Last data update: 2014.03.03
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surveillance
Package: surveillance
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Version: 1.12.1
Date: 2016-05-18
Authors@R: c(MH = person("Michael", "Höhle",
email = "hoehle@math.su.se",
role = c("aut", "ths")),
SM = person("Sebastian", "Meyer",
email = "Sebastian.Meyer@ifspm.uzh.ch",
role = c("aut", "cre")),
MP = person("Michaela", "Paul", role = "aut"),
LH = person("Leonhard", "Held",
email = "Leonhard.Held@uzh.ch",
role = c("ctb", "ths")),
person("Thais", "Correa", role = "ctb"),
person("Mathias", "Hofmann", role = "ctb"),
person("Christian", "Lang", role = "ctb"),
person("Juliane", "Manitz", role = "ctb"),
person("Andrea", "Riebler", role = "ctb"),
person("Daniel", "Sabanés Bové", role = "ctb"),
MS = person("Maëlle", "Salmon", role = "ctb"),
DS = person("Dirk", "Schumacher", role = "ctb"),
person("Stefan", "Steiner", role = "ctb"),
person("Mikko", "Virtanen", role = "ctb"),
person("Wei", "Wei", role = "ctb"),
person("Valentin", "Wimmer", role = "ctb"),
person("R Core Team", role = "ctb",
comment = "A few code segments are modified versions of
code from base R"))
Author: Michael Höhle [aut, ths], Sebastian Meyer [aut, cre],
Michaela Paul [aut], Leonhard Held [ctb, ths],
Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb],
Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Sabanés Bové [ctb],
Maëlle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb],
Mikko Virtanen [ctb], Wei Wei [ctb], Valentin Wimmer [ctb], R Core Team [ctb]
(A few code segments are modified versions of code from base R)
Maintainer: Sebastian Meyer <Sebastian.Meyer@ifspm.uzh.ch>
Depends: R (>= 3.2.0), methods, grDevices, graphics, stats, utils, sp
(>= 1.0-15), xtable (>= 1.7-0), polyCub (>= 0.4-3)
Imports: Rcpp (>= 0.11.0), MASS, Matrix, nlme, spatstat (>= 1.36-0)
LinkingTo: Rcpp
Suggests: parallel, grid, xts, gridExtra, lattice, colorspace, scales,
animation, msm, spc, quadprog, memoise, polyclip, rgeos,
gpclib, maptools, intervals, spdep, numDeriv, maxLik, gsl,
testthat (>= 0.11.0), coda, splancs, gamlss, INLA (>=
0.0-1458166556), runjags, ggplot2, MGLM, knitr
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of Höhle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available monitoring procedures is
given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>.
For the retrospective analysis of epidemic spread, the package provides
three endemic-epidemic modeling frameworks with tools for visualization,
likelihood inference, and simulation. 'hhh4' estimates models for
(multivariate) count time series following Paul and Held (2011)
<doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>.
'twinSIR' models the susceptible-infectious-recovered (SIR) event
history of a fixed population, e.g, epidemics across farms or networks,
as a multivariate point process as proposed by Höhle (2009)
<doi:10.1002/bimj.200900050>. 'twinstim' estimates self-exciting point
process models for a spatio-temporal point pattern of infective events,
e.g., time-stamped geo-referenced surveillance data, as proposed by
Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>.
A recent overview of the implemented space-time modeling frameworks
for epidemic phenomena is given by Meyer et al. (2015)
<http://arxiv.org/abs/1411.0416>.
License: GPL-2
URL: http://surveillance.r-forge.r-project.org/
Additional_repositories: https://www.math.ntnu.no/inla/R/stable
BugReports: https://r-forge.r-project.org/tracker/?group_id=45
Encoding: latin1
VignetteBuilder: utils, knitr
NeedsCompilation: yes
Packaged: 2016-05-17 22:48:20 UTC; sebastian
Repository: CRAN
Date/Publication: 2016-05-18 06:53:12
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'surveillance' ...
