Edits to be made to existing tutorials

[beverlytan]

This issue thread will consist of all the edits that need to be made to improve existing Coding Club tutorials!

[beverlytan]

MCMCglmm tutorial

• The graphs for the trace plots of the models (the caterpillar ones) all have this dark shadow towards the bottom. Replace the files with ones without those shadows (they could still be screencaps, just better screencaps).

[Completed]

[beverlytan]

Occurrence tutorial

• The functions to do with coordinate cleaner do not work. Looks like there have been changes made to these functions in the package so this needs updating.
• Maybe the package got updated or something like that, this is the package repo that might have more info

[Pull request submitted]

[beverlytan]

Use of ggplot in tutorials

• Currently in the various tutorials when we use ggplot, sometime there is an object created, e.g. graph <- ggplot()... and other times it's just ggplot()
• I think it would be better if we are consistently creating objects when making graphs
• Check through the tutorials and add objects wherever the code is just ggplot().
• Also important that it has to be (object_name <- ggplot()...) e.g. the whole thing has to be in brackets, otherwise the graph is made, but not visualised, because we haven't "called" the object in R. And there should be a little snippet of text in each tutorial after the first ggplot graph that goes like "can't see your graph? maybe you have forgotten to put the brackets around the ggplot code chunk. Want to save your graph? Here is an example code chunk with ggsave"

[Identified problematic tutorials on 6 Jan]

• Problematic tutorials r/e ggplot visualization

  • Coding etiquette
  • Time series
  • Machine learning
  • Qualitative data
  • Spatial data and maps

• Mostly ok, just need to add notes about importance of brackets

  • Data vis 1: supplement
  • Occurrence: supplement
  • Model design: supplement
  • Git for labs: one liner
  • Data vis 2
  • SEEC
  • EVENET
  • Loops and functions
  • Mapping populations
  • GEE
  • Linear models
  • Mixed linear models
  • Generalised linear models in stan
  • INLA

[Completed]

[beverlytan]

Surveys and feedback

• Check that the links to the feedback surveys in all tutorials lead to a survey on the right topic. I think sometimes the links are wrong, e.g. it’s the data vis tutorial, but the modelling feedback survey.

• Similarly, in the separate repos for the data for each tutorial, there is a link to the respective feedback, but it’s not always right.

• Some tutorials don’t have surveys - could you add them? If you go to surveymonkey.com and log in using [email protected] and use the same password as for twitter (I think…), you can see all the past surveys and you can just duplicate a survey and only change the relevant words, the surveys are pretty brief, so shouldn’t take too long I hope.

• Need to create new surveys

  • Intro to GEE
    • https://www.surveymonkey.co.uk/r/VKMZHD3
  • INLA
    • https://www.surveymonkey.co.uk/r/VVGXKZG
  • Ordination
    • https://www.surveymonkey.co.uk/r/VYLPZ29
  • Analyzing qualitative data
    • https://www.surveymonkey.co.uk/r/VMRWSKQ
  • Python crash course
    • https://www.surveymonkey.co.uk/r/VN5XKPR
  • Intro to fortran
    • https://www.surveymonkey.co.uk/r/VG5BK9T
  • Iris python data viz
    • https://www.surveymonkey.co.uk/r/VH6XDVZ
  • Meta-analysis with mcmcglmm has no survey link
    • https://www.surveymonkey.co.uk/r/V537CQ5
  • Machine learning in R has no survey link
    • https://www.surveymonkey.co.uk/r/77YWPQL
  • Numpy Python has no survey link
    • https://www.surveymonkey.co.uk/r/795PKMV
  • Topic modelling in Python has no survey link
    • https://www.surveymonkey.co.uk/r/7C5N3QV

• Easy fix: change on tutorial markdown

  • Manipulation and visualisation of spatial / occurrence
    • Survey link: https://www.surveymonkey.com/r/JYDDZ8F
  • Spatial data and maps
    • Survey link: https://www.surveymonkey.co.uk/r/NMD3N5K

• Other problems

  • Make Github for labs clearer in survey
  • Typo in stan GLM survey
  • Intro to python cc by sa size
  • Python pandas cc by sa size

[Pull requests submitted 15/01]

[beverlytan]

Data visualization 2 tutorial

• Do you want me to change the code for predictions / visualisations such that it's using the ggpredict() that we introduced in the model design tutorial?
  • I think we should have both options - so keeping Haydn's more complicated code, which shows you more of the calculations and the stuff "behind the scenes"
  • But also add the ggpredict() code as you suggest, so essentially making that section be "here are two ways to do the same thing, you decide which one suits your workflow best.”

