sig_scale: Scale fatty acid signature proportions
In qfasar: Quantitative Fatty Acid Signature Analysis in R

Description Usage Arguments Value Details References

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.

1	sig_scale(sig_data, fa_use, scale = 3)

`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.

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.

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.

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.

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