** package 'surveillance' successfully unpacked and MD5 sums checked
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -fpic -g -O2 -c backproj.cc -o backproj.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -fpic -g -O2 -c ks.c -o ks.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -fpic -g -O2 -c stcd-assuncaocorrea.cc -o stcd-assuncaocorrea.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -fpic -g -O2 -c surveillance.c -o surveillance.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -fpic -g -O2 -c twins.cc -o twins.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o surveillance.so backproj.o ks.o stcd-assuncaocorrea.o surveillance.o twins.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/surveillance/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'surveillance'
finding HTML links ... done
LRCUSUM.runlength html
MMRcoverageDE html
R0 html
abattoir html
addFormattedXAxis html
addSeason2formula html
aggregate.disProg html
algo.bayes html
algo.call html
algo.cdc html
algo.compare html
algo.cusum html
algo.farrington html
algo.farrington.assign.weights html
algo.farrington.fitGLM html
algo.farrington.threshold html
algo.glrnb html
algo.hhh html
algo.hhh.grid html
algo.hmm html
algo.outbreakP html
algo.quality html
algo.rki html
algo.rogerson html
algo.summary html
algo.twins html
all.equal html
animate html
anscombe.residuals html
arlCusum html
backprojNP html
bestCombination html
boda html
bodaDelay html
calibration html
campyDE html
categoricalCUSUM html
checkResidualProcess html
coeflist html
compMatrix.writeTable html
correct53to52 html
create.disProg html
create.grid html
deleval html
disProg2sts html
discpoly html
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/discpoly.Rd:12: missing file link 'gpc.poly-class'
earsC html
enlargeData html
epidata html
epidataCS html
finding level-2 HTML links ... done
epidataCS_aggregate html
epidataCS_animate html
epidataCS_permute html
epidataCS_plot html
epidataCS_update html
epidata_animate html
epidata_intersperse html
epidata_plot html
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/epidata_plot.Rd:56: missing file link 'brewer.pal'
epidata_summary html
estimateGLRNbHook html
farringtonFlexible html
find.kh html
findH html
findK html
fluBYBW html
formatPval html
glm_epidataCS html
ha html
hagelloch html
hepatitisA html
hhh4 html
hhh4_W html
hhh4_calibration html
hhh4_formula html
hhh4_methods html
hhh4_plot html
Rd warning: /tmp/RtmptSttFF/Rbuild20209269dd7/surveillance/man/hhh4_plot.Rd:245: missing file link 'grid.arrange'
hhh4_predict html
hhh4_simulate html
hhh4_simulate_plot html
hhh4_update html
hhh4_validation html
husO104Hosp html
imdepi html
influMen html
inside.gpc.poly html
intensityplot html
intersectPolyCircle html
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/intersectPolyCircle.Rd:30: missing file link 'gIntersection'
isScalar html
isoWeekYear html
knox html
ks.plot.unif html
layout.labels html
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/layout.labels.Rd:37: missing file link 'panel.text'
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/layout.labels.Rd:63: missing file link 'panel.text'
linelist2sts html
loglikelihood html
m1 html
magic.dim html
make.design html
makePlot html
marks html
meanResponse html
measles.weser html
measlesDE html
meningo.age html
momo html
multiplicity html
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/multiplicity.Rd:7: missing file link 'multiplicity'
multiplicity.Spatial html
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/multiplicity.Spatial.Rd:38: missing file link 'multiplicity'
nbOrder html
nowcast html
pairedbinCUSUM html
permutationTest html
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/permutationTest.Rd:68: missing file link 'symmetry_test'
pit html
plapply html
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/plapply.Rd:7: missing file link 'parLapply'
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/plapply.Rd:26: missing file link 'parLapply'
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/plapply.Rd:34: missing file link 'clusterSetRNGStream'
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/plapply.Rd:68: missing file link 'parLapply'
plot.atwins html
plot.disProg html
plot.survRes html
poly2adjmat html
polyAtBorder html
predict.ah html
primeFactors html
print.algoQV html
qlomax html
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/qlomax.Rd:13: missing file link 'qlomax'
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/qlomax.Rd:42: missing file link 'Lomax'
ranef html
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/ranef.Rd:9: missing file link 'ranef'
readData html
refvalIdxByDate html
residuals.ah html
residualsCT html
rotaBB html
runifdisc html
salmAllOnset html
salmHospitalized html
salmNewport html
salmonella.agona html
scale.gpc.poly html
shadar html
sim.pointSource html
sim.seasonalNoise html
simHHH html
stK html
stcd html
sts-class html
stsAggregate html
stsBP-class html
stsNC-class html
stsNewport html
stsSlots html
stsXtrct html
sts_animate html
sts_creation html
sts_observation html
stsplot html
stsplot_space html
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/stsplot_space.Rd:66: missing file link 'trans'
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/stsplot_space.Rd:78: missing file link 'heat_hcl'
stsplot_spacetime html
stsplot_time html
sumNeighbours html
surveillance-package html
surveillance.options html
test html
testSim html
toFileDisProg html
toLatex.sts html
twinSIR html
twinSIR_cox html
twinSIR_exData html
twinSIR_intensityplot html
twinSIR_methods html
twinSIR_profile html
twinSIR_simulation html
twinstim html
twinstim_epitest html
twinstim_iaf html
twinstim_iafplot html
twinstim_intensity html
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/twinstim_intensity.Rd:112: missing file link 'Sobj_SpatialGrid'
twinstim_methods html
twinstim_plot html
twinstim_profile html
twinstim_siaf html
twinstim_siaf_simulatePC html
twinstim_simulation html
twinstim_step html
twinstim_tiaf html
twinstim_update html
unionSpatialPolygons html
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/unionSpatialPolygons.Rd:27: missing file link 'gUnaryUnion'
Rd warning: /tmp/RtmpUacs4H/R.INSTALL197e367751e2/surveillance/man/unionSpatialPolygons.Rd:49: missing file link 'gUnaryUnion'
untie html
wrap.algo html
xtable.algoQV html
zetaweights html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (surveillance)
Making 'packages.html' ... done
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