title: "Eidith R Package Setup" output: rmarkdown::html_vignette author: "Noam Ross" vignette: > %\VignetteIndexEntry{Eidith R Package Setup} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}
The eidith R package provides programmatic access and analytical tools for data from the PREDICT Program, housed at the Emerging Infectious Disease Information Technology Hub (EIDITH).
The eidith package contains no data. To access data, you must be a registered EIDITH user with data access privileges. If you have a question about your access level, contact technology@eidith.org.
This package is currently in development. We anticipate additional functionality for common analytical tasks. It also currently only accesses data from PREDICT-1. If you have questions, bug reports, or feature requests, please post them on our issue tracker.
eidith is installed from our own package repository rather than CRAN. To install the latest stable version, run the following command:
install.packages("eidith", repos=c("https://ecohealthalliance.github.io/eidith/", "https://cran.rstudio.com"))
If you wish to install the latest development (unstable) version, you will require the devtools package, like so:
devtools::install_github('ecohealthalliance/eidith@dev')
To download data from EIDITH, you must provide logon credentials. If you run
ed_db_download()
or the ed_get()
functions from the R console, your EIDITH username
and password will be requested. To use these functions in scripts, you
must provide these credentials as environment variables.
You can cache your credentials and login automatically by putting them in a hidden
.Renviron
file, which defines environment variables for your R session. For
more information see the ed_auth()
help file.
The eidith package downloads data from EIDITH and stores it locally on your
computer in a database so you don't have to download from the web repeatedly.
Once you've installed the package, you'll need to populated this database with
the ed_db_download()
command, like so:
library(eidith)
ed_db_download()
This may take a few minutes to complete depending on the speed of your internet connection.
Running ed_db_status()
will give you a summary of the contents of your database.
This is useful to see which countries' data you have access to or the latest
updated you have downloaded.
ed_db_updates()
will check if the online database has been updated since
your last download. If it has, ed_db_download()
may be run again to update your local database with the latest
data. You should also run it after installing a new version of the eidith
package, as a new version may change the structure of the database.
Once you've populated your local database, you can look up EIDITH data with
the table functions, each of which loads data from the different table in the
database: ed_events()
, ed_animals()
, ed_specimens()
, ed_tests()
, and
ed_viruses()
, as well as ed_testspecimen()
, which contains cross-references
between the test and specimen tables. See the help for these functions for more
details.
ed_metadata()
contains a list of all variables across these tables
and some information on them. If you lookup this in R help in RStudio with
?ed_metadata
you'll find this metadata in searchable form.
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