pm_obj_func: Parameterized mean objective function
In qfasar: Quantitative Fatty Acid Signature Analysis in R

Description Usage Arguments Value Details

The utility function pm_obj_func computes the total distance between observed predator signatures and vector of mean diet proportions common to all predators.

1	pm_obj_func(diet, obs_sig, mean_sigs, dist_meas = 1, gamma = 1)

`diet`	A numeric vector of mean diet composition.
`obs_sig`	A numeric matrix containing observed predator signatures, in column-major format.
`mean_sigs`	A numeric matrix of the mean fatty acid signature for each prey type in the prey library, in column-major format.
`dist_meas`	An integer indicator of the distance measure to compute. Default value 1.
`gamma`	The power parameter of the chi-square distance measure. Default value 1.

The total distance between observed and modeled signatures.

This is an internal utility function. Consequently, to increase execution speed, no numeric error checking is performed within pm_obj_func. Rather, error checking is presumed to have occurred at a higher level in the calling sequence.

The argument obs_sig is presumed to be a matrix of predator signatures that has been prepared for analysis, which is best accomplished by a call to the function prep_sig with the predator data. Similarly, the contents of mean_sigs should be mean signatures computed from signatures that were prepared for analysis by a call to the function prep_sig.

The argument diet is presumed to contain non-negative proportions that sum to 1.0.

The arguments dist_meas and gamma must be compatible with the function dist_between_2_sigs.

Please refer to the vignette and documentation for the functions prep_sig, sig_scale, and dist_between_2_sigs for additional details.

diet_obj_func models a predator signature as a mixture of the mean prey-type signatures, with the diet proportions as the mixture proportions, returning the distance between the observed and modeled signatures. The diet composition of a predator is estimated by minimizing this function with respect to the diet using the function Rsolnp::solnp.

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