Indicator: number of new introductions of alien species per year in Belgium

[timadriaens]

Description

Temporal trends in first record rates of alien species (number of first records per year/per x year interval) for alien species (based on Seebens et al. 2017). This indicator provides information on the number of new introductions in time, for instance the rate of increase of alien species introductions and the accumulation rate of alien species (Rabitsch et al. 2016). The information will be updated and refined as the checklist is further supplemented.

Data needs

• Country-level checklist
• Checklist-based
• Breakdowns:
  • environment (marine, terrestrial, freshwater)
  • taxon (kingdom --> family)
  • native range
  • pathway (level 1 and level 2 CBD)
  • invasion stage (introduced, established)
  • source checklist
  • distribution (country-level: Belgium)

Data output

The data retrieved by GBIF would be organized in a (tidy) data.frame

key	nubKey	scientificName	datasetKey	species	genus	family	order	class	phylum	kingdom	rank	speciesKey	taxonomicStatus	acceptedKey	accepted	locationId	locality	country	status	first_observed	last_observed	establishmentMeans	native range	origin	invasion stage	habitat	pathway_level1	pathway_level2

This data should be already filtered as explained in #21 .
This data output will serve as input for the plots based on group_by-like pipes, e.g.

df %>% 
  group_by(class) %>% 
  count()

It is suggested to write these series of group_by() in a function for plotting because of the high number of combinations of information.
See issue #18 about temporal information (first_observed and last_observed) in checklists.

[peterdesmet]

I’ve added column “species” to dataframe. It’s likely we will also rename some of the columns.

[damianooldoni]

Yes, @peterdesmet for sure! Tomorrow I am "blocked" for preparing the hackathon.
Among other things in the to-do-list there is also the "renaming" of some columns.

[damianooldoni]

Column names updated (and few others added) in "data output" table of #17 (comment)

[stijnvanhoey]

with respect to the requeste facet_subplots (aka Breakdowns). Not all are possible yet, we can trakc the progress here:

• environment (marine, terrestrial, freshwater) -> not in data available
• taxon (kingdom --> family)
• native range -> this is new in a property-value way in the input data set, we should revisit this to make sure no pivoting is required for this operation
• pathway (level 1 )
• pathway (level 2 CBD) -> actually this should be the pathway indicator Pathways indicator #27
• distribution (country-level: Belgium) -> locality column

With respect to invasion stage (introduced, established) @timadriaens did request an additional line option:

• establishdmeans-based? -> data on established is not available

For the source checklist, a line based breakdown was requested by @timadriaens ; is this of any value?

• source checklist?

[stijnvanhoey]

Similar to #20 , the facet graphs underneath are included as well as part of the functionality; e.g. for kingdom:

@Yasmine-Verzelen you can further check the consequences of different smoothers.

[damianooldoni]

@Yasmine-Verzelen and @SanderDevisscher: my workflow .Rmd has passed internal reviews and it is now merged in master.
Please, pull from origin to have an updated branch via the following git line:

git pull origin master

Unfortunately you cannot do this via GitHub Desktop. So, the most important stuff is the fact that the database is now 100% tidy! That means that you are now able to make facet_subplots for native range breakdown as well 👍. You can start by importing the new version of file test_data_output_checklist_indicators.tsv. By pulling the master in your branch you get this file updated as well.
I have consequently updated the column names of the table at the very beginning of this issue #17 (comment).
Let me know for anything!

[timadriaens]

Hi, where do I find the latest graphs based on the unified checklist including all the breakdowns, need them for a chapter in the Living Planet Report Belgium @damianooldoni ?

[damianooldoni]

@timadriaens : I will rerun the checklist indicators pipelines and push to master: as written via Hangout I plan it to do on June 24th (25th as backup if unexpected errors occur).

[damianooldoni]

By the way, this issue should be closed as this indicator is now working and it is updated on master.