JASMIN-tips.md

+This page is meant to supplement the [How-to-install](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/wikis/How-to-install) page.
+
+**Activating conda R environment**
+
+On some Linux systems Conda does not run or activate environments properly, this is due to environment paths not being properly set. The following has been found to work on JASMIN
+
+```
+export conda_base=`conda info --base`
+source ${conda_base}/etc/profile.d/conda.sh
+conda activate <your_env>
+``` 
+
+where *\<your_env\>* is the name of the environment you wish to activate.
+
+
+
+**Installing R packages not on Conda forge or available through the *conda install* command**
+
+Many, but not all, R packages can be installed via conda forge, e.g.
+
+```
+conda install -c conda-forge <required_package>
+```
+
+Those not available through conda-forge can still be installed via CRAN by downloading the source code and installing from source. When doing this *pkg-config* needs to be configured properly, with the *PKG_CONFIG_PATH* environment variable set to point at the correct directory for the current environment. e.g.
+
+```
+export PKG_CONFIG_PATH="/home/users/random_user/.conda/envs/r_env0/lib/pkgconfig"
+```
+
+for user *random_user* and environment *r_env0*. Package ggplot2, for example, could then be installed via:
+
+```
+wget https://cran.r-project.org/src/contrib/ggplot2_3.3.1.tar.gz
+R CMD INSTALL ggplot2_3.3.1.tar.gz
+```
+
+When installing a package via this method it is likely that the first attempt will fail due to missing dependencies.  If this happens install those dependencies and then try again.
+
+
+
+**Running new_merge_ids_year.R interactively**
+
+The script *new_merge_ids_year.R* is typically run in batch mode, e.g.
+
+`Rscript new_merge_ids_year.R <year1> <year2>`
+
+Where *\<year1\>* and *\<year2\>* are the first and last year to run respectively. For testing purposes the script can also be run interactively by starting R, setting the variable *args2* to first and last year and then sourcing the script.
+
+```
+R
+args2 <- c(1980,1980)
+source('new_merge_ids_year.R)
+```
+
+As part of the script the number of arguments are checked and if zero, as is the case when run interactively, the script uses the values in the variable *args2* instead.
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