Summary
Epidemiology
paquet relatif à Debian Med épidémiologie
Ce métapaquet dépend d'outils utiles pour la recherche épidémiologique.
Plusieurs paquets utilisent le langage de donnée GNU R pour des
investigations statistiques. Il peut être intéressant de lire le papier
« Une introduction rapide à R pour l'épidémiologie », disponible à
l'adresse suivante (en anglais) :
http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
Description
For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:
If you discover a project which looks like a good candidate for Debian Med
to you, or if you have prepared an unofficial Debian package, please do not hesitate to
send a description of that project to the Debian Med mailing list
Links to other tasks
|
Debian Med Epidemiology packages
Official Debian packages with high relevance
Epigrass
Outil scientifique pour la simulation et l'analyse de sénarios dans des réseaux épidémiologiques
|
Versions of package epigrass |
Release | Version | Architectures |
sid | 2.4.7-2 | amd64,arm64,armel,armhf,i386,kfreebsd-amd64,mips,mips64el,mipsel,ppc64el,s390x |
squeeze | 2.0.3-1 | all |
jessie | 2.4.0-2 | all |
stretch | 2.4.7-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
wheezy | 2.0.4-3 | all |
Debtags of package epigrass: |
field | medicine |
interface | x11 |
role | program |
scope | application |
uitoolkit | qt |
use | analysing, viewing |
works-with | db |
x11 | application |
|
License: DFSG free
|
Epigrass est un logiciel pour visualiser, analyser et simuler les
processus épidémiques sur des réseaux géo-référencés.
EpiGrass peut interagir avec le SIG (Système d'Information Géographique)
GRASS à partir duquel il peut obtenir des cartes et autres informations
géo-référencées. Cependant, EpiGrass ne requiert pas l'installation du SIG
GRASS pour la plupart de ses fonctionnalités.
The package is enhanced by the following packages:
epigrass-doc
|
|
R-cran-diagnosismed
medical diagnostic test accuracy analysis toolkit
|
Versions of package r-cran-diagnosismed |
Release | Version | Architectures |
squeeze | 0.2.3-1 | all |
wheezy | 0.2.3-2 | all |
jessie | 0.2.3-3 | all |
stretch | 0.2.3-4 | all |
buster | 0.2.3-6 | all |
sid | 0.2.3-6 | all |
Debtags of package r-cran-diagnosismed: |
devel | lang:r |
field | medicine |
interface | commandline |
role | program |
use | analysing |
|
License: DFSG free
|
DiagnosisMed is a GNU R package to analyze the accuracy of data from
diagnostic tests evaluating health conditions. It was designed to be
used by health professionals. This package helps estimating sensitivity
and specificity from categorical and continuous test results including
some evaluations of indeterminate results, or compare different
categorical tests, and estimate reasonable cut-offs of tests and display
it in a way commonly used by health professionals. No graphical
interface is available yet.
|
|
R-cran-epi
analyse épidémiologique GNU R
|
Versions of package r-cran-epi |
Release | Version | Architectures |
stretch | 2.7-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
squeeze | 1.1.15-1 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
wheezy | 1.1.33-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
jessie | 1.1.67-4 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
buster | 2.32-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.32-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 2.34 |
Debtags of package r-cran-epi: |
field | medicine |
interface | commandline |
role | program |
|
License: DFSG free
|
Fonctions pour analyses démographiques et épidémiologiques dans le
diagramme Lexis, c'est-à-dire des données de suivi de cohorte ou
d'enregistrement, ce qui inclut des données censurées par intervalles et
des représentations de données de différents états. Ce paquet contient
également des fonctions utiles pour la classification et le tracé de
courbes. Il contient des séries de données épidémiologiques.
Le paquet Epi se concentre principalement sur l'épidémiologie
« classique » des maladies chroniques. Le paquet a grandi hors des cours
de pratique statistique en épidémiologie en utilisant R. (pour plus
d'info : http://www.pubhealth.ku.dk/~bxc/SPE).
