How To Install r-cran-surveillance on Ubuntu 18.04
Introduction
In this tutorial we learn how to install r-cran-surveillance on Ubuntu 18.04.
What is r-cran-surveillance
r-cran-surveillance is:
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.
There are three methods to install r-cran-surveillance on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install r-cran-surveillance Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install r-cran-surveillance using apt-get by running the following command:
sudo apt-get -y install r-cran-surveillance
Install r-cran-surveillance Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-cran-surveillance using apt by running the following command:
sudo apt -y install r-cran-surveillance
Install r-cran-surveillance Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install r-cran-surveillance using aptitude by running the following command:
sudo aptitude -y install r-cran-surveillance
How To Uninstall r-cran-surveillance on Ubuntu 18.04
To uninstall only the r-cran-surveillance package we can use the following command:
sudo apt-get remove r-cran-surveillance
Uninstall r-cran-surveillance And Its Dependencies
To uninstall r-cran-surveillance and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove r-cran-surveillance
Remove r-cran-surveillance Configurations and Data
To remove r-cran-surveillance configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge r-cran-surveillance
Remove r-cran-surveillance configuration, data, and all of its dependencies
We can use the following command to remove r-cran-surveillance configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-cran-surveillance
References
Summary
In this tutorial we learn how to install r-cran-surveillance package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
