est_diet: Estimate predator diet composition
In qfasar: Quantitative Fatty Acid Signature Analysis in R
Description
Usage
Arguments
Value
Details
References
Examples
Description
est_diet estimates the diet of one or more predators.
Usage
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Arguments
pred_sigs
A vector or matrix of predator signatures ready for
analysis, intended to be the object sig_scale returned by a call to
the function prep_sig with the predator data frame.
pred_uniq_types
A character vector of the unique predator types,
intended to be the object uniq_types returned by a call to the
function prep_sig with the predator data frame.
pred_loc
A vector or matrix giving the first and last locations of the
signatures of each predator type within pred_sigs, intended to be
the object loc returned by a call to the function
prep_sig with the predator data frame.
prey_sigs
A matrix of prey signatures ready for analysis, intended to
be the object sig_scale returned by a call to the function
prep_sig with the prey data frame or the object
sig_part returned by make_prey_part.
prey_uniq_types
A character vector of the unique prey types, intended
to be the object uniq_types returned by a call to the function
prep_sig with the prey data frame.
prey_loc
A matrix giving the first and last locations of the
signatures of each prey type within prey_sigs, intended to be the
object loc returned by a call to the function
prep_sig with the prey data frame.
cc
A vector of calibration coefficients, intended to be a subset of
the object cc returned by the function prep_fa or the
object cc returned by the function cc_aug.
space
An integer indicator of the estimation space to be used. Default
value 1.
dist_meas
An integer indicator of the distance measure to be used.
Default value 1.
gamma
The power parameter of the chi-square distance measure. Default
value 1.
ind_boot
The number of bootstrap replications to use in the estimation
of the variance of an individual predator's diet. Default value 100.
mean_meth
An integer indicator of the estimation method for mean diet.
Default value 1.
var_meth
An integer indicator of the estimation method for the
variance of mean diet. Default value 1 (bootstrap estimator).
mean_boot
The number of bootstrap replications to use, needed only if
the bootstrap method of estimating the variance of meat diet is selected
(var_meth == 1). Default value 100.
Value
A list containing the following elements:
- pred_sigs
A numeric matrix of predator signatures, potentially
transformed to the prey space.
- prey_sigs
A numeric matrix of prey signatures, potentially
transformed to the predator space.
- mean_sigs
A numeric matrix of mean prey-type signatures, potentially
transformed to the predator space.
- est_ind
A numeric matrix of the estimated diet compositions of
individual predators.
- conv
A logical vector indicating whether the optimization function
successfully converged.
- obj_func
A numeric vector of the values of the objective function at
each predator's estimated diet.
- mod_sigs
A numeric matrix of the modeled signature of each predator
at its estimated diet.
- var_ind
A numeric array containing the estimated variance matrix for
the estimated mean diet of each predator.
- est_mean
A numeric matrix containing the estimated mean diet of each
predator type.
- conv_mean
A logical vector indicating whether the estimated mean
diet of each predator type is based on at least one diet estimate that
converged.
- var_mean
A numeric array containing the estimated variance matrix
for the estimated mean diet of each predator type.
- err_code
An integer error code (0 if no error is detected).
- err_message
A string contains a brief summary of the execution.
Details
est_diet estimates the diet of one or more predators. It implements a
variety of estimation options, and is therefore one of the more complicated
functions in qfasar. Please read the following information and the
Diet Estimation section of the vignette for a description of the options.
The objects passed via the arguments pred_sig, pred_uniq_types,
and pred_loc are presumed to be the objects sig_scale,
uniq_types, and loc, respectively, returned by a call to the
function prep_sig with the predator data frame.
The objects passed via the arguments prey_sig, prey_uniq_types,
and prey_loc are presumed to be the objects sig_scale,
uniq_types, and loc, respectively, returned by a call to the
function prep_sig with the prey data frame.
The object passed via the argument cc is presumed to be a subset of
the object cc returned by a call to the function
prep_fa with the fatty acid suite data frame. Use the logical
vector use returned by prep_fa to subset the list of
all calibration coefficients to the suite to be used for diet estimation.
Alternatively, if signature augmentation is used, pass the object cc
returned by the funtion cc_aug.
Bromaghin et al. (2015) introduced the terms prey space and
predator space. These terms refer to the simplexes in which the prey
and predator signatures reside. The spaces differ due to predator metabolism
of ingested prey tissue and the resulting modification of signature
proportions. The calibration coefficients cc provide a one-to-one
mapping or transformation between the prey and predator spaces. Diet
estimation can be performed in either space. Iverson et al. (2004) used
calibration coefficients to map predator signatures to the prey space, while
Bromaghin et al. (2013) took the opposite approach and mapped prey signatures
to the predator space. Simulation work has not revealed any strong reason
to prefer one space over the other (Bromaghin et al. 2015). However, be aware
that some distance measures will produce different diet estimates in the two
spaces. Please see the vignette for more information.
Estimation space options:
space == 1 Estimation in the predator space, the default value.
space == 2 Estimation in the prey space.
qfasar implements three distance measures that have been used by QFASA
practitioners and researchers: Aitchison, Kullback-Leibler, and chi-square.
The argument gamma is a parameter of the chi-square distance measure
and its value must be strictly greater than 0 and less than or equal to 1.
The distance measure options are:
dist_meas == 1 yields the Aitchison distance measure (Stewart et al.
2014). This is the default value.
dist_meas == 2 yields the Kullback-Leibler distance measure of
Iverson et al. (2004).
dist_meas == 3 yields the chi-square distance measure (Stewart et
al. 2014).
Please refer to the vignette for additional information about distance
measures.
The covariance matrix of each estimated diet can be estimated by bootstrap
sampling the prey library. The signatures of each prey type are
independently sampled with replacement and the predator diet is
estimated with the bootstrapped library. This is replicated ind_boot
times and the covariance matrix is estimated from the replicated estimates
(Beck et al. 2007, Bromaghin et al. 2015). If you do not wish to estimate
variances for the individual diet estimates, pass a bootstrap sample size
of 0 via the argument ind_boot.
qfasar implements two methods of estimating the mean diet of each
class of predator. The first is the empirical mean of the estimated diets.
In the second method, called the parameterized mean method, the
model is parameterized with a single vector of diet proportions common to all
predators and mean diet is estimated by minimizing the distance between the
signature modeled from the mean diet proportions and each predator's
observed signature, summed over all predators. The parameterized mean method
has not yet been thoroughly tested and its inclusion is intended to
facilitate future research. Our limited and unpublished work with the
parameterized mean estimator suggests it may perform well when predator
signatures are homogeneous, but may be more sensitive to the presence of
predators with quite different signatures than the empirical estimator.
The options for mean_meth are:
mean_meth == 0 skips estimation of mean diet.
mean_meth == 1 yields the empirical estimate of mean diet. This is the
default value.
mean_meth == 2 yields the parameterized mean estimate of mean diet.
qfasar implements two methods of estimating the variance of mean diet
estimates, the variance estimator of Beck et al. (2007) and a bootstrap
estimator, controlled by the argument var_meth. The bootstrap
estimator draws independent samples of each prey type to form a bootstrap
prey library and a random sample of each predator type, with sample sizes
equal to the observed sample sizes. Mean diet is estimated using the method
indicated by mean_meth. The argument mean_boot controls the
number of times this is repeated, and the replications are used to estimate
the covariance matrix for each predator type. Unpublished work suggests
that the bootstrap estimator is more reliable. Note that if using the
parameterized-mean estimator for mean diet composition, the Beck estimator
is not appropriate. The options for
var_meth are:
var_meth == 0 skips variance estimation for mean diets.
var_meth == 1 yields the bootstrap estimator. This is the default
value.
var_meth == 2 yields the Beck et al. (2007) estimator.
NOTE: The numerical optimization and bootstrap sampling performed by
est_diet are numerically intensive and can cause long runs times.
Patience is advised! The primary factors causing slow execution are the
number of predator signatures, the number of predator and prey types, and
bootstrap sample sizes.
References
Beck, C.A., S.J. Iverson, W.D. Bowen, and W. Blanchard. 2007. Sex differences
in grey seal diet reflect seasonal variation in foraging behaviour and
reproductive espenditure: evidence from quantitative fatty acid signature
analysis. Journal of Animal Ecology 76:490-502.
Bromaghin, J.F., M.M. Lance, E.W. Elliott, S.J. Jeffries, A.
Acevedo-Gutierrez, and J.M. Kennish. 2013. New insights into the diets of
harbor seals (Phoca vitulina) in the Salish Sea revealed by analysis
of fatty acid signatures. Fishery Bulletin 111:13-26.
Bromaghin, J.F., K.D. Rode, S.M. Budge, and G.W. Thiemann. 2015. Distance
measures and optimization spaces in quantitative fatty acid signature
analysis. Ecology and Evolution 5:1249-1262.
Iverson, S.J., C. Field, W.D. Bowen, and W. Blanchard. 2004.
Quantitative fatty acid signature analysis: A new method of
estimating predator diets. Ecological Monographs 74:211-235.
Stewart, C., S. Iverson, and C. Field. 2014. Testing for a change in diet
using fatty acid signatures. Environmental and Ecological Statistics
21:775-792.
Examples
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20
est_diet(pred_sigs = matrix(c(0.05, 0.10, 0.30, 0.55,
0.04, 0.11, 0.29, 0.56,
0.10, 0.06, 0.35, 0.49,
0.05, 0.15, 0.35, 0.45), ncol=4),
pred_uniq_types = c("Pred_1", "Pred_2"),
pred_loc = matrix(c(1, 3, 2, 4), ncol=2),
prey_sigs = matrix(c(0.06, 0.09, 0.31, 0.54,
0.05, 0.09, 0.30, 0.56,
0.03, 0.10, 0.30, 0.57,
0.08, 0.07, 0.30, 0.55,
0.09, 0.05, 0.33, 0.53,
0.09, 0.06, 0.34, 0.51,
0.09, 0.07, 0.34, 0.50,
0.08, 0.11, 0.35, 0.46,
0.06, 0.14, 0.36, 0.44), ncol=9),
prey_uniq_types = c("Prey_1", "Prey_2", "Prey_3"),
prey_loc = matrix(c(1, 4, 7, 3, 6, 9), ncol=2),
cc = c(0.75, 1.00, 1.50, 1.15),
space = 1, dist_meas = 1, ind_boot = 2,
mean_meth = 0)
qfasar documentation built on March 20, 2020, 1:10 a.m.
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Description Usage Arguments Value Details References Examples
Description
est_diet estimates the diet of one or more predators.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
Arguments
pred_sigs |
A vector or matrix of predator signatures ready for
analysis, intended to be the object |
pred_uniq_types |
A character vector of the unique predator types,
intended to be the object |
pred_loc |
A vector or matrix giving the first and last locations of the
signatures of each predator type within |
prey_sigs |
A matrix of prey signatures ready for analysis, intended to
be the object |
prey_uniq_types |
A character vector of the unique prey types, intended
to be the object |
prey_loc |
A matrix giving the first and last locations of the
signatures of each prey type within |
cc |
A vector of calibration coefficients, intended to be a subset of
the object |
space |
An integer indicator of the estimation space to be used. Default value 1. |
dist_meas |
An integer indicator of the distance measure to be used. Default value 1. |
gamma |
The power parameter of the chi-square distance measure. Default value 1. |
ind_boot |
The number of bootstrap replications to use in the estimation of the variance of an individual predator's diet. Default value 100. |
mean_meth |
An integer indicator of the estimation method for mean diet. Default value 1. |
var_meth |
An integer indicator of the estimation method for the variance of mean diet. Default value 1 (bootstrap estimator). |
mean_boot |
The number of bootstrap replications to use, needed only if the bootstrap method of estimating the variance of meat diet is selected (var_meth == 1). Default value 100. |
Value
A list containing the following elements:
- pred_sigs
A numeric matrix of predator signatures, potentially transformed to the prey space.
- prey_sigs
A numeric matrix of prey signatures, potentially transformed to the predator space.
- mean_sigs
A numeric matrix of mean prey-type signatures, potentially transformed to the predator space.
- est_ind
A numeric matrix of the estimated diet compositions of individual predators.
- conv
A logical vector indicating whether the optimization function successfully converged.
- obj_func
A numeric vector of the values of the objective function at each predator's estimated diet.
- mod_sigs
A numeric matrix of the modeled signature of each predator at its estimated diet.
- var_ind
A numeric array containing the estimated variance matrix for the estimated mean diet of each predator.
- est_mean
A numeric matrix containing the estimated mean diet of each predator type.
- conv_mean
A logical vector indicating whether the estimated mean diet of each predator type is based on at least one diet estimate that converged.
- var_mean
A numeric array containing the estimated variance matrix for the estimated mean diet of each predator type.
- err_code
An integer error code (0 if no error is detected).
- err_message
A string contains a brief summary of the execution.
Details
est_diet estimates the diet of one or more predators. It implements a
variety of estimation options, and is therefore one of the more complicated
functions in qfasar. Please read the following information and the
Diet Estimation section of the vignette for a description of the options.
The objects passed via the arguments pred_sig, pred_uniq_types,
and pred_loc are presumed to be the objects sig_scale,
uniq_types, and loc, respectively, returned by a call to the
function prep_sig with the predator data frame.
The objects passed via the arguments prey_sig, prey_uniq_types,
and prey_loc are presumed to be the objects sig_scale,
uniq_types, and loc, respectively, returned by a call to the
function prep_sig with the prey data frame.
The object passed via the argument cc is presumed to be a subset of
the object cc returned by a call to the function
prep_fa with the fatty acid suite data frame. Use the logical
vector use returned by prep_fa to subset the list of
all calibration coefficients to the suite to be used for diet estimation.
Alternatively, if signature augmentation is used, pass the object cc
returned by the funtion cc_aug.
Bromaghin et al. (2015) introduced the terms prey space and
predator space. These terms refer to the simplexes in which the prey
and predator signatures reside. The spaces differ due to predator metabolism
of ingested prey tissue and the resulting modification of signature
proportions. The calibration coefficients cc provide a one-to-one
mapping or transformation between the prey and predator spaces. Diet
estimation can be performed in either space. Iverson et al. (2004) used
calibration coefficients to map predator signatures to the prey space, while
Bromaghin et al. (2013) took the opposite approach and mapped prey signatures
to the predator space. Simulation work has not revealed any strong reason
to prefer one space over the other (Bromaghin et al. 2015). However, be aware
that some distance measures will produce different diet estimates in the two
spaces. Please see the vignette for more information.
Estimation space options:
space == 1 Estimation in the predator space, the default value.
space == 2 Estimation in the prey space.
qfasar implements three distance measures that have been used by QFASA
practitioners and researchers: Aitchison, Kullback-Leibler, and chi-square.
The argument gamma is a parameter of the chi-square distance measure
and its value must be strictly greater than 0 and less than or equal to 1.
The distance measure options are:
dist_meas == 1 yields the Aitchison distance measure (Stewart et al. 2014). This is the default value.
dist_meas == 2 yields the Kullback-Leibler distance measure of Iverson et al. (2004).
dist_meas == 3 yields the chi-square distance measure (Stewart et al. 2014).
Please refer to the vignette for additional information about distance measures.
The covariance matrix of each estimated diet can be estimated by bootstrap
sampling the prey library. The signatures of each prey type are
independently sampled with replacement and the predator diet is
estimated with the bootstrapped library. This is replicated ind_boot
times and the covariance matrix is estimated from the replicated estimates
(Beck et al. 2007, Bromaghin et al. 2015). If you do not wish to estimate
variances for the individual diet estimates, pass a bootstrap sample size
of 0 via the argument ind_boot.
qfasar implements two methods of estimating the mean diet of each
class of predator. The first is the empirical mean of the estimated diets.
In the second method, called the parameterized mean method, the
model is parameterized with a single vector of diet proportions common to all
predators and mean diet is estimated by minimizing the distance between the
signature modeled from the mean diet proportions and each predator's
observed signature, summed over all predators. The parameterized mean method
has not yet been thoroughly tested and its inclusion is intended to
facilitate future research. Our limited and unpublished work with the
parameterized mean estimator suggests it may perform well when predator
signatures are homogeneous, but may be more sensitive to the presence of
predators with quite different signatures than the empirical estimator.
The options for mean_meth are:
mean_meth == 0 skips estimation of mean diet.
mean_meth == 1 yields the empirical estimate of mean diet. This is the default value.
mean_meth == 2 yields the parameterized mean estimate of mean diet.
qfasar implements two methods of estimating the variance of mean diet
estimates, the variance estimator of Beck et al. (2007) and a bootstrap
estimator, controlled by the argument var_meth. The bootstrap
estimator draws independent samples of each prey type to form a bootstrap
prey library and a random sample of each predator type, with sample sizes
equal to the observed sample sizes. Mean diet is estimated using the method
indicated by mean_meth. The argument mean_boot controls the
number of times this is repeated, and the replications are used to estimate
the covariance matrix for each predator type. Unpublished work suggests
that the bootstrap estimator is more reliable. Note that if using the
parameterized-mean estimator for mean diet composition, the Beck estimator
is not appropriate. The options for
var_meth are:
var_meth == 0 skips variance estimation for mean diets.
var_meth == 1 yields the bootstrap estimator. This is the default value.
var_meth == 2 yields the Beck et al. (2007) estimator.
NOTE: The numerical optimization and bootstrap sampling performed by
est_diet are numerically intensive and can cause long runs times.
Patience is advised! The primary factors causing slow execution are the
number of predator signatures, the number of predator and prey types, and
bootstrap sample sizes.
References
Beck, C.A., S.J. Iverson, W.D. Bowen, and W. Blanchard. 2007. Sex differences in grey seal diet reflect seasonal variation in foraging behaviour and reproductive espenditure: evidence from quantitative fatty acid signature analysis. Journal of Animal Ecology 76:490-502.
Bromaghin, J.F., M.M. Lance, E.W. Elliott, S.J. Jeffries, A. Acevedo-Gutierrez, and J.M. Kennish. 2013. New insights into the diets of harbor seals (Phoca vitulina) in the Salish Sea revealed by analysis of fatty acid signatures. Fishery Bulletin 111:13-26.
Bromaghin, J.F., K.D. Rode, S.M. Budge, and G.W. Thiemann. 2015. Distance measures and optimization spaces in quantitative fatty acid signature analysis. Ecology and Evolution 5:1249-1262.
Iverson, S.J., C. Field, W.D. Bowen, and W. Blanchard. 2004. Quantitative fatty acid signature analysis: A new method of estimating predator diets. Ecological Monographs 74:211-235.
Stewart, C., S. Iverson, and C. Field. 2014. Testing for a change in diet using fatty acid signatures. Environmental and Ecological Statistics 21:775-792.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | est_diet(pred_sigs = matrix(c(0.05, 0.10, 0.30, 0.55,
0.04, 0.11, 0.29, 0.56,
0.10, 0.06, 0.35, 0.49,
0.05, 0.15, 0.35, 0.45), ncol=4),
pred_uniq_types = c("Pred_1", "Pred_2"),
pred_loc = matrix(c(1, 3, 2, 4), ncol=2),
prey_sigs = matrix(c(0.06, 0.09, 0.31, 0.54,
0.05, 0.09, 0.30, 0.56,
0.03, 0.10, 0.30, 0.57,
0.08, 0.07, 0.30, 0.55,
0.09, 0.05, 0.33, 0.53,
0.09, 0.06, 0.34, 0.51,
0.09, 0.07, 0.34, 0.50,
0.08, 0.11, 0.35, 0.46,
0.06, 0.14, 0.36, 0.44), ncol=9),
prey_uniq_types = c("Prey_1", "Prey_2", "Prey_3"),
prey_loc = matrix(c(1, 4, 7, 3, 6, 9), ncol=2),
cc = c(0.75, 1.00, 1.50, 1.15),
space = 1, dist_meas = 1, ind_boot = 2,
mean_meth = 0)
|
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