qfasar: Quantitative Fatty Acid Signature Analysis in R

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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.

Author
Jeffrey F. Bromaghin [aut, cre]
Date of publication
2016-12-02 22:37:00
Maintainer
Jeffrey F. Bromaghin <jbromaghin@usgs.gov>
License
Unlimited
Version
1.1.1

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

Files in this package

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