make_pred_sigs: Simulate predator signatures

In qfasar: Quantitative Fatty Acid Signature Analysis in R

Description

make_pred_sigs generates predator signatures based on a specified predator diet composition and bootstrap sampling signatures from a prey library.

Usage

make_pred_sigs(prey_sigs, prey_loc, cc, diet, prey_ss, n_pred)

Arguments

prey_sigs	A matrix of prey signatures in the prey space, intended to be the object sig_scale returned by a call to the function prep_sig, or the object sig_part returned by a call to the function make_prey_part.
prey_loc	A matrix giving the first and last locations of the signatures of each prey type within prey_sigs, intended to be the object loc returned by a call to one of the functions prep_sig or make_prey_part.
cc	A numeric vector containing the calibration coefficients.
diet	A numeric vector specifying the predator diet composition as proportions.
prey_ss	An integer vector specifying the bootstrap sample size to use for each prey type.
n_pred	An integer specifying the number of predator signatures to generate.

Value

A list containing the following elements:

sim_pred_sigs

A numeric matrix containing simulated predator signatures in the predator space.

err_code

An integer error code (0 if no error is detected).

err_message

A string containing a brief summary of the results.

Details

QFASA simulation studies often require the generation of predator signatures given a specified diet, against which subsequent estimates of diet composition can then be compared (e.g., Bromaghin et al. 2016). Given a specified diet, a bootstrap sample of each prey type is drawn and mean prey-type signatures are computed. A predator signature is then generated by multiplying the mean bootstrapped prey signatures by the diet proportions. Finally, the calibration coefficients are then used to transform the predator signatures to the predator space (Bromaghin et al. 2015).

References

Bromaghin, J.F., S.M. Budge, and G.W. Thiemann. 2016. Should fatty acid signature proportions sum to 1 for diet estimation? Ecological Research 31:597-606.

Bromaghin, J.F., K.D. Rode, S.M. Budge, and G.W. Thiemann. 2015. Distance measures and optimization spaces in quantitative fatty acid signature analysis. Ecology and Evolution 5:1249-1262.

Examples

make_pred_sigs(prey_sigs = matrix(c(0.06, 0.09, 0.31, 0.54,
                                  0.05, 0.09, 0.30, 0.56,
                                  0.03, 0.10, 0.30, 0.57,
                                  0.08, 0.07, 0.30, 0.55,
                                  0.09, 0.05, 0.33, 0.53,
                                  0.09, 0.06, 0.34, 0.51,
                                  0.09, 0.07, 0.34, 0.50,
                                  0.08, 0.11, 0.35, 0.46,
                                  0.06, 0.14, 0.36, 0.44), ncol = 9),
               prey_loc = matrix(c(1, 4, 7, 3, 6, 9), ncol=2),
               cc = c(0.75, 1.05, 0.55, 1.75),
               diet = c(0.25, 0.25, 0.50),
               prey_ss = c(5, 3, 7),
               n_pred = 50)

qfasar documentation built on March 20, 2020, 1:10 a.m.