| Version: | 1.0.4 |
| Date: | 2020-09-17 |
| Title: | Predict Fish Year-Class Strength from Survey Data |
| LazyData: | yes |
| Description: | Predict fish year-class strength by calibration regression analysis of multiple recruitment index series. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.1.1 |
| NeedsCompilation: | no |
| Packaged: | 2020-09-23 14:02:32 UTC; colin |
| Author: | Colin Millar [aut, cre], Marc Taylor [aut] |
| Maintainer: | Colin Millar <colin.millar@ices.dk> |
| Repository: | CRAN |
| Date/Publication: | 2020-09-25 13:10:02 UTC |
Predict Fish Year-Class Strength from Survey Data
Description
Predict fish year-class strength by calibration regression analysis of multiple recruitment index series.
Details
Functions:
rct3 | run a calibrated regression to predict rectruitment |
print.rct3 | print a rct3 object |
summary.rct3 | summarise a rct3 object |
#' Data sets:
recdata | example dataset of recruitment and survey indices |
References
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
Print an rct3 fit
Description
Print an rct3 fit showing the model settings and predicted recruitments
Usage
## S3 method for class 'rct3'
print(x, digits = max(3, getOption("digits") - 3), ...)
Arguments
x |
an object of class rct3 - an output from the rct3 function. |
digits |
optional integer for how much to round the values in the output tables. |
... |
additional arguments to print.data.frame |
Value
invisibly returns a summary data frame.
See Also
rct3 run a calibrated regression to predict rectruitment.
summary.rct3 summarise a rct3 object
rct3-package gives an overview of the package.
Examples
# 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$rct3.summary["WAP"])
Run a calibrated regression to predict recruitment
Description
Function to run a calibrated regression to predict recruitment using the method decribed by Shepherd (1997)
Usage
rct3(
formula,
data,
predictions = NULL,
shrink = FALSE,
power = 3,
range = 20,
min.se = 0.2,
old = TRUE
)
Arguments
formula |
a formula to define which surveys to use in the recruitment estimation. |
data |
a dataframe with one column named 'yearclass' and other columns with the recruitment and the survey index relavent for that recruitment value |
predictions |
which yearclasses to make recruitment predictions for |
shrink |
shrink predictions to the VPA mean? |
power |
the power to use 0 - no weighting, 2 - bisquare, 3 - tricubic |
range |
the year range to use in the time tapered weighting |
min.se |
the minimum standard error used in the weighting of predictions |
old |
default TRUE, defines how to treat zero values. In the origional implmentation al values were transformed using log(x + 1), old=TRUE maintains this. |
Value
Object of class rct3.
Note
This function was written based on the publication by Shepherd (1997) with additional reverse engeneering by comparing results to previous examples run using the RCT3 ver3.1 dos program
References
J. G. Shepherd, Prediction of year-class strength by calibration regression analysis of multiple recruit index series, ICES Journal of Marine Science, Volume 54, Issue 5, October 1997, Pages 741–752, https://doi.org/10.1006/jmsc.1997.0222
See Also
rct3-package gives an overview of the package.
Examples
# load recruitment data
data(recdata)
formula <- recruitment ~ NT1 + NT2 + NT3 +
NAK1 + NAK2 + NAK3 +
RT1 + RT2 + RT3 +
EC01 + ECO2 + ECO3
my_rct3 <- rct3(formula, recdata, predictions = 2012:2017, shrink = TRUE)
# see a short summary
my_rct3
# for a full summary do:
summary(my_rct3)
# the components are here:
my_rct3$rct3
my_rct3$rct3.summary
# predicted recruitment
t(my_rct3$rct3.summary["WAP"])
Recruitment and survey index data
Description
data.frame containing recruitment (age 3) and survey indices from several surveys over ages 1 to 3
Usage
recdata
Format
Data frame containing 14 columns:
yearclass | the yearclass |
recruitment | the recruiment (age 3) for that yearclass |
NT1 | The age 1 survey index from 'NT' survey |
NT2 | The age 2 survey index from 'NT' survey |
... | and so on |
See Also
rct3 run a calibrated regression to predict rectruitment.
rct3-package gives an overview of the package.
Summarise an rct3 fit
Description
Print an rct3 fit showing the model settings, a summary of the prediction for each yearclass and the overall predicted recruitments
Usage
## S3 method for class 'rct3'
summary(object, digits = max(3, getOption("digits") - 3), ...)
Arguments
object |
an object of class rct3 - an output from the rct3 function. |
digits |
optional integer for how much to round the values in the output tables. |
... |
additional arguments to print.data.frame |
Value
invisibly returns a summary data frame.
See Also
rct3 run a calibrated regression to predict rectruitment.
rct3-package gives an overview of the package.
Examples
# 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"])