R package for users of data from https://motus.org

See the motus package site for detailed usage information

## Installation

### Updating

If you are updating your version of motus from a version <1.5.0 to >= 1.5.0 (i.e. from when motusClient was a separate package), you will have best results if you first remove motus and motusClient and reinstall from scratch:

remove.packages(c("motus", "motusClient"))

Now you can install v1.5.0+ as follows.

### New Installation

Users: the ‘master’ branch is what you want. You can install it from R by doing:

install.packages("remotes")              ## if you haven't already done this
remotes::install_github("motusWTS/motus@master")   ## the lastest stable version

Developers: the ‘betaX’ branches are for work-in-progress. Install the one you want

install.packages("remotes")                       ## if you haven't already done this
remotes::install_github("motusWTS/motus@beta3")   ## the beta branch for version 3+

### Troubleshooting

#### General Problems

Many, many, problems arise from conflicts between R packages which may be out of date. If you have a problem that you can’t seem to resolve, try the following steps in order (stopping when the problem goes away). If you have a problem installing motus, try Step 2 first.

1. Update motus and packages that motus depends on. (You may first need to install the remotes package). Re-start R
remotes::update_packages("motus")
1. Update all your packages. Re-start R
remotes::update_packages()
1. Update R https://cran.r-project.org/. (You may have to reinstall packages)

#### Specific Problems

Some known installation problems are listed below. If all else fails, uninstalling R and/or R Studio, and reinstalling the latest R version typically works. Depending on how much customization you have made to your R configuration, this may be the quickest option available.

cannot remove prior installation of package

If you get errors “cannot remove prior installation of package …” (e.g. dplyr) while trying to install motus, this could be due to having multiple R sessions active. You can try the following:

1. find out your R package library location: Sys.getenv("R_LIBS_USER") or .libPaths()
2. close any session of R and/or R Studio
3. in the library folder, manually delete the package that failed to remove (e.g. dplyr)
4. restart R and manually install the package again e.g. install.packages("dplyr")

Another possible cause of this problem relates to file permissions in your library folders (e.g. libraries installed in c:\program files\R\R-3.x.x\library). To confirm this, you can try running R “as administrator” (right-clicking the R icon), or use SUDO R (Linux/Ubuntu) and trying installation again. If this resolves your problem, you should consider setting your libraries in a new folder where your logged in user has full access:

# confirm the libPaths location(s)
.libPaths()
# add a new libPaths default location
.libPaths("c:/users/myusername/R/win-libraries")