qfasar (version 1.2.1)

prep_fa: Prepare fatty acid information analysis

Description

The function prep_fa processes the information in a fatty acid suites data frame and prepares that information for application to fatty acid signatures.

Usage

prep_fa(df_fa)

Arguments

df_fa

A data frame containing fatty acid names, calibration coefficients, and 0/1 definitions of fatty acid suites. qfasar has strict formatting requirements for df_fa; please see Details and/or the vignette.

Value

A list containing the following elements:

cc

A numeric vector of calibration coefficients.

use

A logical vector defining a fatty acid suite.

fa_names

A character vector of fatty acid names.

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 function is designed to be called by the user after the fatty acid data frame has been read. The data frame should contain a complete list of all fatty acids in the prey and predator signature data, one or more sets of calibration coefficients with an indicator of which set to use, one or more fatty acid suite definitions with an indicator of which suite to use, and optional comments. Please refer to the vignette for additional information.

The fatty acid data frame must strictly meet the following formatting requirements.

• The first row must contain a header for each column.

• The second row must list "use_me" in the first column, a 1 in the column for the set of calibration coefficients to be used, a 1 in the column for the fatty acid suite to be used, and a 0 in all other columns.

• Starting with row three, the first column must contain fatty acid names, which must exactly match the corresponding components of the headers in any prey and predator signature data frames.

• Starting with row three, Columns 2 to k must contain calibration coefficients for each fatty acid. Multiple sets of calibration coefficients can be in the data frame. The set to be used must contain a 1 in Row 1 and the others must contain a 0 in Row 1.

• Columns k+1 to m must contain one or more definitions of fatty acid suites. Membership in a suite is defined by 0/1 indicators, with a 1 indicating membership. Definitions for multiple suites can be in the data frame. For example, two columns could contain indicators defining membership in the dietary and extended-dietary suites of fatty acids (Iverson et al. 2004). The suite to be used must contain a 1 in Row 1 and the others must contain a 0 in Row 1.

• An optional last column can contain comments.

• Please see the vignette for examples of how to format this data frame.

References

Iverson, S.J., C. Field, W.D. Bowen, and W. Blanchard. 2004. Quantitative fatty acid signature analysis: A new method of estimating predator diets. Ecological Monographs 74:211-235.

Examples

# NOT RUN {
prep_fa(data.frame(fa = c("use_me", "fa_1", "fa_2", "fa_3"),
                   cc = c(1, 0.75, 1.25, 1.0),
                   use = c(1, 1, 1, 1)))

prep_fa(data.frame(fa = c("use_me", "fa_1", "fa_2", "fa_3"),
                   cc1 = c(0, 0.75, 1.25, 1.00),
                   cc2 = c(1, 1.2, 0.8, 0.9),
                   use_1 = c(0, 1, 1, 0),
                   use_2 = c(1, 1, 1, 0)))

# }