Description Usage Arguments Value Note References See Also Examples
Function to run a calibrated regression to predict recruitment using the method decribed by Shepherd (1997)
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formula |
a formula to define which surveys to use in the recruitment estimation. |
data |
a dataframe with one column named 'yearclass' and other columns with the recruitment and the survey index relavent for that recruitment value |
predictions |
which yearclasses to make recruitment predictions for |
shrink |
shrink predictions to the VPA mean? |
power |
the power to use 0 - no weighting, 2 - bisquare, 3 - tricubic |
range |
the year range to use in the time tapered weighting |
min.se |
the minimum standard error used in the weighting of predictions |
old |
default TRUE, defines how to treat zero values. In the origional implmentation al values were transformed using log(x + 1), old=TRUE maintains this. |
Object of class rct3
.
This function was written based on the publication by Shepherd (1997) with additional reverse engeneering by comparing results to previous examples run using the RCT3 ver3.1 dos program
J. G. Shepherd, Prediction of year-class strength by calibration regression analysis of multiple recruit index series, ICES Journal of Marine Science, Volume 54, Issue 5, October 1997, Pages 741–752, https://doi.org/10.1006/jmsc.1997.0222
rct3-package
gives an overview of the package.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | # load recruitment data
data(recdata)
formula <- recruitment ~ NT1 + NT2 + NT3 +
NAK1 + NAK2 + NAK3 +
RT1 + RT2 + RT3 +
EC01 + ECO2 + ECO3
my_rct3 <- rct3(formula, recdata, predictions = 2012:2017, shrink = TRUE)
# see a short summary
my_rct3
# for a full summary do:
summary(my_rct3)
# the components are here:
my_rct3$rct3
my_rct3$rct3.summary
# predicted recruitment
t(my_rct3$rct3.summary["WAP"])
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