Une introduction rapide à R pour l'épidémiologie est disponible ici :
http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
Attention, les pages 38 à 120 correspondent aux pages de manuels pour le
paquet Epi.
Epi n'est pas le seul paquet R pour l'analyse épidémiologique, un paquet
ayant plus d'affinité avec l'épidémiologie des maladies infectieuses est
le paquet epitools, qui est aussi disponible dans Debian.
Epi est utilisé par de département de biostatistique de l'université de
Copenhague.
|
|
R-cran-epibasix
GNU R Elementary Epidemiological Functions
|
Versions of package r-cran-epibasix |
Release | Version | Architectures |
buster | 1.5-1 | all |
stretch | 1.3-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.5-1 | all |
squeeze | 1.1-2 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
wheezy | 1.1-3 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
jessie | 1.3-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
Debtags of package r-cran-epibasix: |
field | medicine |
interface | commandline |
role | program |
|
License: DFSG free
|
Elementary Epidemiological Functions for a Graduate Epidemiology /
Biostatistics Course.
This package contains elementary tools for analysis of common epidemiological
problems, ranging from sample size estimation, through 2x2 contingency table
analysis and basic measures of agreement (kappa, sensitivity/specificity).
Appropriate print and summary statements are also written to facilitate
interpretation wherever possible. This package is a work in progress, so
any comments or suggestions would be appreciated. Source code is commented
throughout to facilitate modification. The target audience includes graduate
students in various epi/biostatistics courses.
Epibasix was developed in Canada.
|
|
R-cran-epicalc
GNU R Epidemiological calculator
|
Versions of package r-cran-epicalc |
Release | Version | Architectures |
stretch | 2.15.1.0-2 | all |
sid | 2.15.1.0-4 | all |
wheezy | 2.14.1.6-1 | all |
squeeze | 2.11.1.0-1 | all |
jessie | 2.15.1.0-1 | all |
buster | 2.15.1.0-4 | all |
Debtags of package r-cran-epicalc: |
devel | lang:r |
field | medicine, statistics |
interface | commandline |
role | program |
|
License: DFSG free
|
Functions making R easy for epidemiological calculation.
Datasets from Dbase (.dbf), Stata (.dta), SPSS(.sav), EpiInfo(.rec) and
Comma separated value (.csv) formats as well as R data frames can be
processed to do make several epidemiological calculations.
|
|
R-cran-epir
fonctions de GNU R pour l’analyse de données épidémiologiques
|
Versions of package r-cran-epir |
Release | Version | Architectures |
squeeze | 0.9-26-1 | all |
wheezy | 0.9-38-1 | all |
jessie | 0.9-59-1 | all |
stretch | 0.9-79-1 | all |
buster | 0.9-99-1 | all |
sid | 0.9-99-1 | all |
Debtags of package r-cran-epir: |
devel | lang:r |
field | medicine |
interface | commandline |
role | program |
use | analysing |
|
License: DFSG free
|
Il s’agit d’un paquet pour l’analyse de données épidémiologiques. Il
contient des fonctions pour directement ou indirectement ajuster les
fréquences de maladies, quantifier les mesures d’association sur la base
d’une ou plusieurs couches de données de comptage présentées dans un
tableau de contingence, et calculer l’intervalle de confiance entre le
risque d’incidence et le taux d’incidence estimés. Il fournit aussi
diverses fonctions pour la méta-analyse, l’interprétation de diagnostics et
le calcul de taille d’échantillon.
|
|
R-cran-epitools
outils GNU R d’épidémiologie pour les données et graphiques
|
Versions of package r-cran-epitools |
Release | Version | Architectures |
sid | 0.5-10-2 | all |
wheezy | 0.5-6-1 | all |
buster | 0.5-10-2 | all |
squeeze | 0.5-5-1 | all |
jessie | 0.5-7-1 | all |
stretch | 0.5-7-1 | all |
Debtags of package r-cran-epitools: |
field | medicine |
interface | commandline |
role | program |
|
License: DFSG free
|
Il s’agit d’outils de GNU R pour l’épidémiologie de santé publique et
l’analyse de données. Epitools fournit des outils numériques et des
solutions de programmation qui ont été utilisées et testées, en situation
réelle, dans des applications d’épidémiologie.
