Open SanderDevisscher opened 4 years ago
@timadriaens @damianooldoni "per regio van oorsprong", is this variable "native range" in the data? Because I found 150 different values for that - which might not be ideal to show in stacked barplot
> unique(exotenData[, "native range"])
native range
1:
2: North America
3: North Pacific Ocean
4: Eastern Asia (WGSRPD:38)
5: Europe (WGSRPD:1)
---
146: Eurasia
147: central Italy
148: western Italy
149: northern coastal areas of the western Mediterranean
150: Mediterranean & Portugal
Also, multiple values are separated by "," or "&", not by "|" as indicated https://docs.google.com/spreadsheets/d/1LeXXbry2ArK2rngsmFjz_xErwE1KwQ8ujtvHNmTVA6E/edit#gid=808615322
@damianooldoni @mvarewyck
How hard is it to translate native range into this ? analog to habitat being translated into marine, freshwater, terrestrial.
native range | Azië | Afika | Noord-Amerika | Zuid-Amerika | Antartica | Europa | Oceanië |
---|---|---|---|---|---|---|---|
North America | FALSE | FALSE | TRUE | FALSE | FALSE | FALSE | FALSE |
North Pacific Ocean | FALSE | FALSE | FALSE | FALSE | FALSE | FALSE | TRUE |
Eastern Asia (WGSRPD | FALSE | FALSE | FALSE | FALSE | FALSE | FALSE | FALSE |
Europe (WGSRPD | FALSE | FALSE | FALSE | FALSE | FALSE | TRUE | FALSE |
Eurasia | TRUE | FALSE | FALSE | FALSE | FALSE | TRUE | FALSE |
central Italy | FALSE | FALSE | FALSE | FALSE | FALSE | TRUE | FALSE |
western Italy | FALSE | FALSE | FALSE | FALSE | FALSE | TRUE | FALSE |
northern coastal areas of the western Mediterranean | FALSE | FALSE | FALSE | FALSE | FALSE | TRUE | FALSE |
Mediterranean & Portugal | FALSE | FALSE | FALSE | FALSE | FALSE | TRUE | FALSE |
Also, multiple values are separated by "," or "&", not by "|" as indicated https://docs.google.com/spreadsheets/d/1LeXXbry2ArK2rngsmFjz_xErwE1KwQ8ujtvHNmTVA6E/edit#gid=808615322
@damianooldoni can you look into this ?
yes, that's one of the problems with the current checklist, in principle they should have been mapped at checklist level using the World Geographical Scheme for Recording Plant Species Distribution (WGSRPD, https://web.archive.org/web/20160125135239/http://www.nhm.ac.uk/hosted_sites/tdwg/TDWG_geo2.pdf) and the UN geoscheme (https://en.wikipedia.org/wiki/United_Nations_geoscheme) for other species.
@SanderDevisscher: it's a long recoding and it's just tedious to write it:
df %>%
mutate(Azië = if_else(native_range == "Eurasia", TRUE, FALSE),
Afrika = FALSE, #no TRUE values in table above
Noord-Amerika = if_else(native_range == "North America", TRUE, FALSE),
etc.
)
@timadriaens, should we do this mapping for TrIAS indicators report as well? Or it's something you want only for RShyny visualization webpage?
@timadriaens : I ask again our TrIAS colleagues about possibility of mapping it at checklist publication level or while unifiying the checklists.
@damianooldoni I think very often, checklists will have more detailed (and not very standardized) information on native range. And it would be "a pitty" (and not very stimulating to the checklist owner to keep track of such detail) actually if this went lost at checklist publication level. I don't know what is the best place - and there is always the option of keeping a verbatim field - but it is us who have made the very pragmatic decision to use WGSRPD for plants and UN geoscheme for animals, these are very crude anyway.
So in the logic of preserving as much detail in the source checklists as possible, I would say it is more something for the flow to the unified. And of course, this should first of all be in the TrIAS indicators.
@SanderDevisscher: it's a long recoding and it's just tedious to write it:
df %>% mutate(Azië = if_else(native_range == "Eurasia", TRUE, FALSE), Afrika = FALSE, #no TRUE values in table above Noord-Amerika = if_else(native_range == "North America", TRUE, FALSE), etc. )
@timadriaens, should we do this mapping for TrIAS indicators report as well? Or it's something you want only for RShyny visualization webpage?
@damianooldoni what about grepl ? or a manual mapping list ?
@SanderDevisscher : yes, a file containing the mapping seems way better.
Is the UN Geocode scheme this one: https://en.wikipedia.org/wiki/United_Nations_geoscheme?
If we're going to standardize it anyway, why not use one scheme for all?
because the botanists wanted their own thing see this issue
there is of course also the issue of marine species where native range requires a dedicated vocab
Regarding botanists: well, I think we (authors of the unified checklist) can choose to which extend we want to aggregate (including using the same scheme for plants and animals, marine taxa are indeed separate). The source data will always be available. So, it comes down to making a decision.
@SanderDevisscher @timadriaens @damianooldoni
I assume dealing with native_range
is still ongoing?