[Issue #155, waiting for advice]

[beverlytan]

Model design tutorial

• Update the image files in the tutorial to also reflect the new theme (default CC theme)

[Completed]

[beverlytan]

Other generic edits

• Ordination tutorial: Fix graphs, points, numbers and titles

• Data clustering tutorial: Remove ggmap and create the map using ggplot

[Pull requests submitted 19/01]

[gndaskalova]

On the twitter front @beverlytan , there is a new tutorial on machine learning by Sam that you could tweet about sometime over the next few weeks (no rush at all) - https://ourcodingclub.github.io/2018/10/15/machine-learning.html

I'll go fix those gigantic license images in the tutorial now, since they look quite ugly, my bad, that was me trying to "fix" things and then making them worse!

[Completed]

[gndaskalova]

Happy new year @beverlytan !

Great work on the data vis 2 tutorial! I was wondering if you could update the colours on the final plot too so that they are the same as the other ones you made earlier in the tutorial? No rush on it, just whenever.

Thanks!

[Completed]

[gndaskalova]

Hi @beverlytan ,

Apologies for behind a bit behind on tasks here, I'll catch up over the weekend hopefully.

Just got a comment "to bring up to date" this tutorial https://ourcodingclub.github.io/2017/11/11/popchange.html from the online feedback form, could you go through it to see if there is indeed anything that needs updating?

Thanks!

[Pull request submitted 19/01]

[gndaskalova]

Hey @beverlytan , me again!

Just noticed the resolution of this graph in the functions and loops tutorials is a bit low, could you please swap the image file with a better one and increase the size of the graph in the tutorial a bit as well?

Thanks very much!

[Completed]

[gndaskalova]

Hey @beverlytan

John just added to this tutorial https://ourcodingclub.github.io/2017/02/08/funandloops.html could you please tweet about it sometime next week?

And in general, for the next semester, feel free to tweet about previous tutorials, those that haven't received much attention in the past, etc. Maybe something like 1 tweet about the tutorial from the workshop that happened in that week, and one tweet about some other tutorial, as a rough guideline.

[Completed]

[gndaskalova]

Hey @beverlytan

Thank you very much for sorting out the surveys, that will help us with keeping the tutorials up to date (and working)!

I just remembered that the links to the surveys are also in the README files in the repositories that hold the data for each tutorial - those ones are less urgent to fix, but whenever you can, can you check them as well? Then our surveys would all be sorted out!

[Completed]

[beverlytan]

Hi @gndaskalova , this is regarding the ordination tutorial edits

• For the first PCOA plot, for some reason my graph is the opposite of what is on the tutorial and I dont understand enough of the tutorial to fix the problem - so I'm not sure what you want me to do here. Should I leave the old plot or upload this for some reason flipped one? (I tried to work out why it was flipped but couldnt really fix it). This is the graph I get instead, with the same code as per the tutorial:

• I also don't know how to develop the graph for "ordexample2.png", that was just an example of the final result, and so haven't managed to change the font size / screenshots. But i think because it's an example it should be ok.

• Uploaded other problematic figures with better font sizes

[Pull requests submitted on 19/01]

[beverlytan]

Things left to do as of 6 Feb

• Resolve Data vis 2 tutorial: mixed effect models #155 data viz 2 tutorial
• Resolve above comment: fixing ordination tutorial

[gndaskalova]

Hey @beverlytan

I will aim to go through the pull requests over the weekend and answer your questions too.

Someone just said in the online feedback survey that the stargazer part of the mixed effects models tutorial didn't work for them, could you please look into that when you can?

Thanks!

[beverlytan]

@gndaskalova just checked, and stargazer is working fine!

[gndaskalova]

Hi @beverlytan - if you can, could you please check out the pull request for the programming in C tutorial? Essentially if you could complete the tutorial and see all the code and formatting and such works, and then I can merge the pull request afterwards?