Beaucoup de problèmes pratiques dans l’analyse de données de santé publique
ont besoin de programmation ou des logiciels particuliers, et les
chercheurs pourraient faire de la programmation en double. Souvent, des
analyses simples, telles que la construction d’intervalles de confiance, ne
sont pas calculées et par conséquent compliquent les inférences
statistiques appropriées pour de petites aires géographiques. Il existe de
nombreux exemples où des outils numériques simples et utiles qui
amélioreraient le travail d’épidémiologistes dans des départements locaux
ne sont pas facilement disponibles pour le problème à résoudre. La
disponibilité de ces outils encouragerait une plus large utilisation des
méthodes appropriées et promouvrait les pratiques de santé publique basées
sur des éléments probants.
|
|
R-cran-lexrankr
extractive summarization of text with the LexRank algorithm
|
Versions of package r-cran-lexrankr |
Release | Version | Architectures |
buster | 0.5.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.5.0-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
An R implementation of the LexRank algorithm implementing stochastic
graph-based method for computing relative importance of textual units
for Natural Language Processing. The technique on the problem
of Text Summarization (TS) is tested. Extractive TS relies on the concept of
sentence salience to identify the most important sentences in a
document or set of documents. Salience is typically defined in terms of
the presence of particular important words or in terms of similarity to
a centroid pseudo-sentence.
|
|
R-cran-seroincidence
GNU R seroincidence calculator tool
|
Versions of package r-cran-seroincidence |
Release | Version | Architectures |
sid | 2.0.0-1 | all |
buster | 2.0.0-1 | all |
stretch | 1.0.5-1 | all |
|
License: DFSG free
|
Antibody levels measured in a cross-sectional population samples can be
translated into an estimate of the frequency with which seroconversions
(new infections) occur. In order to interpret the measured
cross-sectional antibody levels, parameters which predict the decay of
antibodies must be known. In previously published reports (Simonsen et
al. 2009 and Versteegh et al. 2005), this information has been obtained
from longitudinal studies on subjects who had culture-confirmed
Salmonella and Campylobacter infections. A Bayesian back-calculation
model was used to convert antibody measurements into an estimation of
time since infection. This can be used to estimate the seroincidence in
the cross-sectional sample of population. For both the longitudinal and
cross-sectional measurements of antibody concentrations, the indirect
ELISA was used. The models are only valid for persons over 18 years. The
seroincidence estimates are suitable for monitoring the effect of
control programmes when representative cross-sectional serum samples are
available for analyses. These provide more accurate information on the
infection pressure in humans across countries.
|
|
R-cran-sf
|
Versions of package r-cran-sf |
Release | Version | Architectures |
buster | 0.7-2+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.7-2+dfsg-1 | amd64,arm64,armel,armhf,i386,kfreebsd-amd64,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Support for simple features, a standardized way to encode spatial vector
data. Binds to 'GDAL' for reading and writing data, to 'GEOS' for
geometrical operations, and to 'PROJ' for projection conversions and
datum transformations.
|
|
R-cran-sjplot
GNU R data visualization for statistics in social science
|
Versions of package r-cran-sjplot |
Release | Version | Architectures |
sid | 2.6.2-1 | all |
buster | 2.6.2-1 | all |
|
License: DFSG free
|
Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are
commonly used in social sciences) can be visualized using this package,
including simple and cross tabulated frequencies, histograms, box plots,
(generalized) linear models, mixed effects models, principal component
analysis and correlation matrices, cluster analyses, scatter plots,
stacked scales, effects plots of regression models (including
interaction terms) and much more. This package supports labelled data.
