sig_scale {qfasar}

Scale fatty acid signature proportions

Description

The utility function sig_scale implements the three options for scaling fatty acid signature data summarized by Bromaghin et al. (2016). A logical vector denotes the subset of all fatty acids to be used in the analysis. The fatty acids that are not to be used are censored and one of three scaling options is implemented. See Details.

Usage

sig_scale(sig_data, fa_use, scale = 3)

Arguments

sig_data

A numeric matrix containing prey signature data as proportions in column-major. These data should have previously been processed by sig_rep_zero.

fa_use

A logical vector denoting the fatty acids to be used, of length equal to the total number of fatty acids. This vector originates from a data file required by qfasar. See the vignette for details.

scale

An integer indicator of the desired scaling option. See Details. Default value 3.

Value

A list containing the following elements:

n_fa

The number of fatty acids in the processed signatures.

sig

A numeric matrix of processed signatures in column-major format.

err_code

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

err_message

A string contains a brief summary of the execution.

Details

This is an internal utility function.

The argument scale must be one of three integer values and its value denotes the scaling option that will be implemented:

• scale == 1. The proportions within each censored signature are scaled to sum to 1.0. This option is not recommended for routine use in QFASA applications, as Bromaghin et al. (2016) found that it can meaningfully bias diet estimates under some conditions. It is implemented here to provide compatibility with original methods and to facilitate potential future research.

• scale == 2. The proportions within each censored signature are not scaled, so each signature will have a different partial sum.

• scale == 3. Each censored signature is augmented with an additional proportion whose value equals the sum of the censored proportions, so that the proportions in each signature sum to 1. This is the default option.

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.