lwCompPreds: Constructs plots of predicted weights at given lengths among...

Description Usage Arguments Value IFAR Chapter Author(s) References Examples

View source: R/lwCompPreds.R

Description

Constructs plots of predicted weights at given lengths among different groups. These plots allow the user to explore differences in predicted weights at a variety of lengths when the weight-length relationship is not the same across a variety of groups.

Usage

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lwCompPreds(
  object,
  lens = NULL,
  qlens = c(0.05, 0.25, 0.5, 0.75, 0.95),
  qlens.dec = 1,
  base = exp(1),
  interval = c("confidence", "prediction", "both"),
  center.value = 0,
  lwd = 1,
  connect.preds = TRUE,
  show.preds = FALSE,
  col.connect = "gray70",
  ylim = NULL,
  main.pre = "Length==",
  cex.main = 0.8,
  xlab = "Groups",
  ylab = "Predicted Weight",
  yaxs = "r",
  rows = round(sqrt(num)),
  cols = ceiling(sqrt(num))
)

Arguments

object

An lm object (i.e., returned from fitting a model with lm). This model should have log(weight) as the response and log(length) as the explanatory covariate and an explanatory factor variable that describes the different groups.

lens

A numeric vector that indicates the lengths at which the weights should be predicted.

qlens

A numeric vector that indicates the quantiles of lengths at which weights should be predicted. This is ignored if lens is non-null.

qlens.dec

A single numeric that identifies the decimal place that the lengths derived from qlens should be rounded to (Default is 1).

base

A single positive numeric value that indicates the base of the logarithm used in the lm object in object. The default is exp(1), or the value e.

interval

A single string that indicates whether to plot confidence (="confidence"), prediction (="prediction"), or both (="both") intervals.

center.value

A single numeric value that indicates the log length used if the log length data was centered when constructing object.

lwd

A single numeric that indicates the line width to be used for the confidence and prediction interval lines (if not interval="both") and the prediction connections line. If interval="both" then the width of the prediction interval will be one less than this value so that the CI and PI appear different.

connect.preds

A logical that indicates whether the predicted values should be connected with a line across groups or not.

show.preds

A logical that indicates whether the predicted values should be plotted with a point for each group or not.

col.connect

A color to use for the line that connects the predicted values (if connect.preds=TRUE).

ylim

A numeric vector of length two that indicates the limits of the y-axis to be used for each plot. If null then limits will be chosen for each graph individually.

main.pre

A character string to be used as a prefix for the main title. See details.

cex.main

A numeric value for the character expansion of the main title. See details.

xlab

A single string for labeling the x-axis.

ylab

A single string for labeling the y-axis.

yaxs

A single string that indicates how the y-axis is formed. See par for more details.

rows

A single numeric that contains the number of rows to use on the graphic.

cols

A single numeric that contains the number of columns to use on the graphic.

Value

None. However, a plot is produced.

IFAR Chapter

7-Weight-Length.

Author(s)

Derek H. Ogle, derek@derekogle.com

References

Ogle, D.H. 2016. Introductory Fisheries Analyses with R. Chapman & Hall/CRC, Boca Raton, FL.

Examples

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# add log length and weight data to ChinookArg data
ChinookArg$logtl <- log(ChinookArg$tl)
ChinookArg$logwt <- log(ChinookArg$w)
# fit model to assess equality of slopes
lm1 <- lm(logwt~logtl*loc,data=ChinookArg)
anova(lm1)

# set graphing parameters so that the plots will look decent
op <- par(mar=c(3.5,3.5,1,1),mgp=c(1.8,0.4,0),tcl=-0.2)
# show predicted weights (w/ CI) at the default quantile lengths
lwCompPreds(lm1,xlab="Location")
# show predicted weights (w/ CI) at the quartile lengths
lwCompPreds(lm1,xlab="Location",qlens=c(0.25,0.5,0.75))
# show predicted weights (w/ CI) at certain lengths
lwCompPreds(lm1,xlab="Location",lens=c(60,90,120,150))
# show predicted weights (w/ just PI) at certain lengths
lwCompPreds(lm1,xlab="Location",lens=c(60,90,120,150),interval="prediction")
lwCompPreds(lm1,xlab="Location",lens=c(60,90,120,150),connect.preds=FALSE,show.preds=TRUE)

# fit model with a different base (plot should be the same as the first example)
ChinookArg$logtl <- log10(ChinookArg$tl)
ChinookArg$logwt <- log10(ChinookArg$w)
lm1 <- lm(logwt~logtl*loc,data=ChinookArg)
lwCompPreds(lm1,base=10,xlab="Location")
## return graphing parameters to original state
par(op)

FSA documentation built on July 17, 2021, 5:07 p.m.

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