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Open-Source — ultimaker (Ultimaker) / debian-backup — Project

A certifiably-awesome open-source package repository curated by Ultimaker, hosted by Cloudsmith.

Note: Packages in this repository are licensed as GNU General Public License v3.0 or later (dependencies may be licensed differently).

r-cran-surveillance 1.16.2-1

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One-liner (summary)

GNU R package for the Modeling and Monitoring of Epidemic Phenomena

Description

Implementation of statistical methods for the modeling and change-point detection in time series of counts, proportions and categorical data, as well as for the modeling of continuous-time epidemic phenomena, e.g., discrete-space setups such as the spatially enriched Susceptible-Exposed-Infectious-Recovered (SEIR) models, or continuous-space point process data such as the occurrence of infectious diseases. Main focus is on outbreak detection in count data time series originating from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics or social sciences.

Currently, the package contains implementations of many typical outbreak detection procedures such as Farrington et al (1996), Noufaily et al (2012) or the negative binomial LR-CUSUM method described in Höhle and Paul (2008). A novel CUSUM approach combining logistic and multinomial logistic modelling is also included. Furthermore, inference methods for the retrospective infectious disease models in Held et al (2005), Held et al (2006), Paul et al (2008), Paul and Held (2011), Held and Paul (2012), and Meyer and Held (2014) are provided.

Continuous self-exciting spatio-temporal point processes are modeled through additive-multiplicative conditional intensities as described in Höhle (2009) ('twinSIR', discrete space) and Meyer et al (2012) ('twinstim', continuous space).

The package contains several real-world data sets, the ability to simulate outbreak data, visualize the results of the monitoring in temporal, spatial or spatio-temporal fashion.

Note: Using the 'boda' algorithm requires the 'INLA' package, which is available from <http://www.r-inla.org/download>.

License

Unknown

Size

5.5 MB

Downloads

Status	Completed
Checksum (MD5)	03f2f2a8d79006e53a9762dd26cfeba7
Checksum (SHA-1)	78bf657336c3383893173e055c13405f0598357f
Checksum (SHA-256)	05df513d1f8a6e7216c57c8f60a0c1f997674e95ae9922c7bd819f7ae8e2c618
Checksum (SHA-512)	42a61e2b7067eb3a13918a0074d413084781c405429f77414e7f93678ca9dd23f7…
GPG Signature	Download
GPG Fingerprint	c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution	debian/buster - Debian - 10 (Buster)
Storage Region	Dublin, Ireland
Type	Binary (contains binaries and binary artifacts)
Uploaded At	1 year, 1 month ago
Uploaded By
Slug Id	r-cran-surveillance_1162-1_armhfdeb-y2yp
Unique Id	xdfJ9WyPvTYB
Version (Raw)	1.16.2-1
Version (Parsed)	Major: 1 Minor: 16 Patch: 2 Pre (Str): (empty) Pre (Num Array): 1 Type: SemVer (Strict)
	extended metadata
Homepage	https://cran.r-project.org/package=surveillance
Installed Size	6.7 MB
Maintainer	Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Priority	optional
Section	gnu-r

Dependencies

Checksum (md5)

8e52de8a278027aed31898c2bee7e0e2

Depends	libc6	>=2.4
Depends	libgcc1	>=1:3.5
Depends	libstdc++6	>=5.2
Depends	r-api-3.5
Depends	r-base-core	>=3.5.1-1
Depends	r-cran-mass
Depends	r-cran-matrix
Depends	r-cran-nlme
Depends	r-cran-polycub	>=0.6.0
Depends	r-cran-rcpp	>=0.11.1
Depends	r-cran-sp	>=1.0-15
Depends	r-cran-spatstat	>=1.36-0
Depends	r-cran-xtable	>=1.7-0
Recommends	r-cran-maxlik
Recommends	r-cran-memoise
Recommends	r-cran-spdep
Recommends	r-cran-testthat	>=0.10.0
Suggests	r-cran-animation
Suggests	r-cran-coda
Suggests	r-cran-colorspace
Suggests	r-cran-ggplot2
Suggests	r-cran-gridextra	>=2.0.0
Suggests	r-cran-gsl
Suggests	r-cran-knitr
Suggests	r-cran-lattice
Suggests	r-cran-maptools
Suggests	r-cran-msm
Suggests	r-cran-numderiv
Suggests	r-cran-polyclip
Suggests	r-cran-quadprog
Suggests	r-cran-scales
Suggests	r-cran-spc
Suggests	r-cran-testthat	>=0.11.0
Suggests	r-cran-xts

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These instructions assume you have setup the repository first (or read it).

To install/use r-cran-surveillance @ version 1.16.2-1 ...

To install packages, you can quickly setup the repository automatically (recommended):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E bash

If you need to force a specific distribution, release/version, architecture, or component (if supported), you can also do that (e.g. if your system is compatible but not identical):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E distro=debian codename=buster arch=ARCH component=COMPONENT bash

or ... you can manually configure it yourself before installing packages:

apt-get install -y debian-keyring  # debian only
apt-get install -y debian-archive-keyring  # debian only
apt-get install -y apt-transport-https
# For Debian Stretch, Ubuntu 16.04 and later
keyring_location=/usr/share/keyrings/ultimaker-debian-backup-archive-keyring.gpg
# For Debian Jessie, Ubuntu 15.10 and earlier
keyring_location=/etc/apt/trusted.gpg.d/ultimaker-debian-backup.gpg
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/gpg.C334EFCB2C4F9BE3.key' |  gpg --dearmor >> ${keyring_location}
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/config.deb.txt?distro=debian&codename=buster&component=main' > /etc/apt/sources.list.d/ultimaker-debian-backup.list
sudo chmod 644 ${keyring_location}
sudo chmod 644 /etc/apt/sources.list.d/ultimaker-debian-backup.list
apt-get update

sudo apt-get install r-cran-surveillance=1.16.2-1

Warning: Note that this package is for Debian 10 (Buster) / armhf and may only work for that configuration.

Still stuck? Need help? Don't panic. Just contact us for help (even if you're not a customer).

Previous Version: 1.16.2-1

Next Version: 1.16.2-1

r-cran-surveillance 1.16.2-1	debian/buster deb arm64 main latest 5.5 MB — 1 year, 1 month ago	7
r-cran-surveillance 1.16.2-1	debian/buster deb armhf main latest 5.5 MB — 1 year, 1 month ago	7
r-cran-surveillance 1.16.2-1	debian/buster deb arm64 main latest 5.5 MB — 1 year, 1 month ago	7

r-cran-surveillance 1.16.2-1

One-liner (summary)

Description

License

Size

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This package has 168 files/directories.

r-cran-surveillance

r-cran-surveillance

r-cran-surveillance

Dependencies

Checksum (md5)