telfer

Telfer's change index is designed to assess the relative change in range size of species between two time periods (Telfer et al, 2002). This function can take multiple time periods and will complete all pairwise comparisons.

Telfer's method has two additional features that the user can parameterise. The first (min_sq) specifies the minimum number of squares occupied in the first time period in order for a trend to be calculated for a species. This ensures that potentially inaccurate large changes are not generated. The second is the ability to switch on or off iterations and to specify how many iterations should be used. Iterations are used to account for increased variation in the logit proportions close to zero and one (see Telfer et al, 2002).

# Load the library
library(sparta)

# Load example dataset
data(ex_dat)

# Passing data as an R object
telfer_out <- telfer(Data=ex_dat,
                     time_periods=data.frame(start=c(1980,1990,2000),end=c(1989,1999,2009)),
                     min_sq=2,
                     useIterations=T,
                     iterations=20,
                     site_col='hectad',
                     sp_col='CONCEPT',
                     start_col='TO_STARTDATE',
                     end_col='Date')

In this example we have chosen to include only species with a minimum of 2 observations in the first time period and have used 20 iterations.

head(telfer_out)

     CONCEPT  telfer_1_2  telfer_1_3 telfer_2_3
1  Species 1 -1.21339352 -0.82309449  0.9064044
2 Species 10  0.06179485  0.72776298  0.2046855
3 Species 11 -0.73669784 -0.05795487         NA
4 Species 12 -2.64829773 -1.44161144         NA
5 Species 13 -0.29153414  0.39549882 -0.1944723
6 Species 14  1.18890474 -0.26671483 -0.8862288

The output column names indicate the time periods compared and NA's indicate species time period combinations that did not meet the min_sq specified.

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###References

Telfer, M.G., Preston, C.D., & Rothery, P. (2002) A general method for measuring relative change in range size from biological atlas data. Biological Conservation, 107, 99–109.