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qfasar (version 1.2.1)

Quantitative Fatty Acid Signature Analysis in R

Description

An implementation of Quantitative Fatty Acid Signature Analysis (QFASA) in R. QFASA is a method of estimating the diet composition of predators. The fundamental unit of information in QFASA is a fatty acid signature (signature), which is a vector of proportions describing the composition of fatty acids within lipids. Signature data from at least one predator and from samples of all potential prey types are required. Calibration coefficients, which adjust for the differential metabolism of individual fatty acids by predators, are also required. Given those data inputs, a predator signature is modeled as a mixture of prey signatures and its diet estimate is obtained as the mixture that minimizes a measure of distance between the observed and modeled signatures. A variety of estimation options and simulation capabilities are implemented. Please refer to the vignette for additional details and references.

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Version

Install

install.packages('qfasar')

Monthly Downloads

146

Version

1.2.1

License

Unlimited

Maintainer

Jeff Bromaghin

Last Published

March 19th, 2020

Functions in qfasar (1.2.1)

dist_between_2_sigs

Compute the distance between two fatty acid signatures
comp_chi_gamma

Compute gamma parameter of chi-square distance measure
diet_pool

Pool diet estimates to combined prey types
dist_sigs_2_mean

Distance between fatty acid signatures and their mean
diet_obj_func

Diet estimation objective function
dist_pairs_map

Creats a map of the distance between pairs of fatty acid signatures
cc_aug

Calibration coefficient for an augmented signature proportion
add_cc_err

Add error to the calibration coefficients
dimac

Diversive magnetic clustering
adj_diet_fat

Adjust diet composition estimates for prey fat content
make_ghost

Make a ghost prey signature
gof

Goodness-of-fit for modeled predator signatures
find_boot_ss

Find realistic bootstrap sample sizes
make_pred_sigs

Simulate predator signatures
lopo

Leave-one-prey-out analysis
lopo_pool

Pool lopo results to original prey types
make_diet_grid

Generate a regular grid of diet compositions
make_diet_rand

Generate random diet compositions
est_diet

Estimate predator diet composition
dist_sum_pairwise

Distance between pairs of fatty acid signatures
prep_sig

Prepare fatty acid signature data for analysis
sig_rep_zero

Replace invalid fatty acid signature proportions
pm_obj_func

Parameterized mean objective function
make_prey_part

Make prey partition
pred_beyond_prey

Identify predator signature proportions beyond range of prey
prep_fa

Prepare fatty acid information analysis
sig_scale

Scale fatty acid signature proportions