There is no specific deadline on this.

[20 March update: seems like the file is blank, cannot progress at the moment]

[gndaskalova]

Hey @beverlytan

Hope you are doing well!

I have another task if you're up for it!

Could you please go through all the Coding Club tutorials that use the Living Planet Database and make sure there is always a link to the Living Planet Database website and a reference for the data? Same for the repositories that have the data for each tutorial, the reference can go in the readme file.

Thank you!

[Tutorials checked, Pull requests submitted 20 March]

[gndaskalova]

Hey @beverlytan

Got another task for you if you're up for it! It is not time-sensitive so whenever you can.

We got permission to publish a tutorial from the Stirling Coding Club on our website and I was wondering if you could do the actual posting?

This is the tutorial https://stirlingcodingclub.github.io/SCC_R_package/notebook/Rpackage_notes.html

The Rmd file for the tutorial is here, so essentially you'll need to convert the Rmd file to a normal md one as that's what our website uses (and you can check out existing md files in the posts folder of our repo to see the syntax) and match the formatting of the tutorial with how we format ours.
https://github.com/StirlingCodingClub/SCC_R_package/blob/master/notebook/Rpackage_notes.Rmd

You can call it "Creating your own R package" or something like that.

Feel free to edit the tutorial as well if you see somewhere where that is needed as you go through the text.

Thanks very much!
Gergana

[Pull requests submitted 20 March]

[beverlytan]

Hi @gndaskalova, okie dokes i'll get to that.

Also, i'll try to get to these tasks on Thursday this week, 20 March (I'm meeting my prof on Thursday so realistically will only work on CC things after that meeting) and finish the forms then so that you can submit it on Friday, so that it'll come together with the accounts for this semester. I saw that you wanted the forms in by the 18th but was wondering if this would be ok instead?

I'm just thinking that payment will take a while, and i'm likely going to close my bank account in July, so want to get the forms in asap! I completely didn't think this through until now, let me know if that's ok.

[gndaskalova]

That's fine about the forms! Yeah, we should definitely submit your forms asap then. If you don't finish all the tasks before I submit the forms, that's okay, you can estimate how long they'll take you and you can add hours for covering the twitter form until you go off for fieldwork, is that alright @beverlytan ?

[beverlytan]

Okay @gndaskalova , will update you on Thursday night! Also, wanted to ask if I have to resubmit a signed copy of my passport and visa stuff, cuz Isla had previously signed the first set of forms I submitted but it was dated 28 Nov?

[gndaskalova]

You'll need to check that with Lisa when you submit the forms, so we will see!

[beverlytan]

Just an update!

Things left to do 20 March

• Resolve data vis Data vis 2 tutorial: mixed effect models #155: @sandra-ab working on this
• Ordination tutorial, questions for @gndaskalova above
• Go through Programming in C pull request: but file is currently blank

[gndaskalova]

Hey @beverlytan

Hmm, okay, I will check about the C programming tutorial later.

Thanks for posting the how to make a package tutorial! Here is what it currently looks like - I was wondering if you could make the screenshots smaller as some are really in your face and a bit blurry? And I was thinking back to your DS tutorial, you had nice annotations on your screenshots there, maybe on some of the screenshots for the R package one, where the text says things like "here we can see..." you can add a circle or something, so that people can see exactly where the "here" is?

https://ourcodingclub.github.io/2019/03/20/writing-r-package.html

Oh and the tutorial needs a header - this is the blank file https://github.com/ourcodingclub/tutorials-in-progress/blob/master/resources/tutheaderbl.png

So perhaps you can add "How to make your own R package" and with smaller text something else below as you see fit? 48pt bold Arial for the main title and 30pt regular Arial for the sub-title - that's the CC general style.

Thanks very much!

[gndaskalova]

Hey @beverlytan

There is a new tutorial to advertise on Twitter! It is Maude's spatial analysis in R (rasters and remote-sensing one), so quite exciting!

https://ourcodingclub.github.io/2019/03/26/spatial.html

Can you tweet about it when you can, and use the logo for it as the image. Thank you!

[Tweeted 19 Apr]