Identical demes for different countries

I just looked at a build in auspice and saw my zambia-specific build had entries assigned to New Zealand. On closer inspection it seems that one of the zambia divisions (Southern) is assigned a lat/long in New Zealand. While I can obviously delete the NZ entry and replace / update it with a Zambian one, this would break any global builds with a NZ Southern entry. So is it possible to have multiple identical named entries in the lat/long list / is there any way to filter by region / country to select the correct division? Appreciate any advice on how to resolve this. Thanks in advance!

Hi @dbridges,

unfortunately no. This is a short-coming of our format to specify lat-longs that we baked into the system long ago now knowing what was comingā€¦ Our current way of handling this is suffixing ambiguous entries with shorthands for country or state like:

Palma ES
Palma BR

we need to tackle this more comprehensively, but for the time being this hopefully helps.
richard

Thanks @rneher - good to know I am not missing something obvious. Am sure you, and the rest of the team, have a 1001 things on the to-do-list so totally understand. Pretty sure Iā€™m not going to be able to provide any real support, but if there is something I can do let me knowā€¦

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Do you mean that lat/lon is assigned by a country code? And there are conflicting country codes, like for Zambia and New Zealand?

@dbridges can you post the example here?

Hi @abitrolly.

The issue is that the lat-long details are derived from the github /default/lat_longs.tsvfile. Sample metadata (country / division etc) are matched via the name. So for example, Zambia and NZ both have an area called ā€˜Southernā€™. In the lat long sheet the NZ entry is called ā€˜Southernā€™ and the Zambian one is called ā€˜Southern Zambiaā€™. Considering our samples are from Zambia I could edit the tsv file, but this would assign NZ/Southern to a Zambian location unless I remember to switch it back / edit the NZ entries.

Essentially the matching needs to be changed to take into account higher level metadata e.g. match on multiple columns i.e. Region > Country > Division > Location so that divisions / locations that are not unique between countries / regions are correctly identified. By the way I have no idea how the information is taken into the workflow so this may be a poor suggestion!

This has been on our to-do list, as you correctly identify the problems that are occurring, but we just havenā€™t implemented it. In the meantime, if you are focusing on Zambia there shouldnā€™t be any major issue if you do lose the lat/longs for the south of New Zealand!

Found the line.

It looks like an easy fix on the data level. Adding country name in a square brackets after the district name to disambiguate the records.

@james can this break anything?

It looks like itā€™s already there on line 13747! Therefore changing your metadata so that the ā€œdivisionā€ field is now ā€œSouthern Zambiaā€ should do the trick.

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