community_stability is missing the species.var argument

[I-Hickman]

Hello,

I am trying to use the community_stability function, however, it requires species.var argument (as per Hallett et al. 2016) for the desired output. It is missing this info both in the description of the function and in the function itself, i.e. won't allow me to run the code with the species.var argument.

Here is the what happens when I run the code:

Community.stability <- community_stability(

• df = sp_abundnace_site,
• time.var = "Year",
• species.var = "Species",
• abundance.var = "avg",
• replicate.var = "Site"
• )
  Error in community_stability(df = sp_abundnace_site, time.var = "Year", :
  unused argument (species.var = "Species")

Here is what is says in the help section - in the Details section it mentions species.var, but it is not in the code

Usage
community_stability(df, time.var, abundance.var, replicate.var = NA)

Details
The input data frame needs to contain columns for time, species and abundance; time.var, species.var and abundance.var are used to indicate which columns contain those variables. If multiple replicates are included in the data frame, that column should be specified with replicate.var. Each replicate should reflect a single experimental unit - there should be a single community represented within each time point and replicate.

Here is the code from Hallett et al. 2016:

community_stability(df = knz_001d,
time.var = "year",
species.var = "species",
abundance.var = "abundance",
replicate.var = "subplot" )

Please correct me if I am wrong!
Thank you in advance,
Iris

[mbjones]

Hi @iris-hickman -- thanks for the report. I think what you are seeing is a documentation error -- the species.var is not in the arguments list for community_stability, and I think the reference you see is due to a documentation editing issue in the details section (basically, a copy/paste error from other parts of the docs). I'll ask @laurenmh to confirm, and I'll put in a PR to fix the documentation with the next release. Removing species.var from your code allows it to run, like so:

library(codyn)
community_stability(df = knz_001d,
    time.var = "year",
    abundance.var = "abundance",
    replicate.var = "subplot" )
#>    subplot stability
#> 1      A_1  4.123316
#> 2      A_2  3.986904
#> 3      A_3  6.514939
#> 4      A_4  4.322140
#> 5      A_5  3.415329
#> 6      B_1  4.479464
#> 7      B_2  3.442573
#> 8      B_3  3.551204
#> 9      B_4  3.937452
#> 10     B_5  3.282738
#> 11     C_1  3.165395
#> 12     C_2  3.703476
#> 13     C_3  3.744142
#> 14     C_4  5.057938
#> 15     C_5  3.207514
#> 16     D_1  4.497318
#> 17     D_2  6.222124
#> 18     D_3  4.504468
#> 19     D_4  6.197067
#> 20     D_5  5.246663

^{Created on 2022-06-14 by the reprex package (v2.0.1)}

Thanks again for the report.

[mbjones]

@laurenmh I pushed the fix to sha 5ce6e1d on develop -- let me know if this looks right to you please.