|
|
R-cran-surveillance
GNU R package for the Modeling and Monitoring of Epidemic Phenomena
|
Versions of package r-cran-surveillance |
Release | Version | Architectures |
wheezy | 1.2-1-3 (contrib) | amd64,i386 |
squeeze | 1.2-1-1 (contrib) | amd64,i386 |
jessie | 1.8-0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 1.16.2-1 | amd64,arm64,armel,armhf,hurd-i386,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.16.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.13.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package r-cran-surveillance: |
field | medicine |
interface | commandline |
role | program |
|
License: DFSG free
|
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.
|
|
Official Debian packages with lower relevance
R-cran-cmprsk
GNU R subdistribution analysis of competing risks
|
Versions of package r-cran-cmprsk |
Release | Version | Architectures |
stretch | 2.2-7-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.2-7-4 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.2-7-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
This GNU R package supports estimation, testing and regression modeling
of subdistribution functions in competing risks, as described in Gray
(1988), A class of K-sample tests for comparing the cumulative incidence
of a competing risk.
|
|
R-cran-msm
modèles de Markov multi-état et caché en temps continu
|
Versions of package r-cran-msm |
Release | Version | Architectures |
buster | 1.6.6-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.6.6-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.6.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.4-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
wheezy | 1.1-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
squeeze | 0.9.7-1 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
Debtags of package r-cran-msm: |
interface | commandline |
role | program |
|
License: DFSG free
|
Fonctions pour adapter des modèles de Markov temporels cachés et continus à
des données longitudinales. Les taux de transitions de Markov et le
processus de sortie de Markov caché peuvent être modélisés en terme de co-
variables. Une variété de schémas d'observation sont permis, qui
comprennent une surveillance des processus à des temps arbitraires, une
observation complète des processus, et des états censurés.
|
|
Packaging has started and developers might try the packaging code in VCS
Epifire
model the spread of an infectious disease in a population
|
Versions of package epifire |
Release | Version | Architectures |
VCS | 3.34.0+dfsg-1 | all |
|
License: BSD-3-clause
Debian package not available
Version: 3.34.0+dfsg-1
|
EpiFire is a C++ applications programming interface (API) that does
two things:
- Model the spread of an infectious disease in a population
- Generate and manipulate networks of nodes and edges
While the network code can be used independently from the
epidemiological code and vice versa—they are conceptually and
functionally distinct—from the beginning, the libraries were developed
to be compatible with each other. What EpiFire excels at is simulating
the stochastic spread of disease on contact networks.
|
Netepi-analysis
network-enabled tools for epidemiology and public health practice
|
Versions of package netepi-analysis |
Release | Version | Architectures |
VCS | 0.9.0-2 | all |
|
License: HACOS
Debian package not available
Version: 0.9.0-2
|
NetEpi, which is short for "Network-enabled Epidemiology", is a
collaborative project to create a suite of free, open source software
tools for epidemiology and public health practice. Anyone with an
interest in population health epidemiology or public health
informatics is encouraged to examine the prototype tools and to
consider contributing to their further development. Contributions
which involve formal and/or informal testing of the tools in a wide
range of circumstances and environments are particularly welcome, as
is assistance with design, programming and documentation tasks.
This is a tool for conducting epidemiological analysis of data sets,
both large and small, either through a Web browser interface, or via
a programmatic interface. In many respects it is similar to the
analysis facilities included in the Epi Info suite, except that
NetEpi Analysis is designed to be installed on servers and accessed
remotely via Web browsers, although it can also be installed on
individual desktop or laptop computers.
The software was developed by New South Wales Department of Health.
|
Netepi-collection
network-enabled tools for epidemiology and public health practice
|
Versions of package netepi-collection |
Release | Version | Architectures |
VCS | 1.8.4-2 | all |
|
License: HACOS
Debian package not available
Version: 1.8.4-2
|
NetEpi, which is short for "Network-enabled Epidemiology", is a
collaborative project to create a suite of free, open source software
tools for epidemiology and public health practice. Anyone with an
interest in population health epidemiology or public health
informatics is encouraged to examine the prototype tools and to
consider contributing to their further development. Contributions
which involve formal and/or informal testing of the tools in a wide
range of circumstances and environments are particularly welcome, as
is assistance with design, programming and documentation tasks.
NetEpi Case Manager is a tool for securely collecting structured
information about cases and contacts of communicable (and other)
diseases through Web browsers and the Internet. New data collection
forms can be designed and deployed quickly by epidemiologists, using
a "point-and-click" interface, without the need for knowledge of or
training in any programming language. Data can then be collected from
users of the system, who can be located anywhere in the world, into a
centralised database. All that is needed by users of the system is a
relatively recent Web browser and an Internet connection ("NetEpi" is
short for "Network-enabled Epidemiology"). In many respects, NetEpi
Case Manager is like a Web-enabled version of the data entry
facilities in the very popular Epi Info suite of programmes published
by the US Centers for Disease Control and Prevention, and in the
Danish EpiData project, which is available for several languages. The
software was developed by the Centre for Epidemiology and Research of
the New South Wales Department of Health, with contributions from
Population Health Division of the Australian Government Department of
Health and Ageing.
The software was developed by New South Wales Department of Health.
|
Shiny-server
put Shiny web apps online
|
Versions of package shiny-server |
Release | Version | Architectures |
VCS | 1.5.6.875+dfsg-1 | all |
|
License: AFFERO-3
Debian package not available
Version: 1.5.6.875+dfsg-1
|
Shiny Server lets you put shiny web applications and interactive
documents online. Take your Shiny apps and share them with your
organization or the world.
Shiny Server lets you go beyond static charts, and lets you manipulate
the data. Users can sort, filter, or change assumptions in real-time.
Shiny server empower your users to customize your analysis for their
specific needs and extract more insight from the data.
|
Ushahidi
web platform for information collection
|
Versions of package ushahidi |
Release | Version | Architectures |
VCS | 2.7.4-1 | all |
|
License: LGPL-3+
Debian package not available
Version: 2.7.4-1
|
Ushahidi is a platform that allows information collection,
visualization and interactive mapping, allowing anyone to submit
information through text messaging using a mobile phone, email or web
form.
It can be used to monitor epidemic diseases, measuring the impact of
natural disasters, uncovering corruption, and empowering peace makers.
|
No known packages available but some record of interest (WNPP bug)
framework for creating agent based simulations
|
|
License: BSD
Debian package not available
|
Repast Simphony is a free and open source agent-based modeling toolkit
that simplifies model creation and use. Repast Simphony offers users a
rich variety of features including the following:
- Fluid model component development using any mixture of Java, Groovy,
and flowcharts in each project;
- A pure Java point-and-click model execution environment that includes
built-in results logging and graphing tools as well as automated
connections to a variety of optional external tools including the R
statistics environment, *ORA and Pajek network analysis plugins, A
live agent SQL query tool plugin, the VisAD scientific visualization
package, the Weka data mining platform, many popular spreadsheets,
the MATLAB computational mathematics environment, and the iReport
visual report designer;
- An extremely flexible hierarchically nested definition of space
including the ability to do point-and-click and modeling and
visualization of 2D environments; 3D environments; networks including
full integration with the JUNG network modeling library as well as
Microsoft Excel spreadsheets and UCINET DL file importing; and
geographical spaces including 2D and 3D Geographical Information
Systems (GIS) support;
- A range of data storage "freeze dryers" for model check pointing
and restoration including XML file storage, text file storage, and
database storage;
- A fully concurrent multithreaded discrete event scheduler;
- Libraries for genetic algorithms, neural networks, regression, random
number generation, and specialized mathematics;
- An automated Monte Carlo simulation framework which supports multiple
modes of model results optimization;
- Built-in tools for integrating external models;
- Distributed computing with Terracotta;
- Full object-orientation;
- Optional end-to-end XML simulation
- A point-and-click model deployment system
|
|