vbgfCI_time {fishboot} | R Documentation |
VBGF plot and CI
Description
This function plots a swarm of von Bertalanffy growth functions (VBGF), as length vs time (age) curves, based on the results of bootstrap runs, with confidence intervals (CI).
Usage
vbgfCI_time(
res,
CI = 95,
agemax = NULL,
plot = TRUE,
add_legend = TRUE,
add_max_dens_legend = TRUE,
xlab = "Relative time",
ylab = "Length",
perm.col = adjustcolor("grey50", 0.1),
perm.lwd = 1,
ci.col = "black",
ci.lty = 2,
ci.lwd = 1,
maxd.col = "black",
maxd.lty = 1,
maxd.lwd = 2,
...
)
Arguments
res |
Object with |
CI |
|
agemax |
|
plot |
|
add_legend |
|
add_max_dens_legend |
logical. Should maximum density line be added (Default: 'add_max_dens_legend = TRUE'). |
xlab |
Label for x-axis |
ylab |
Label for y-axis |
perm.col , perm.lwd |
Color and width for each resample estimate line. |
ci.col , ci.lty , ci.lwd |
Color, type and width for CI line. |
maxd.col , maxd.lty , maxd.lwd |
Color, type and width for maximum density line. |
... |
Extra arguments passed to the main plot function. |
Details
Each thin grey line represents the output of a single bootstrap run. The most
likely optimum (i.e., the mode of the posterior distribution) is shown as a
thick black line. The dashed lines show the upper and lower limits of the 95
confidence envelope. The input used for plotting is usually the result of a
bootstrapped growth analysis (i.e. a lfqBoot
object generated by
fishboot functions such as ELEFAN_SA_boot,
ELEFAN_GA_boot, grotag_boot, or grolenage_boot).
Value
A list
containing:
$limCI
A
data.frame
with CI limits by time.$inCI
A
data.frame
with logical values defining whether bootstrapping samples are within each of the defined CIs.$density
The multivariate kernel density estimates for each sample.
$max_dens
A
list
with the VBGF parameter combination having the maximum density estimate.
Examples
data(alba_boot) # lfqBoot object
vbgfCI_time(res = alba_boot)
vbgfCI_time(res = alba_boot, CI = c(50, 95),
ci.col = c("red", "orange"))
data(bonito_boot) # grotagBoot object
LinfK_scatterhist(res = bonito_boot)