Could you update whenever this is ready for me to continue working on the plot?
@damianooldoni what is the status of the native range
issue ?
values have largely been standardized by @peterdesmet see this issue but not sure this is already updated in the unified @damianooldoni ?
@damianooldoni can you make sure the mapping find its way into data_input_checklist_indicators.tsv
It has not been included in the unified checklist, because:
As said and argumented here, I definitely think they should be part of it, yes. Otherwise, breakdowns of indicators based on native ranges are impossible.
This is now republished with standardized native range in the unified checklist. Can you reprocess and see if that solve the issue?
Thanks @peterdesmet . I will asap process unified checklist data to include these changes.
@SanderDevisscher @timadriaens @damianooldoni
I imported the update of the checklist. So now there are 25 different values for native_range
.
> table(exotenData[, "native_range"], exclude = NULL)
Africa Americas Asia
1380 211 566
Australia and New Zealand Caribbean Central America
192 5 25
Central Asia Eastern Africa Eastern Asia
13 24 2549
Eastern Europe Europe Melanesia
2587 2511 1
Micronesia Middle Africa Northern Africa
2 14 23
Northern America South America Southeastern Asia
1205 553 52
Southern Africa Southern Asia Southern Europe
15 75 83
Western Africa Western Asia Western Europe
19 28 18
<NA>
603
Concerning the requested graph:
maar in de stijl van FIGUUR: Gerapporteerd aantal per jaar en per regio van de grofwildjacht pagina. Dus per jaar een stacked bar chart met de verschillende regios
Do I write the code for this graph? If so, be aware that the style might differ from the graphs that are currently used for aantal geïntroduceerde uitheemse soorten per jaar and Cumulatief aantal uitheemse soorten as they come from the TRiAS package. Or is there code available?
Do I write the code for this graph?
Yes, if it were up to me!
If so, be aware that the style might differ from the graphs that are currently used for aantal geïntroduceerde uitheemse soorten per jaar and Cumulatief aantal uitheemse soorten as they come from the TRiAS package.
I think it is best we overwrite the TrIAS style with the Inbotheme style or at least use a similar style as the rest of the app.
Or is there code available?
Not that I know of. Shall I make a basis for you to start from or would you like to start from scratch ?
Note: the regions can be grouped in 5 continents: https://en.wikipedia.org/wiki/United_Nations_geoscheme
If so, be aware that the style might differ from the graphs that are currently used for aantal geïntroduceerde uitheemse soorten per jaar and Cumulatief aantal uitheemse soorten as they come from the TRiAS package.
I think it is best we overwrite the TrIAS style with the Inbotheme style or at least use a similar style as the rest of the app.
Okay, I will give that a go.
Or is there code available?
Not that I know of. Shall I make a basis for you to start from or would you like to start from scratch ?
Thanks, I have the code from grofwildjacht to start from. So it's okay
Note: the regions can be grouped in 5 continents: https://en.wikipedia.org/wiki/United_Nations_geoscheme
Do you prefer to display on continent level (in that case I regroup)? Or on native_range
level as in raw data?
Note: the regions can be grouped in 5 continents: https://en.wikipedia.org/wiki/United_Nations_geoscheme
Do you prefer to display on continent level (in that case I regroup)? Or on
native_range
level as in raw data?
Maybe add a unit type filter or a switch (to increase details-level => default continent)
First version of the plot:
First version of the plot:
Ziet er goed uit maar wel lage aantallen, Is dit gefilterd ?
@mvarewyck @eadriaensen is it possible to add an option to choose between the relative and absolute numbers for this graph ? Default should be relative.
Title should be "aandeel geïntroduceerde uitheemse soorten per jaar per regio van oorsprong" when relative and "aantal geïntroduceerde uitheemse soorten per jaar per regio van oorsprong" when absolute.
It would be good to implement the code for this plot in the trias package, for sake of uniformity - and given the limited remaining project hours. In that case, the option to display relative or absolute numbers should ideally be implemented in the function there as an argument.
If so, I can easily implement a tick box for the user in the app to switch between relative and absolute
The current code, used for the graph : exoten_indicatorYearByNativeRange.zip
@SanderDevisscher is this possible?
@damianooldoni can you look into this ?
I agree with @eadriaensen; it is better to develop this functionality in the trias
package for sake of uniformity.
But I go on holiday on Thursday. No time to do it this afternoon or tomorrow.
As maintainer of the trias
package I am more than happy to accept contributions and PRs. @SanderDevisscher or somebody else involved: maybe have you some time to give a try? I can review it when I come back (~2 weeks). And in the meanwhile you can use the trias package in development branch for the shiny app instead of the master?
Thanks
@damianooldoni I'll give it a go
Gebaseerd op deze indicator: https://trias-project.github.io/indicators/indicator_introductions_per_year.html maar in de stijl van
FIGUUR: Gerapporteerd aantal per jaar en per regio
van de grofwildjacht pagina. Dus per jaar een stacked bar chart met de verschillende regiosMet deze data: https://github.com/trias-project/indicators/blob/master/data/interim/data_input_checklist_indicators.tsv
en de volgende selectie opties: