Quantitative Fatty Acid Signature Analysis
Computes within species variance-covariance matrices on transformed sc...
Produces a dendrogram using distances between the mean FA signatures o...
Each prey fatty acid signature is systematically removed from the supp...
Generate a pseudo predator parametrically from multivariate normal dis...
Generate a pseudo predator by sampling with replacement from prey data...
FUNCTION TO GENERATE ns PSEUDO SEALS WHERE ns IS THE NUMBER OF ROWS IN...
FUNCTION TO GENERATE ns SEALS FOR EACH OF ny YEARS
Find the pair of starting species with the best (lowest) IC value amon...
Finds the species combination with the best# (lowest) IC value achieva...
Returns individual confidence intervals and simultaneous confidence in...
Returns the distance between two compositional vectors using Aitchison...
Used to provide additional information on various model components eva...
Used in solnp() as the objective function to be minimized when Aitch...
Returns diet estimates corresponding to a sample of predators based on...
Measure of Repeatability for Diet Estimates (Balanced Case)
Finds the species combination with the best (lowest) IC value achievab...
Calculate p-value of a given prey type diet proportion under the preda...
Calculate bias correction for confidence intervals from `beta.meths.CI...
Calculate bias correction for confidence intervals.
Find simultaneous and individual confidence intervals for diet proport...
Called by create.d.mat() to compute the chi-square distance.
Returns the distance between two compositional vectors using the chi-s...
Calculate p-value corresponding to a specified null value using bootst...
Generate pseudo predators with ith predator having true diet given by ...
Bootstrap statistic function: in this case it is the mean (meanBEZI) o...
Repeatability in Diet Estimates
Generate bootstrap replicates of diet proportion estimates for given p...
Confidence Intervals for Diet Proportions
Called by testfordiff.ind.boot.fun() to create a matrix of distances...
CALCULATE CS DISTANCE BETWEEN EACH TWO PREDATORS IN dataset
Used to provide additional information on various model components eva...
Used in solnp() as the objective function to be minimized when chi-s...
Bootstrap ran.gen function:
Roxygen commands
Get nll and IC values for a pair of species (this is used in forward s...
Get nll and IC values for a given model (note that the model is determ...
Returns diet estimates corresponding to a sample of predators based on...
Generate pseudo predators with ith predator having true diet given by ...
Returns the distance between two compositional vectors using Kullback-...
Used to provide additional information on various model components eva...
Used in solnp() as the objective function to be minimized when Kullb...
Get simplified MLE estimates
Returns the geometric mean of a compositional vector
Returns the multivariate mean FA signature of each prey group entered ...
Modifies the zeros for a sample of FA signatures using the multiplicat...
Modifies the zeros for a single FA signature using the multiplicative ...
Multiplicative replacement of zeroes
Find simultaneous confidence intervals for diet proportions of a singl...
Bootstrap statistic function: in this case it is the mean (meanBEZI) o...
Returns simplified MLE diet estimates corresponding to a sample of pre...
Returns MUFASA diet estimates corresponding to a sample of predators.
Returns QFASA diet estimates corresponding to a sample of predators.
Simultaneous estimation of diet composition and calibration coefficien...
Simultaneous maximum unified fatty acid signature analysis
Generate a single pseudo predator FA signature
Returns sum(alpha) and used in solnp().
QFASA: A package for Quantitative Fatty Acid Signature Analysis
RETURNS RHO AND THE BOOTSTRAP SAMPLE DETERMINED BY ind.
FUNCTION TO BE PASSED TO bootstrap::jackknife.
Find root (i.e. solve f(pio) = PVAL(pio) = alpha1 using either uniroot...
Splits prey database into a simulation set (1/3) and a modelling set (...
Called by testfordiff.ind.boot().
Called by testfordiff.ind.pval().
Test for a difference between two independent samples of compositional...
Generate bootstrap replicates of diet proportion estimates for given p...
Measure of (unadjusted) repeatability
Measure of Repeatability for Diet Estimates (Unbalanced/Missing Value ...
RETURNS RHO AND THE BOOTSTRAP SAMPLE DETERMINED BY ind.
FUNCTION TO BE PASSED TO bootstrap::jackknife.
Measure of (unadjusted) repeatability with missing values
Use uniroot() to find roots and compare with bisection outcome
Reintroduce excluded species to diet estimates as forced zeroes
Accurate estimates of the diets of predators are required in many areas of ecology, but for many species current methods are imprecise, limited to the last meal, and often biased. The diversity of fatty acids and their patterns in organisms, coupled with the narrow limitations on their biosynthesis, properties of digestion in monogastric animals, and the prevalence of large storage reservoirs of lipid in many predators, led to the development of quantitative fatty acid signature analysis (QFASA) to study predator diets.