Pipeline broken

[IainMoppett]

There seem to be a lot of aspects of the pipeline that don't work. NHS Digital have recently updated their system but not having tried the code before I don't know whether the problems stem from that. For those that want to try:

• HES APC data are comma separated, so the separator needs to be set to "," not "|".
• The process seems to fail silently - if the various functions that write 'data' don't execute properly there is no error message so the user needs to hunt down the relevant function. (The logs are are useful tool here).
• I'm not sure if the comorbidity package is working with current versions - I couldn't get it to work but maybe I was doing something wrong. For those that want to calculate Elixhauser and Charlson the package 'coder' seems to do the trick.