Install R package ctrdata
Ralf Herold
2022-03-20
Source:vignettes/ctrdata_install.Rmd
ctrdata_install.Rmd
Install package ctrdata
on a R system
The R Project website (https://www.r-project.org/) provides installers for the R system. It can be used with software products and graphical user interfaces such as R Studio, or Microsoft R Open, or from Visual Studio Code.
General information on the ctrdata
package is available
here: https://github.com/rfhb/ctrdata.
In R, execute:
install.packages("ctrdata")
For using the development version of package ctrdata
,
install from GitHub:
# install preparatory package
install.packages(c("devtools", "httr"))
devtools::install_github("rfhb/ctrdata")
Either of the above should install package ctrdata
into
the user’s library.
Internet access via proxy
Functions in package ctrdata
that start with
ctr...
require access to trial registers over the internet
via the https
protocol. Many organisastions use transparent
proxies that may not require users to do any configurations.
However, if necessary, package ctrdata
can use proxy
settings set by users in their R session such as follows:
Sys.setenv(https_proxy = "your_proxy.server.domain:8080") # if needed
Sys.setenv(https_proxy_user = "your_userid:your_password") # if needed
Additional installation aspects
The command line tools perl
, sed
and
php
(5.2 or higher) are required for
ctrLoadQueryIntoDb()
, the main function of package
ctrdata
. No other function in this package has this
requirement.
MS Windows
For this requirement on MS Windows, the Cygwin
environment has to be installed, into the local directory
c:\cygwin
(or any folder corresponding to
c:\cygw*
). The installation of a minimal Cygwin environment
on MS Windows can be done with the help of package ctrdata
in R as follows:
ctrdata::installCygwinWindowsDoInstall()
To update or correct the Cygwin installation:
ctrdata::installCygwinWindowsDoInstall(force = TRUE)
If internet access requires to specify a proxy (see above):
ctrdata::installCygwinWindowsDoInstall(proxy = "proxy.server.domain:8080")
To install Cygwin manually, download the setup executable from here. In a MS Windows command window or Powershell window, use the following command line. The parameters are explained here.
setup-x86_64.exe --no-admin --quiet-mode --verbose --upgrade-also --root c:/cygwin
--site http://www.mirrorservice.org/sites/sourceware.org/pub/cygwin/
--packages perl,php-jsonc,php-simplexml
macOS, Linux and other operating systems
The command line tools perl
, sed
and
php
(5.2 or higher) may already be available by default in
some Linux and macOS systems. They are checked when running
ctrLoadQueryIntoDb()
; alternatively, check with
(ctrdata:::checkBinary())
.
Databases to use
At this time, a PostgreSQL, an SQLite or a remote or local MongoDB
database can be used with the package ctrdata
. A full
SQLite database is provided in the R package RSQLite
. Suggested
installation instructions for PostgreSQL are here and for a local
MongoDB server are here;
a remote MongoDB database server is accessible here.
If available, a PostgreSQL or MongoDB local server is recommended for notably faster performance than SQLite.
Purpose | Function call | Reference |
---|---|---|
Create SQLite database connection | dbc <- nodbi::src_sqlite(dbname = "name_of_my_database", collection = "name_of_my_collection") |
nodbi::src_sqlite() |
Create PostgreSQL database connection |
dbc <- nodbi::src_postgres(dbname = "name_of_my_database") ;
dbc[["collection"]] <- "name_of_my_collection"
|
nodbi::src_postgres() |
Create MongoDB database connection | dbc <- nodbi::src_mongo(db = "name_of_my_database", collection = "name_of_my_collection") |
nodbi::src_mongo() |
Subsequently, use connection dbc with
ctrdata functions |
ctrdata::{ctr,db}*(con = dbc, ...) |
Attach package ctrdata
After completing the installation, attach the package from the user’s library. This will also check the availability of the additional installation requirements as mentioned above:
Remember to respect the registers’ terms and conditions (see
ctrOpenSearchPagesInBrowser(copyright = TRUE)
). Please cite
this package in any publication as follows: Ralf Herold (2022). ctrdata:
Retrieve and Analyze Clinical Trials in Public Registers. R package
version 1.9.0. https://cran.r-project.org/package=ctrdata