est_iec: Estimate IEC site scores.
In ngwalton/iec: Index of Ecological Condition (IEC)

Description Usage Arguments Details Value References See Also

est_iec estimates the Index of Ecological Condition (IEC) for each site in sp based on the biotic response curves (BRC) in brc.

1	est_iec(sp, brc, method = "pa", n_reps = 30, keep_zeros = TRUE)

`sp`	community data frame (sites as rows, taxa as columns, observations as values).
`brc`	BRC data frame generated by `est_brc`.
`method`	one of `"pa"` (default; CalcPA) or `"q"` (CalcQ).
`n_reps`	scalar integer setting the number of random starts for optimization (default is 30).
`keep_zeros`	logical indicating if all taxa are used in scoring (`TRUE`; default) or only detected taxa.

An Index of Ecological Condition (IEC) score is estimated for each site (row) in data frame sp. This score is based on the Biotic Response functions (curves) in brc (output from est_brc). The column names in sp and column 1 of brc must contain the same taxa in the same order.

The default method treats observations as presence/absence (method = "pa"). When using pa, it is essential to use BR functions based on probability or probability-like (e.g., scaled to 0-1) observation data (est_brc). Note that input records do not need to be coded as presence/absence as the method simply checks for 0 or > 0.

When quantitative observations are available and were used to generate BR functions, set method to "q". As with "pa" it is important to match the type of data used to score the sites with the type of data used to estimate the BR functions. For example, if the data used to construct the BR functions in est_brc were probabilities, then the data used to score the sites (sp) should also be probabilities If BR functions were constructed using log transformed (e.g. log1p) count data, then the observations used to score the sites in est_iec should be transformed in the same way.

n_reps determines the number of times the optimization function (nlminb) is run with different starting values. n_reps can be set to any positive integer, but the authors recommend against using values of less than 10 except for testing purposes. Larger values will take longer to process. The default value is 30. If keep_zeros = TRUE (default), all taxa in brc are used for scoring the sites. But if keep_zeros = FALSE, only those taxa detected at a given site are used to score that site. With the latter option, the number of taxa used to score each site may vary.

A data frame containing the IEC scores for each site in sp and the corresponding likelihood of the score.

Gnass Giese, E.E., R.W. Howe, A.T. Wolf, N.A. Miller, and N.G. Walton. 2015. Sensitivity of breeding birds to the "human footprint" in western Great Lakes forest landscapes. Ecosphere 6(6):90. http://dx.doi.org/10.1890/ES14-00414.1

Howe, R.W., R. R. Regal, J.M. Hanowski, G.J. Niemi, N.P. Danz, and C.R. Smith. 2007a. An index of ecological condition based on bird assemblages in Great Lakes coastal wetlands. Journal of Great Lakes Research 33 (Special Issue 3): 93-105.

Howe, R.W., R. R. Regal, G.J. Niemi, N.P. Danz, J.M. Hanowski. 2007b. A probability-based indicator of ecological condition. Ecological Indicators 7:793-806.

est_brc to generate biotic response curves.

ngwalton/iec documentation built on May 23, 2019, 4:43 p.m.