ELEFAN_SA_boot {fishboot} | R Documentation |
Bootstraped ELEFAN_SA
Description
This function performs a bootstrapped fitting of a von
Bertalanffy growth function (VBGF) via the ELEFAN_SA
function. Most of the arguments are simply passed to the function within many
permutations (resampling) of the original lfq
data. Partial
(repeated fitting on original data) and full bootstrap (with resampling)
routines are possible, depending on resample
.
Usage
ELEFAN_SA_boot(
lfq,
seasonalised = FALSE,
init_par = list(Linf = 50, K = 0.5, t_anchor = 0.5, C = 0, ts = 0),
low_par = NULL,
up_par = NULL,
SA_time = 60 * 1,
maxit = NULL,
nb.stop.improvement = NULL,
SA_temp = 1e+05,
MA = 5,
addl.sqrt = FALSE,
agemax = NULL,
seed = NULL,
nresamp = 10,
resample = TRUE,
parallel = FALSE,
outfile = NA
)
Arguments
lfq |
a length frequency object of the class |
seasonalised |
logical; indicating if the seasonalised von Bertalanffy growth function should be applied (default: FALSE). |
init_par |
a list providing the Initial values for the components to be optimized. When set to NULL the following default values are used:
|
low_par |
a list providing the lower bounds for components. When set to NULL the following default values are used:
|
up_par |
a list providing the upper bounds for components. When set to NULL the following default values are used:
|
SA_time |
numeric; Maximum running time in seconds (default : 60 * 1). |
maxit |
Integer. Maximum number of iterations of the algorithm. Default is NULL. |
nb.stop.improvement |
Integer. The program will stop when there is no any improvement in 'nb.stop.improvement' steps. Default is NULL |
SA_temp |
numeric; Initial value for temperature (default : 1e5). |
MA |
number indicating over how many length classes the moving average should be performed (defalut: 5, for more information see lfqRestructure). |
addl.sqrt |
Passed to lfqRestructure. Applied an additional square-root transformation of positive values according to Brey et al. (1988). (default: FALSE, for more information see lfqRestructure). |
agemax |
maximum age of species; default NULL, then estimated from
|
seed |
seed value for random number reproducibility. |
nresamp |
|
resample |
|
parallel |
Whether a |
outfile |
|
Details
If resample = TRUE
, a full non-parametric bootstrap is
performed with resampling from the original length-frequencies by using the
function lfqResample. Otherwise, if resample = FALSE
, a partial
bootstrap is performed, reflecting solution variation due only to the search
algorithm, with repeated fitting to the original data (no resampling is
performed).
Value
An object of class lfqBoot
containing 2 levels:
$bootRaw
A
data.frame
of fitted VBGF parameters (columns) by resampling (rows).$seed
A
numeric
vector of seed values set prior to each resampling call to lfqResample.
References
Brey, T., Soriano, M., and Pauly, D. 1988. Electronic length frequency analysis: a revised and expanded user's guide to ELEFAN 0, 1 and 2.
Efron, B., & Tibshirani, R. (1986). Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy. Statistical Science, 54-75.
Mildenberger, T., Taylor, M. H., & Wolff, A. M., 2017. TropFishR: an R package for fisheries analysis with length-frequency data. Methods in Ecology and Evolution, 8(11), 1520-1527.
Pauly, D. 1981. The relationship between gill surface area and growth performance in fish: a generalization of von Bertalanffy's theory of growth. Meeresforsch. 28:205-211.
Pauly, D. and N. David, 1981. ELEFAN I, a BASIC program for the objective extraction of growth parameters from length-frequency data. Meeresforschung, 28(4):205-211.
Schwamborn, R., Mildenberger, T. K., & Taylor, M. H., 2019. Assessing sources of uncertainty in length-based estimates of body growth in populations of fishes and macroinvertebrates with bootstrapped ELEFAN. Ecological Modelling, 393, 37-51.
Schwamborn, R., Freitas, M. O., Moura, R. L., & Aschenbrenner, A. 2023. Comparing the accuracy and precision of novel bootstrapped length-frequency and length-at-age (otolith) analyses, with a case study of lane snapper (Lutjanus synagris) in the SW Atlantic. Fisheries Research, 264, 106735.
Scrucca, L., 2013. GA: a package for genetic algorithms in R. Journal of Statistical Software, 53(4), 1-37.
von Bertalanffy, L., 1938. A quantitative theory of organic growth. Human Biology 10, 181-213.
Examples
# load data
data("alba", package = "TropFishR")
# Define settings (for demo only, fast settings)
MA <- 7
low_par <- list(Linf = 9, K = 0.4, t_anchor = 0.5, C = 0, ts = 0)
up_par <- list(Linf = 11, K = 0.6, t_anchor = 0.8, C = 1, ts = 1)
init_par <- list(Linf = 10, K = 0.5, t_anchor = 0.6, C = 0.5, ts = 0.5)
SA_time <- 1.5
SA_temp <- 1e5
nresamp <- 2
# Non-parallel bootstrapped curve fiting
res <- ELEFAN_SA_boot(lfq = alba, MA = MA, seasonalised = FALSE,
init_par = init_par, up_par = up_par, low_par = low_par,
SA_time = SA_time, SA_temp = SA_temp,
nresamp = nresamp)
res
# Define settings (for demo only)
MA <- 7
low_par <- list(Linf = 8, K = 0.1, t_anchor = 0, C = 0, ts = 0)
init_par <- list(Linf = 12, K = 0.5, t_anchor = 0.5, C = 0.5, ts = 0.5)
up_par <- list(Linf = 15, K = 5, t_anchor = 1, C = 1, ts = 1)
SA_time <- 10
SA_temp <- 1e5
nresamp <- 12
# parallel version
res <- ELEFAN_SA_boot(lfq = alba, MA = MA, seasonalised = FALSE,
init_par = init_par, up_par = up_par, low_par = low_par,
SA_time = SA_time, SA_temp = SA_temp,
nresamp = nresamp,
parallel = TRUE)
res