Whether the abundance of species can be taken in to rarity and endemism in Biodiverse? How to set the points or based as the groups?
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Song Houjuan
Jul 29, 2020, 9:28:01 PM7/29/20
to Biodiverse Users
Hi all,
I like this software very much, very flexible, but I also encountered problems in the process of using it.
I have some fields plot data, including the site number, species and its abundance, and geographic coordinates. I would like to calculate the rarity and endemism of each plot based on the abundance information of species, such as the rarity of site 'VAST1_1'. However, I have some troubles in set the site as the groups, not according to the coordinates. In addition, I would like know whether the abundance of species can be taken into the calculation of rarity and endemism in Biodiverse. Hope you can give me some suggestions. Thanks a lot.
with warm regards,
Houjuan
Shawn Laffan
Jul 30, 2020, 1:53:09 AM7/30/20
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Hello Houjan,
To import the data using the plot names as the group you can choose that column and specify it as type "Text group".
The data will not plot like a map, nor can they be analysed using their geographic positions, because the system does not know the coordinates. However, the will treat each one as a distinct unit and the spatial conditions that do not need location will work (e.g. sp_self_only() and sp_match_text()).
https://github.com/shawnlaffan/biodiverse/wiki/SpatialConditions
In regards to endemism and rarity, the rarity indices are all based on the abundances. They are calculated in the same way as the endemism indices except that abundances are used instead of ranges. The endemism indices are all based on ranges, calculated as the number of groups each label (taxon) occurs in.
Formulae are at:
https://github.com/shawnlaffan/biodiverse/wiki/Indices#rarity-central and https://github.com/shawnlaffan/biodiverse/wiki/Indices#endemism-central
Regards,
Shawn.
To import the data using the plot names as the group you can choose that column and specify it as type "Text group".
The data will not plot like a map, nor can they be analysed using their geographic positions, because the system does not know the coordinates. However, the will treat each one as a distinct unit and the spatial conditions that do not need location will work (e.g. sp_self_only() and sp_match_text()).
https://github.com/shawnlaffan/biodiverse/wiki/SpatialConditions
In regards to endemism and rarity, the rarity indices are all based on the abundances. They are calculated in the same way as the endemism indices except that abundances are used instead of ranges. The endemism indices are all based on ranges, calculated as the number of groups each label (taxon) occurs in.
Formulae are at:
https://github.com/shawnlaffan/biodiverse/wiki/Indices#rarity-central and https://github.com/shawnlaffan/biodiverse/wiki/Indices#endemism-central
Regards,
Shawn.
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-- Prof Shawn Laffan, FMSSANZ School of Biological, Earth and Environmental Sciences UNSW, Sydney 2052, Australia Tel +61 2 9385 8093 http://www.bees.unsw.edu.au/staff/shawn-laffan https://shawnlaffan.github.io/biodiverse (free diversity analysis software) International Journal of Geographical Information Science http://www.tandf.co.uk/journals/ijgis UNSW CRICOS Provider Code 00098G
Song Houjuan
Aug 2, 2020, 4:20:49 AM8/2/20
to Biodiverse Users
Hi Shawn,
Thanks for your fast reply. The problem of taking point as group has been resolved perfectly. However, I meet another question.
I found that no matter whether I take the abundance of species into calculating rarity of a plot, I get the same value. My approach is that the site is Text group, species in each site is label, and the abundance of each species in each site is label or Include_columns. I am not sure whether this is right. In another words, how to use the abundance of species to calculate the raity and endemism, which type of the species and abundance when calculating rarity for each Text_group.
Thanks a lot.
Shawn Laffan
Aug 2, 2020, 6:07:56 AM8/2/20
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Hello Houjan,
There are two issues here. The first is a technical question, the second is more conceptual. I'll respond to the technical question first.
For tabular data, if your input data have a field with abundances then you can specify it as a sample_count column. Otherwise the abundances are estimated from the input rows. The total abundance of a label across all groups is the number of rows in which that label occurs. The abundance for a label in a group is the number of times that label and group combination are calculated. This matters most when aggregating point observations to coarser cells. For your data I am guessing it will be one row per population, so the abundances for each label in each group will be 1.
For example, you might have a table of two populations (plots) with two taxa that looks like this:
plot,taxon,abundance
p1a,spp1,5
p1a,spp2,3
p2b,spp1,5
p2b,spp1,3
p2b,spp2,5
If you import them using text groups based on the "plot" field, but do not specify a sample_count column, then taxon "spp1" will have an abundance of 1 in group "p1a" and 2 in group "p2b", as it occurs in one and two rows respectively. Total abundance across groups will be 3 as it is found in three rows.
If you do specify a sample_count column, then taxon "spp1" will have an abundance of 5 in group "p1a" and 8 in group "p2b" (sum of 3 and 5). Its total abundance will be 13.
