qfasar: Quantitative Fatty Acid Signature Analysis in R
Version 1.2.0

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.

AuthorJeffrey F. Bromaghin [aut, cre]
Date of publication2017-01-10 00:04:44
MaintainerJeffrey F. Bromaghin <jbromaghin@usgs.gov>
LicenseUnlimited
Version1.2.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("qfasar")

Getting started

Package qfasar"

Popular man pages

add_cc_err: Add error to the calibration coefficients
find_boot_ss: Find realistic bootstrap sample sizes
lopo_pool: Pool lopo results to original prey types
make_ghost: Make a ghost prey signature
make_prey_part: Make prey partition
pred_beyond_prey: Identify predator signature proportions beyond range of prey
sig_rep_zero: Replace invalid fatty acid signature proportions
See all...

All man pages Function index File listing

Man pages

add_cc_err: Add error to the calibration coefficients
adj_diet_fat: Adjust diet composition estimates for prey fat content
cc_aug: Calibration coefficient for an augmented signature proportion
comp_chi_gamma: Compute gamma parameter of chi-square distance measure
diet_obj_func: Diet estimation objective function
diet_pool: Pool diet estimates to combined prey types
dimac: Diversive magnetic clustering
dist_between_2_sigs: Compute the distance between two fatty acid signatures
dist_pairs_map: Creats a map of the distance between pairs of fatty acid...
dist_sigs_2_mean: Distance between fatty acid signatures and their mean
dist_sum_pairwise: Distance between pairs of fatty acid signatures
est_diet: Estimate predator diet composition
find_boot_ss: Find realistic bootstrap sample sizes
gof: Goodness-of-fit for modeled 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
make_ghost: Make a ghost prey signature
make_pred_sigs: Simulate predator signatures
make_prey_part: Make prey partition
pm_obj_func: Parameterized mean objective function
pred_beyond_prey: Identify predator signature proportions beyond range of prey
prep_fa: Prepare fatty acid information analysis
prep_sig: Prepare fatty acid signature data for analysis
sig_rep_zero: Replace invalid fatty acid signature proportions
sig_scale: Scale fatty acid signature proportions

Functions

Files

inst
inst/doc
inst/doc/qfasar.Rmd
inst/doc/qfasar.R
inst/doc/qfasar.html
tests
tests/testthat.R
tests/testthat
tests/testthat/test_pred_beyond_prey.R
tests/testthat/test_adj_diet_fat.R
tests/testthat/test_est_diet.R
tests/testthat/test_dimac.R
tests/testthat/test_make_ghost.R
tests/testthat/test_find_boot_ss.R
tests/testthat/test_make_diet_grid.R
tests/testthat/test_comp_chi_gamma.R
tests/testthat/test_make_prey_part.R
tests/testthat/test_prep_sig.R
tests/testthat/test_diet_pool.R
tests/testthat/test_prep_fa.R
tests/testthat/test_cc_aug.R
tests/testthat/test_lopo.R
tests/testthat/test_lopo_pool.R
NAMESPACE
R
R/pred_beyond_prey.R
R/dimac.R
R/lopo_pool.R
R/find_boot_ss.R
R/sig_rep_zero.R
R/pm_obj_func.R
R/make_pred_sigs.R
R/sig_scale.R
R/prep_sig.R
R/dist_sum_pairwise.R
R/make_ghost.R
R/dist_pairs_map.R
R/prep_fa.R
R/est_diet.R
R/diet_obj_func.R
R/dist_sigs_2_mean.R
R/lopo.R
R/comp_chi_gamma.R
R/make_diet_grid.R
R/make_prey_part.R
R/cc_aug.R
R/add_cc_err.R
R/make_diet_rand.R
R/dist_between_2_sigs.R
R/gof.R
R/adj_diet_fat.R
R/diet_pool.R
vignettes
vignettes/qfasar.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/comp_chi_gamma.Rd
man/cc_aug.Rd
man/dist_sum_pairwise.Rd
man/prep_sig.Rd
man/pm_obj_func.Rd
man/adj_diet_fat.Rd
man/dimac.Rd
man/prep_fa.Rd
man/pred_beyond_prey.Rd
man/make_diet_rand.Rd
man/make_ghost.Rd
man/make_pred_sigs.Rd
man/dist_sigs_2_mean.Rd
man/lopo_pool.Rd
man/make_prey_part.Rd
man/diet_pool.Rd
man/est_diet.Rd
man/sig_rep_zero.Rd
man/dist_between_2_sigs.Rd
man/make_diet_grid.Rd
man/dist_pairs_map.Rd
man/find_boot_ss.Rd
man/diet_obj_func.Rd
man/lopo.Rd
man/sig_scale.Rd
man/add_cc_err.Rd
man/gof.Rd
qfasar documentation built on May 19, 2017, 4:40 p.m.

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