plot.VFP: Plot VFP-Ojbects.
In VFP: Variance Function Program
plot.VFP R Documentation
Plot VFP-Ojbects.
Description
Function takes an object of class 'VFP' and plots a fitted variance-function
either on the original variance-scale ('type="vc"') or on the CV-scale ("cv").
The corresponding 100x(1-alpha)% confidencen interval around the variance-function
can be plotted either as lines ('ci.type="lines') or as per default as CI-band.
Usage
## S3 method for class 'VFP'
plot(
x,
model.no = NULL,
type = c("vc", "sd", "cv"),
add = FALSE,
alpha = 0.05,
ci.col = "gray90",
ci.type = c("band", "lines", "none"),
dispersion = NULL,
browse = FALSE,
BG = "white",
Title = list(),
Xlabel = list(),
Ylabel = list(),
Line = list(),
Points = list(),
Grid = list(),
Crit = list(),
ylim = NULL,
xlim = NULL,
Prediction = NULL,
Pred.CI = NULL,
Model = TRUE,
CI.method = c("chisq", "t", "normal"),
use.log = FALSE,
Npred = 200,
...
)
Arguments
x
(VFP) object as returned by function 'fit.vfp'
model.no
(integer) specifying which model to plot, must be one of the fitted models
type
(character) either "vc" to generate a plot on the original
variance-scale or "cv" to plot it on the coefficient of variation
scale, i.e. CV = 100*sqrt(VC)/Mean or "log" to plot after a variance
stabilizing transformation. The latter will not work if 'Prediction' is specified!.
add
(logical) TRUE = the current (im)precision profile is added to an existing plot,
FALSE = a new plot will be generated
alpha
(numeric) value specifying the 100x(1-alpha)% confidencen interval
to be plotted around the function
ci.col
(character) string specifying a color used for the CI-region
ci.type
(character) either "band" to plto the CI as polygon, or "lines" to
plot the CI-bounds as two separate line using color 'ci.col'
dispersion
(numeric) NULL = the dispersion parameter will be estimated,
numeric value = the dispersion parameter will be used as specified
browse
(logical) TRUE = if multiple models were fitted, all will be displayed one after
the other in increasing order of their respective AIC, mouse-klick on the plot
triggers switch to the next model
BG
(character) string specifying a background color
Title
(list) passed to function mtext controlling content and style of
the main title
Xlabel
(list) passed to function mtext controlling the labeling
of the X-axis
Ylabel
(list) passed to function mtext controlling the labeling
of the Y-axis
Line
(list) passed to function lines controlling the visual appearance
of the line representing the fitted variance-function
Points
(list) passed to function points controlling how
data used to fit a variance function shall be plotted
Grid
(list) passed to function addGrid controlling the appearance
of a grid, set to NULL to omit
Crit
(list) passed to function legend per default used to present
the optimality criterion for choosing the best fitting model, per default this
is AIC and additionally residual sum of squares (RSS) is shown for the plotted
model in the upper-right corner
ylim
(numeric) vector of length two specifying plot-limits in Y-direction, if NULL
these will be automatically determined
xlim
(numeric) vector of length two specifying plot-limits in X-direction, if NULL
these will be automatically determined
Prediction
(list) with elements 'y' specifying values on VC-, SD- or CV-scale depending on
'type' for which predictions on the X-axis are requested or 'x' specifying mean-values
on the X-axis for which predictions on the Y-axis are requested; furthermore,
all graphical parameters accepted by function lines indicating predictions;
NULL to omit (default);
additionally to arguments accepted by function 'lines', one can specify parameters
'x.line' and 'y.line' used to indicated values at the respective axis in margin-lines see
mtext for details; 'cex' and 'font' for specifying how these values are plotted.
The same color as lines is used per default but can be changed setting 'text.col'.
Can also be (numeric) vector (not a list) which results in using default graphical settings.
See also parameter Pred.CI.
Pred.CI
(list) with all parameters accepted by function rect; if not NULL,
the 100x(1-alpha)% CI of predicted values will be added as a semi-transparent rectangle
per default (see examples).