On the more conceptual side:
Endemism does not use abundances. It uses the range of each label (taxon), calculated as the number of groups the taxon occurs in. It is useful to think of the range as a 2D footprint, where you have extent but no depth or height. Some refer to endemism as geographic rarity, though.
Endemism can be absolute, where a taxon is found in one place and nowhere else. However, this is very dependent on the definition of the "place". The alternative is relative endemism, in that a taxon's range is relatively small but might span several places. An example is where a taxon with a small range is found in both Cape York Peninsula and New Guinea. It is not absolutely endemic to either place, but is still range restricted.
It is also useful to note that a taxon might be found in very few places (is range restricted), but is abundant in those locations where it is found.
See Crisp et al (2001) for some discussion of the above points. https://doi.org/10.1046/j.1365-2699.2001.00524.x
Rarity itself is a function of abundances. A rare taxon is usually found in few places (is range restricted, and at its most extreme it is found in only one place), but there are relatively few individuals across its range.
The ENDW_WE and RAREW_WE indices are calculated in the same way, with the difference being that the endemism calculations work with fractions of ranges in the sample, while the rarity calculations use the fractions of abundances.
https://github.com/shawnlaffan/biodiverse/wiki/Indices#rarity-whole
https://github.com/shawnlaffan/biodiverse/wiki/Indices#endemism-whole
Hopefully the above helps, but please let me know what else needs to be clarified.
The above might also be more detailed than you were needing, but will likely be useful for others who come later.
Regards,
Shawn.
There are two issues here. The first is a technical question, the second is more conceptual. I'll respond to the technical question first.
For tabular data, if your input data have a field with abundances then you can specify it as a sample_count column. Otherwise the abundances are estimated from the input rows. The total abundance of a label across all groups is the number of rows in which that label occurs. The abundance for a label in a group is the number of times that label and group combination are calculated. This matters most when aggregating point observations to coarser cells. For your data I am guessing it will be one row per population, so the abundances for each label in each group will be 1.
For example, you might have a table of two populations (plots) with two taxa that looks like this:
plot,taxon,abundance
p1a,spp1,5
p1a,spp2,3
p2b,spp1,5
p2b,spp1,3
p2b,spp2,5
If you import them using text groups based on the "plot" field, but do not specify a sample_count column, then taxon "spp1" will have an abundance of 1 in group "p1a" and 2 in group "p2b", as it occurs in one and two rows respectively. Total abundance across groups will be 3 as it is found in three rows.
If you do specify a sample_count column, then taxon "spp1" will have an abundance of 5 in group "p1a" and 8 in group "p2b" (sum of 3 and 5). Its total abundance will be 13.
On the more conceptual side:
Endemism does not use abundances. It uses the range of each label (taxon), calculated as the number of groups the taxon occurs in. It is useful to think of the range as a 2D footprint, where you have extent but no depth or height. Some refer to endemism as geographic rarity, though.
Endemism can be absolute, where a taxon is found in one place and nowhere else. However, this is very dependent on the definition of the "place". The alternative is relative endemism, in that a taxon's range is relatively small but might span several places. An example is where a taxon with a small range is found in both Cape York Peninsula and New Guinea. It is not absolutely endemic to either place, but is still range restricted.
It is also useful to note that a taxon might be found in very few places (is range restricted), but is abundant in those locations where it is found.
See Crisp et al (2001) for some discussion of the above points. https://doi.org/10.1046/j.1365-2699.2001.00524.x
Rarity itself is a function of abundances. A rare taxon is usually found in few places (is range restricted, and at its most extreme it is found in only one place), but there are relatively few individuals across its range.
The ENDW_WE and RAREW_WE indices are calculated in the same way, with the difference being that the endemism calculations work with fractions of ranges in the sample, while the rarity calculations use the fractions of abundances.
https://github.com/shawnlaffan/biodiverse/wiki/Indices#rarity-whole
https://github.com/shawnlaffan/biodiverse/wiki/Indices#endemism-whole
Hopefully the above helps, but please let me know what else needs to be clarified.
The above might also be more detailed than you were needing, but will likely be useful for others who come later.
Regards,
Shawn.
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Song Houjuan
Aug 2, 2020, 8:28:53 AM8/2/20
to Biodiverse Users
Hi Shawn,
Your explanation is very clear. I have been benefited from your help and I got a deeper understanding of rarity and endemism. I am very grateful to you.
Thanks again.
Warm regarding,
Houjuan
在 2020年7月30日星期四 UTC+8上午9:28:01，Song Houjuan写道：
在 2020年7月30日星期四 UTC+8上午9:28:01，Song Houjuan写道：
Shawn Laffan
Aug 4, 2020, 12:23:20 AM8/4/20
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You're welcome Houjuan.
Regards,
Shawn.
Regards,
Shawn.
with warm regards,
Houjuan
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