📈Plots📈

[dill]

1. [x] time series of temporal strandings (lines!)
   • all(??)/mysts/odonts
   • underneath for 25(??) year periods, maps of total # individuals and # stranding events
   • historical events! (WWI/WW2/moratorium, Ellen has list)
   • check dots?
2. [x] species composition measles plot (Dave)
   • phylopic

Appendix plots

1. [ ] facet wrap of times series per species
2. [ ] decadal gifs! 👾 (Ellen)
   • pick one that's good
   • split myst/odont

[dill]

e82bed3 has the first draft of the measles plot, without the fiddly phylopic thing for now. Perhaps want to group sp. by something useful?

[nhcooper123]

Also probably want to remove the Species ylab as it's obvious, italicise species names, maybe add some horizontal lines to make it easier to line stuff up across years? Do we want to highlight specific events? Basically though this is amazeballs. 🐳

[dill]

Not sure what you mean by "add some horizontal lines to make it easier to line stuff up across years"?

Rest is done in 1280cee

On 09/11/2017 16:32, Natalie Cooper wrote:

Also probably want to remove the Species ylab as it's obvious, italicise species names, maybe add some horizontal lines to make it easier to line stuff up across years? Do we want to highlight specific events? Basically though this is amazeballs. 🐳

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[nhcooper123]

This looks great to me! @EllenJCoombs what do you think? My horizontal line comment is me being tired and meaning vertical lines and you already have the grey grid in the background so that's all good, thanks! 👍

[dill]

Cool, no worries on the vertical/horiz then :)

I added a first draft of the megaplot to 7f50714. Let me know what you think. Currently missing:

1. historical events
2. is this the right data?
3. what about little lines along the x axis in the time series showing what the lengths are for the plots below?

[dill]

oh maybe also there's too much whitespace?

[dill]

oh just spotted that the first column is weird in the pdf? But it looks fine in the graphics window?

[EllenJCoombs]

Measles plot looks amazing! Thanks a lot :)

[nhcooper123]

I can't see the megaplot, am I being stupid?

[dill]

no it's me...

helps if I push...

On 14/11/2017 17:11, Natalie Cooper wrote:

I can't see the megaplot, am I being stupid?

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[nhcooper123]

[resists urge to post a link to Salt-N-Pepa]

Yeah the first and last column are weirdly aligned on my PDF too, but maybe just a PDF issue. Ellen can probably tweak most of the rest the plot easily (we will want to remove Parvorder for example).

@EllenJCoombs can you give Dave a list of the events you're interested in adding? Or Dave can you just add an arrow at world war 1 to show Ellen how to do this? Then she can handle the rest and ask you if she gets stuck?

Less white space would be good, but not essential. We need a legend for the maps I think.

and I should have said straight off - this looks awesome. Thanks

[EllenJCoombs]

Haha, BEHOLD THE MEGAPLOT. Love it. Thank you - it looks awesome! I've had a go at adding arrows and texts to my own plots using annotate, "rect" and "segement":

Moratorium 1986 (adds shaded period)

p <- p + annotate("rect", xmin=1985, xmax=1986, ymin=0, ymax=60, alpha=.3, fill="gray44") + geom_text( aes(x = 1985, y = 60, label = "Moratorium comes into effect: 1985/1986 season start"), size = 3)

This code adds arrows to the plot

CSIP

p <- p + annotate("segment", x = 1990, xend = 1990, y = - 0, yend = -10, colour="black", size=0.5, arrow=arrow(length=unit(0.1,"cm"))) + geom_text( aes(x = 1990, y = -12, label = "CSIP programme starts"), size = 3)

If that's the best way to do it then I will give it a go on megaplot! The only thing I'm struggling with is making the arrow tip drop below the x axis (at the moment the x axis drops below everything (i.e. below the data, arrows and arrow text) leaving a big gap between the axis and the data)

Thinking of putting the following, any suggestions would be great :)

• WWI (1914 - 1918, I did this as a shaded segment/period)
• WWII (1939 - 1945, as a shaded segment/period)
• 1945 - Increase in post-war fishing and whaling effort (arrow)
• 1985/86 season - Commercial whaling moratorium (arrow)
• 1990 - CSIP programme starts (arrow)

[dill]

Fixed this in aeab3ab

Ellen: those annotations look good to me!

On 14/11/2017 17:25, Natalie Cooper wrote:

[resists urge to post a link to Salt-N-Pepa]

Yeah the first and last column are weirdly aligned on my PDF too, but maybe just a PDF issue. Ellen can probably tweak most of the rest the plot easily (we will want to remove Parvorder for example).

@EllenJCoombs https://github.com/ellenjcoombs can you give Dave a list of the events you're interested in adding? Or Dave can you just add an arrow at world war 1 to show Ellen how to do this? Then she can handle the rest and ask you if she gets stuck?

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[EllenJCoombs]

Thanks Dave. You also asked if this is the right data...it is thanks! I'm going to remove all of the unknowns (sorry, I should have sent you the dataset with these removed), as well as the species with only 1-2 records (Narwhals, Belugas, Melon-headed, Blainville's beaker, Dwarf sperm) as we discussed. Thanks again, love the beaker comments.

[Googles Salt-N-Pepa]

[nhcooper123]

It's probably not a big issue right now that these are the correct and final data, as this code can be re-run on the correct data easily enough. Ellen we can chat about this, but I think there will need to be some tidying for reproducibility pipeline purposes at some point, probably resulting in a .Rmd file(s) with the analysis pipeline from raw data to paper (as suggested by Dave pre meeting up in St Andrews). We can think about the best way to do this. I'll raise a new issue :)