You cannot put references in pdf_output? Finally, after long (definitely too long) break I came with something hopefully useful. Recently I was working on some templates for reports for my previous work. Long story short I wanted to create a bookdown package, that will contain full template of report, which will be converted into html and pdf files. Since I was working with people who had no knowledge on R, LaTeX, HTML, or other programming stuff, I decided that i will have single file in RMarkdown that will compile into both html and tex.

Creating package from dirty code Previously I wrote some post on creating nice, human readable tables from EPPO database. However the code was full of fragile parts, formatting was awful and it needed some refactoring. As I wanted to push myself, I decided it is good time to try to work on making first package. And this means a lot of work. Don’t get me wrong, making package from what I wrote previously would probably take less than several hours of work.

Genereric pest spread models Assessing spread of quarantine pest under new climatic conditions is not an easy task. This kind of model must combine climatic, spatial and pest climatic suitability data. Unfortunately that is not enough in most cases. To make model that resembles reality it should also include pest biology: it’s movement abilities, reproduction, maximum population density, host availability etc. Taking all above into account we may conclude that it is extremely hard to make generic spread model.

A table in human readable format Part III Last two times I showed you how easily you can extract information from EPPO SQLite database, put it into easily understandable table and how to make use of EPPO REST API. Below I show you I will show you how to download files straight into list and use to expand table. Lets prepare our workflow by defining some variables e.g. EPPOcodes.

A table in human readable format Part II Last time i showed you how easily you can extract information from EPPO SQLite database and put it into easily understandable table. Now, I will show you how to expand this table with data obtained from EPPO REST API. But first lets recall one thing we did last time. We defined variable EPPOcodes, which we will use in this part. #query sql for codeid and eppocode sqlEppo %>% dbGetQuery(paste0('SELECT codeid, eppocode FROM t_codes WHERE codeid IN (', paste0(codeIdDB, collapse = ', '),')')) %>% arrange(eppocode) -> EPPOcodes We also need to set some constant variables to build up list of URL links for our REST queries.

A table in human readable format OK, time to run new blog have come. So, for the first post, I decided to write about something more meaningful than just ‘Look on what have I found on the Net…’. And first thing that came into my mind was ‘The Table’. It is actually thing that I made recently, to solve some time consuming issue in my work. I needed to merge data from different data structures in R into one table in human readable format.