LP_est_adjust {Petersen} | R Documentation |
Estimate abundance after empirical adjustments for various factors.
Description
This will take a previous fit and return estimates of abundance after making various empirical adjustments
Usage
LP_est_adjust(
N_hat,
N_hat_SE,
conf_level = 0.95,
tag.retention.est = 1,
tag.retention.se = 0,
tag.reporting.est = 1,
tag.reporting.se = 0,
n1.adjust.est = 1,
n1.adjust.se = 0,
n2.adjust.est = 1,
n2.adjust.se = 0,
m2.adjust.est = 1,
m2.adjust.se = 0,
n.sim = 10000,
trace = FALSE
)
Arguments
N_hat |
Estimate of N that will be adjusted |
N_hat_SE |
SE of the N_hat |
conf_level |
The expected coverage for confidence intervals on N. |
tag.retention.est |
Estimated tag retention probability |
tag.retention.se |
Estimated SE of tag retention probability |
tag.reporting.est |
Estimated tag reporting probability |
tag.reporting.se |
Estimated SE of tag reporting probability |
n1.adjust.est |
Adjustment to "n1". This should typically be a ratio of new n1 to old n1 |
n1.adjust.se |
Adjustment to "n1" uncertainty |
n2.adjust.est |
Adjustment to "n2" This should typically be a ratio of new n2 to old n2 |
n2.adjust.se |
Adjustment to "n2" uncertainty |
m2.adjust.est |
Adjustment to "m2" This should typically be a ratio of new m2 to old m2 |
m2.adjust.se |
Adjustment to "m2" uncertainty |
n.sim |
Number of simulation runs to make |
trace |
If trace flag is set in call when estimating functions |
Details
The estimate and SE are converted to a beta distribution for adjustment factors between 0 and 1 with equivalent mean and SD as the estimate and se. The estimate and se are used in normal distribution for adjustment factors for n1, n2, and m2. These adjustment factors are then simulated a large number of times and then multiplied together to get the mean and sd of all adjustments applied together. Then the abundance is simulated (on the log scale), the product taken, and the mean, sd, ci estimated directly.
Value
An list object with a summary data frame and a data frame with the adjustment factors with the following objects summary A data frame with the adjusted abundance estimates, SE, and CI adjustment a data frame showing the adjustment factors applied for tag retention, tag reporting, n1 n2 or m2. datetime Date and time the adjustment was done
Author(s)
Schwarz, C. J. cschwarz.stat.sfu.ca@gmail.com.
Examples
data(data_rodli)
rodli.fit <- Petersen::LP_fit(data=data_rodli, p_model=~..time)
rodli.est <- Petersen::LP_est(rodli.fit)
res <- Petersen::LP_est_adjust(rodli.est$summary$N_hat, rodli.est$summary$N_hat_SE,
tag.retention.est=.90, tag.retention.se=.05)
res$summary