Give a special color to value 0 in visualization of all deployment features

[damianooldoni]

After meeting with @jimcasaer, we decided to give color black to value 0 in map_dep() as it is a special/sentinel value. This should affect the visualization of all features (rai, n_species, effort, n_obs)

[damianooldoni]

After breaking my head to add zero as special value as stated here, I came to the idea that actually it is not completely right to define 0 as a special value as all variables we want to visualize are continuous! The transitions should be smooth. So, it's just a matter of defining a specific color palette which starts from black.

We can use already predefined palettes with black as extreme value. These are:

• magma
• inferno

We can otherwise make our own palette, not a big deal, just choosing the color we want to pass through, e.g. by passing palette_colors <- c("black", "green", "blue") to arg palette in leaflet::colorNumeric() function

@jimcasaer: give a look to examples below please and tell me which one do you like it most? Are you satisfied with one of these palettes?

"magma" color palette

Extreme values:

Middle range values:

"inferno" color palette

Extreme values:

Middle range values:

A custom palette

Extreme values:

Middle range values:

[damianooldoni]

I think also that the choice of the palette should still be left to the user by adding the argument palette to map_dep(). @jimcasaer: the choice of the favourite palette (see comment above) is sitll important as we can use it as default palette.

[damianooldoni]

Update: I implemented my solution in #80 and merged to main branch so everybody can test it easily by installing the package. Default palette: "inferno".

[jimcasaer]

@damianooldoni sorry for the long delay before taking this up when do you have 5 minutes to discuss this before approving?

[damianooldoni]

We decided to try to get a second layer with only the zeros and those ones with a special marker or symbol. In this way are the zero values easily detectable.

[damianooldoni]

@jimcasaer: in #84 I tackled this issue again. Can you give a look to the results as shown in vignette: https://inbo.github.io/camtrapdp/articles/visualize-deployment-features.html

If you are satisfied with this kind of marker, we can close this issue and give a party 🥳

[jimcasaer]

hmm, the markers are very big !! and blur the total view of the map -- so to be honest: not yet fully satisfied no party time yet

what about using simple circle markers in a specific color for the subset of locations with "0" values

[damianooldoni]

Ok. So, the markers should be scalable like the other circles. Notice I leave the continuous scale in legend from 0 but the values mapped in the legend are all data without 0. This to allow visualizing values which are almost 0 but not 0.

Let's see what you prefer:

Option 1

gray circle markers, with stroke, default opacity

Option 2

gray circle markers, with stroke, fillOpacity = 0.8, opacity of the stroke = 0.8

Option 3

gray circle markers, without stroke, fillOpacity = 0.8

Option 4

black circle markers, with stroke, standard opacity

@jimcasaer: let me know which options you like at most, so I can provide you more examples. It's like selling a suit 😄

[jimcasaer]

@damianooldoni preference for option 4 -- only wondering if red or white would not be better given the background colours of the maps

the suit is almost sold, difficult client

[damianooldoni]

Let's give a try!

white - default opacity

default opacity is way too low, I think.

white - high opacity

Better, but it doesn't stand out, I think.

red - default opacity

red - high opacity

Personally I find red with high opacity the best one. But, be careful: it's the best one if we use default palette! If a user opts for example for `palette = "reds", I think making red circles is not the best option anymore.

Proposal: as we allow the user to pass a different palette than the default one, I strongly recommend to allow him/her to define also the color of these new circles if red is not good.

[jimcasaer]

damiano,

my personal preference is the red - default opacity :-) and yes I like the idea of to have a default palette and default red -- but allowing the user to indicate other palettes and other colours

[damianooldoni]

Great! I will do.

[damianooldoni]

@jimcasaer: done and merged to main in #86. Online documentation and vignette should be automatically updated on the website within few minutes. Let me know what do you think about it.

[jimcasaer]

could it be that the red inside/outside is reversed in comparison to example 3 ?

[damianooldoni]

I have just given a look to the leaflet maps in https://inbo.github.io/camtrapdp/articles/visualize-deployment-features.html It seems everything works as expected. The stroke is more opaque than the circle as expected. Or would you like less opacity of the inner circle in general?

[jimcasaer]

very strange -- my leaflet does the opposite -- when do you have 5 minutes ?

[jimcasaer]

works fine now outside of markdown -- :-) final ideas

• should we not allow a option to cluster also the zero - deployments (cfr non-zero values)
• can the cluster function apply on both zero values and non zero values in the leaflet (I guess not given that the are in reality separate layers in this approach)

[damianooldoni]

The cluster option already exists. By default is cluster = TRUE. You can deactivate clustering via cluster = FALSE. it's very easy to add clustering to cluster deployments with zero values as well.

