class: center, middle  <!-- Do not forget to adapt the presentation title in the header! --> <!-- Adjust the presentation to the session. Focus on the challenges, this is not a coding tutorial. Note, to include figures, store the image in the `/docs/assets/images` folder and use the jekyll base.url reference as done in this template or see https://jekyllrb.com/docs/liquid/tags/#links. using the scale attribute , you can adjust the image size. --> <!-- Adjust the day, month --> # 18 JUNE 2019 ## INBO coding club <!-- Adjust the room number and name --> Herman Teirlinck<br> 01.71 - Frans Breziers --- class: center, middle <!-- Create a new badge using Inkscape based on the assets/images/coding_club_badges.svg file -->  --- class: center, middle Previuos month: <br /> [Rstudio database website](https://db.rstudio.com/) --- class: center, middle Previuos month: <br /> [INBO database tutorial](https://inbo.github.io/tutorials/tutorials/r_database_access/) --- class: center, middle Today: <br /> [dbplyr](https://dbplyr.tidyverse.org/) --- class: center, middle ### How to get started? Check the [Each session setup](https://inbo.github.io/coding-club/gettingstarted.html#each-session-setup) to get started. ### First time coding club? Check the [First time setup](https://inbo.github.io/coding-club/gettingstarted.html#first-time-setup) section to setup. --- class: center, middle  --- class: center, middle ### Share your code during the coding session! <!-- Create a new hackmd file and replace this link (twice!) --> Go to https://hackmd.io/AtaurkBeRXKVgvCQwpE5kw <iframe src="https://hackmd.io/AtaurkBeRXKVgvCQwpE5kw" height="400px" width="800px"></iframe> --- background-image: url(/assets/images/background_challenge_1.png) class: left, middle # Challenge 1 (Installing and) load package `inborutils` use the `connect_inbo_dbase` function from the inborutils package to connect to the database `D0021_00_userFlora`. For more information, check [INBO database tutorial](https://inbo.github.io/tutorials/tutorials/r_database_access/). - Click [`20190618/20190618_challenges.R`](https://github.com/inbo/coding-club/blob/master/src/20190618/20190618_challenges.R) and download* script to `src` subfolder. - Make a connection to `D0021_00_userFlora` - Connect to taxon table `tblTaxon` - Get the names of the columns in `taxon` - Get preview of first 10 rows of `taxon` - Get the first 10 Dutch names in `taxon` - How many taxa are in `taxon` data.frame? - Get the first 10 Dutch names in `taxon` as a "normal" data.frame (tip: check https://dbplyr.tidyverse.org/) - Get the scientific name of 'Geel schorpioenmos' <small>* __Note__: check the getting started instructions on [how to download a single file](https://inbo.github.io/coding-club/gettingstarted.html#each-session-setup)</small> --- class: left, middle ## Intermezzo <p><a href="https://resources.rstudio.com/webinars/best-practices-for-working-with-databases-march-2018-edgar-ruiz?wvideo=vffitvywy6"><img src="https://embedwistia-a.akamaihd.net/deliveries/29b87d8ee942cd844acf0481b9376c52ecda91a2.jpg?origin_v2=1&image_play_button_size=2x&image_crop_resized=960x540&image_play_button=1&image_play_button_color=71a5d4e0" width="400" height="225" style="width: 400px; height: 225px;"></a></p><p><a href="https://resources.rstudio.com/webinars/best-practices-for-working-with-databases-march-2018-edgar-ruiz?wvideo=vffitvywy6">RStudio webinar dbplyr (March 2018)- Edgar Ruiz</a></p> <br> <br> <small>Thanks Floris for the hint!</small> --- background-image: url(/assets/images/background_challenge_2.png) class: left, middle # Challenge 2 We found in Challenge 1 how to get the scientific name of 'Geel schorpioenmos'. We want to reuse the query later on for other species. - Complete the function called `userflora_query_scientificname` in [`20190618/20190618_challenges.R`](https://github.com/inbo/coding-club/blob/master/src/20190618/20190618_challenges.R) to do it. The function has two input arguments: a connection to a table and a dutch plant name. The funcion should return the corresponding scientificname. - Try to extend the function `userflora_dutch_to_scientificname` to work on partial matches, i.e. search for all taxa CONTAINING the input dutch plant name in column `NaamNederlands`. For example, searching all dutch names containing the string `sterkranswier`. Tip: see https://dbplyr.tidyverse.org/articles/sql.html --- background-image: url(/assets/images/background_challenge_3.png) class: left, middle # Challenge 3 - Get taxon groups: table `tblTaxonGroep` - Get relationship between the groups and the taxa in `taxon` - Try to add the group name (Naam) to `taxon` - Try also to count how many taxa are in each group --- class: center, middle <!-- Always try to include some type of reviewing (can be short and entertaining). Remove this slide if no reviewing is included -->  --- class: center, middle INBO Coding club goes to holiday... see you all back in August!  --- class: center, middle  <!-- Adjust the room and date --> Room: Herman Teirlinck - 01.71 - Frans Breziers<br> Date: __29/08/2019__, van 10:00 tot 12:00<br> Title: markdown your report<br> (registration announced via DG_useR@inbo.be)