Tool for analyzing CLS data and generating graphs for survival curves, doubling times
To install this tool from github follow these steps:
First we need devtools to get access to install_github.
devtools provides the infrastructure for installing from github and it has a tool requirement outside of standard R for each O/S to complete. Full details can be found from r-project at: https://www.r-project.org/nosvn/pandoc/devtools.html \ A quick summary:\ for Windows you will need rtools: https://cran.r-project.org/bin/windows/Rtools/ \ for Mac OS you need to install Xcode from the Mac App Store\ For Linux: If you are using ubuntu see below, for other versions you will need to check google for solutions to getting devtools installed to that specific linux.
there are some ubuntu dependencies that are not installed by default that are needed for devtools, so first in a shell:\ sudo apt install libcurl4-openssl-dev libssl-dev libxml2-dev
Depending on the state of your R packages R might prompt you with a message offering to install newer versions of packages than the current binary versions. This is not a necessary step for SPOCK to work assuming you are on R >= 3.6.3. Once devtools is ready to install, install the package and load the library (commands below)
install.packages("devtools")\ library(devtools)\ install_github("https://github.com/labmccormick/SPOCK", build_vignette = TRUE)\
Once you have installed the package above you can now use the built in R vignette utility to get additional information on setting up your data to run SPOCK by running\ browseVignettes("SPOCK")
If when you are installing SPOCK you get an error with conflicting rlang you need to exit out of rstudio and then when you reload rstudio first run install.packages("rlang") and reload library(devtools). This should fix this conflict and allow you to continue installation.