But I would avoid to allow a mix behavior, i.e. cluster = TRUE for deploys with zero values and cluster = FALSE for all other deployments or viceversa. It will result in adding another argument to the function and I don't think you will ever user it. Do you agree on this?

[damianooldoni]

I think I misunderstood your request in my previous comment., @jimcasaer. We can cluster zero values deploys and non zero values deploys apart (as explained in my comment above, and as I will push on main in a while). But we can NOT cluster zero and non-zero values deploys together as they are two different layers, indeed.

A small but maybe important graphic decision.

Do you prefer non-zero deploys on top of zero ones (option 1):

Or viceversa (option 2)?

I think option 1, but I would like your opinion on this. Thanks.

[damianooldoni]

@jimcasaer: Pull Request #87 implements option 1 as described in my comment above. Give me your ok and I can push it to main.

[jimcasaer]

when do you have a moment looks like clustering is not working on both layers

[damianooldoni]

Well, @jimcasaer, it cannot work on main branch as I have still not pushed to main. Should I?

[damianooldoni]

after videocall with @jimcasaer we decided to go for option 1. Unfortunately the merged PR #87 implemented the worng option (option 2). A fast PR is following.

[damianooldoni]

@jimcasaer: does everything work fine now? I hope so. Please let me know. Hopefully we can close this issue.

[jimcasaer]

you can close it :-) good start for the weekend

[damianooldoni]

After @jimcasaer brainstorming with his colleagues, we decided to:

1. add show not show argument (default: show)
2. marker type (default = small cross)
3. marker color (default = white)

[damianooldoni]

@jimcasaer:

1. do you agree on the icon?
2. which size? See examples from 10px up to 25px
3. which color as default? Still white in mind?

library(dplyr)
library(camtrapdp)

# icon from https://icons8.com/icons/set/math
# red (E74C3C) - 10px
icons <- leaflet::icons(
  iconUrl = "https://img.icons8.com/ios-glyphs/30/E74C3C/multiply.png",
  iconWidth = 10,
  iconHeight = 10
)
leaflet::leaflet(mica$deployments) %>% 
  leaflet::addTiles() %>% 
  leaflet::addMarkers(icon = icons)
#> Assuming "longitude" and "latitude" are longitude and latitude, respectively

# black (000000)  - 15px
icons <- leaflet::icons(
  iconUrl = "https://img.icons8.com/ios-glyphs/30/000000/multiply.png",
  iconWidth = 15,
  iconHeight = 15
)
leaflet::leaflet(mica$deployments) %>% 
  leaflet::addTiles() %>% 
  leaflet::addMarkers(icon = icons)
#> Assuming "longitude" and "latitude" are longitude and latitude, respectively

# yellow (F1C40F)  - 20px
icons <- leaflet::icons(
  iconUrl = "https://img.icons8.com/ios-glyphs/30/F1C40F/multiply.png",
  iconWidth = 20,
  iconHeight = 20
)
leaflet::leaflet(mica$deployments) %>% 
  leaflet::addTiles() %>% 
  leaflet::addMarkers(icon = icons)
#> Assuming "longitude" and "latitude" are longitude and latitude, respectively

# white (FFFFFF)  - 25px
icons <- leaflet::icons(
  iconUrl = "https://img.icons8.com/ios-glyphs/30/FFFFFF/multiply.png",
  iconWidth = 25,
  iconHeight = 25
)
leaflet::leaflet(mica$deployments) %>% 
  leaflet::addTiles() %>% 
  leaflet::addMarkers(icon = icons)
#> Assuming "longitude" and "latitude" are longitude and latitude, respectively

^{Created on 2022-03-15 by the reprex package (v2.0.1)}

[jimcasaer]

given the standard palette used in map_dep I would suggest to go for a default black and for the smallest symbol (and now I hope the female part of our team will agree :-) )

[damianooldoni]

Thanks a lot. Could you please check this with your team (or its female part of it) and give me the final GO?

[jimcasaer]

@damianooldoni cluster = FALSE seems to give an error when using map_dep

[damianooldoni]

Yes, you are right. I tried to change this

clusterOptions = if (cluster == TRUE) leaflet::markerClusterOptions() else NULL

with this:

clusterOptions = ifelse(cluster == TRUE,
                                leaflet::markerClusterOptions(),
                                NULL
        )

but R said NO 😄

I revert it and everything should look good again.

[damianooldoni]

Done in https://github.com/inbo/camtraptor/commit/7039d97445e699c2f8acccec7e6402d162ce4265 directly on main. Please reinstall and let me know.

[jimcasaer]

the result is great !! thanks adapted icon size to 5