polygons instead of lines for the number of observed cases. Due cause a number of problems were fixed in the plotting of the legend. Plotting routine now also handles binomial data, where the number of observed cases y are stored in
"observed"
and the denominator data n are stored in"populationFrac"
.Problems with the aggregate function not operating correctly for the populationFrac were fixed.
The
"rogerson"
wrapper function for algo.rogerson was modified so it now works better for distribution"binomial"
. Thus a time varying binomial cusum can be run by callingrogerson( x, control(..., distribution="binomial"))
An experimental implementation of the twins model documented in Held, L., Hofmann, M., Höhle, M. and Schmid V. (2006). A twocomponent model for counts of infectious diseases, Biostatistics, 7, pp. 422–437 is now available as algo.twins.
surveillance 0.99 (20080121)
 Fixed a few small problems which gave warnings in the CRAN distribution
surveillance 0.98 (20080119)
The algo_glrpois function now has an additional
"ret"
arguments, where one specifies the return type. The arguments of the underlying c functions have been changed to include an additional direction and return type value arguments.added restart argument to the algo.glrpois control object, which allows the user to control what happens after the first alarm has been generated
experimental algo.glrnb function is added to the package. All calls to algo.glrpois are now just alpha=0 calls to this function. However, the underlying C functions differentiate between poisson and negative case