qfasar: Quantitative Fatty Acid Signature Analysis in R

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

View on CRAN

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

add_cc_err Man page
adj_diet_fat Man page
cc_aug Man page
comp_chi_gamma Man page
diet_obj_func Man page
diet_pool Man page
dimac Man page
dist_between_2_sigs Man page
dist_pairs_map Man page
dist_sigs_2_mean Man page
dist_sum_pairwise Man page
est_diet Man page
find_boot_ss Man page
gof Man page
lopo Man page
lopo_pool Man page
make_diet_grid Man page
make_diet_rand Man page
make_ghost Man page
make_pred_sigs Man page
make_prey_part Man page
pm_obj_func Man page
pred_beyond_prey Man page
prep_fa Man page
prep_sig Man page
sig_rep_zero Man page
sig_scale Man page

Files

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

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