maes

This function uses the method presented in Maes et al, (2012) to estimate a percentage change in distribution area between two time periods. The formula attempts to account for uneven recording effort between time periods. This method is specifically designed to feed into IUCN red list analyses (criterion A2c). This function can take multiple time periods and will complete all pairwise comparisons.

This method only includes sites that fulfill a criteria set by min_sp. This parameter gives the minimum number of species that must be observed in both time periods for a site to be included. For example, if set to 5, then at least 5 species much be observed in both time period 1 and time period 2 for that site to be included in the analysis.

# Load the library
library(sparta)

# Load example dataset
data(ex_dat)

# Run the analysis
Ma_out<-maes(Data=ex_dat,
             time_periods=(data.frame(start=c(1980,1990,2000),end=c(1989,1999,2009))),
             min_sp=1,
             site_col='hectad',
             sp_col='CONCEPT',
             start_col='TO_STARTDATE',
             end_col='Date')

In this example min_sp has been set to 1 as the example dataset is very sparse.

head(Ma_out)

     CONCEPT 1_2_gridcells1 1_2_relDist1 1_2_gridcells2 1_2_relDist2
1  Species 1            106  0.148044693             74  0.138836773
2 Species 10             28  0.039106145             25  0.046904315
3 Species 11              4  0.005586592              2  0.003752345
4 Species 12              4  0.005586592              0  0.000000000
5 Species 13            125  0.174581006             99  0.185741088
6 Species 14             14  0.019553073             22  0.041275797
   1_2_change 1_3_gridcells1 1_3_relDist1 1_3_gridcells2 1_3_relDist2
1   -6.219689             55  0.076815642             31  0.108771930
2   19.941035             14  0.019553073             13  0.045614035
3  -32.833021              2  0.002793296              1  0.003508772
4 -100.000000              3  0.004189944              0  0.000000000
5    6.392495             66  0.092178771             50  0.175438596
6  111.096221              8  0.011173184              4  0.014035088
  1_3_change 2_3_gridcells1 2_3_relDist1 2_3_gridcells2 2_3_relDist2
1   41.60128             40  0.075046904             38  0.133333333
2  133.28321             18  0.033771107             12  0.042105263
3   25.61404              1  0.001876173              1  0.003508772
4 -100.00000             NA           NA             NA           NA
5   90.32430             52  0.097560976             42  0.147368421
6   25.61404             10  0.018761726              3  0.010526316
  2_3_change
1   77.66667 
2   24.67836
3   87.01754
4         NA
5   51.05263
6  -43.89474

For each pair of time periods being compared 5 columns are produced, prefixed by the index of the time periods being compared.

• gridcells1 and gridcells2 give the number of cells occupied in each time period (1st and 2nd respectively) after removing sites that do not meet the selection criteria.
• relDist1 and relDist2 give the relative distributions for each time period.
• change gives the percentage change between the earlier and latter time period.

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###References

Maes, D., Vanreusel, W., Jacobs, I., Berwaerts, K., Van Dyck, H. (2012) Applying IUCN Red List criteria at a small regional level: A test case with butterflies in Flanders (north Belgium). Biological conservation, 145, 258-266.