Model
(logical) TRUE = plots the fitted model as subtitle below the main title, FALSE = omits this
CI.method
(character) one of "t", "normal", "chisq" specifying which CI-method to use for
deriving confidence intervals
use.log
(logical) TRUE = X- and Y-axis will be log-transformed
Npred
(integer) specifying the number of data points used to plot the fitted model, the larger the
smoother (maybe slower if too large)
...
additional parameters passed forward
Value
(matrix) of predictions at user-specified X- or Y-coordinates is invisibly return in case Prediction is not NULL
Author(s)
Andre Schuetzemeister andre.schuetzeneister@roche.com
See Also
fit.vfp, predict.VFP, predictMean
Examples
library(VCA)
data(VCAdata1)
lst <- anovaVCA(y~(device+lot)/day/run, VCAdata1, by="sample")
mat <- getMat.VCA(lst) # automatically selects "total"
mat
res <- fit.vfp(model.no=1:10, Data=mat)
plot(res)
plot(res, type="cv")
plot(res, type="cv", ci.type="lines", ci.col="red",
Grid=list(col="wheat"), Points=list(pch=2, lwd=2, col="black"))
# same for repeatability
mat.err <- getMat.VCA(lst, "error")
res.err <- fit.vfp(1:10, Data=mat.err)
plot(res.err)
# add predictions to plot, e.g. functional sensitivity
plot(res.err, type="cv", xlim=c(0, 4), Prediction=10)
# variability at X-values are of interest
plot(res.err, type="cv", xlim=c(0, 4), Prediction=list(x=0.5))
# one can specify X- and Y-values in the "Prediction" list-argument
plot(res.err, type="cv", xlim=c(0, 4),
Prediction=list(x=c(0.25, 0.5), y=15))
#######################################################################
# another example using CA19_9 data from CLSI EP05-A3
data(CA19_9)
# fit reproducibility model to data
fits.CA19_9 <- anovaVCA(result~site/day, CA19_9, by="sample")
# fit within-laboratory-model treating site as fixed effect
fits.ip.CA19_9 <- anovaMM(result~site/(day), CA19_9, by="sample")
# the variability "between-site" is not part of "total"
fits.ip.CA19_9[[1]]
fits.CA19_9[[1]]
# extract repeatability
rep.CA19_9 <- getMat.VCA(fits.CA19_9, "error")
# extract reproducibility
repro.CA19_9 <- getMat.VCA(fits.CA19_9, "total")
# extract intermediate-precision (within-lab)
ip.CA19_9 <- getMat.VCA(fits.ip.CA19_9, "total")
# fit model (a+bX)^C (model 8) to all three matrices
mod8.repro <- fit.vfp(repro.CA19_9, 8)
mod8.ip <- fit.vfp(ip.CA19_9, 8)
mod8.rep <- fit.vfp(rep.CA19_9, 8)
# plot reproducibility precision profile first
# leave enough space in right margin for a legend
plot(mod8.repro, mar=c(5.1, 7, 4.1, 15),
type="cv", ci.type="none", Model=FALSE,
Line=list(col="blue", lwd=3),
Points=list(pch=15, col="blue", cex=1.5),
xlim=c(10, 450), ylim=c(0,10),
Xlabel=list(text="CA19-9, kU/L (LogScale) - 3 Patient Pools, 3 QC Materials",
cex=1.5), Title=NULL,
Ylabel=list(text="% CV", cex=1.5),
Grid=NULL, Crit=NULL, log="x")
# add intermediate precision profile
plot (mod8.ip, type="cv", add=TRUE, ci.type="none",
Points=list(pch=16, col="deepskyblue", cex=1.5),
Line=list(col="deepskyblue", lwd=3), log="x")
# add repeatability precision profile
plot(mod8.rep, type="cv", add=TRUE, ci.type="none",
Points=list(pch=17, col="darkorchid3", cex=1.5),
Line=list(col="darkorchid3", lwd=3), log="x")
# add legend to right margin
legend.rm( x="center", pch=15:17, col=c("blue", "deepskyblue", "darkorchid3"),
cex=1.5, legend=c("Reproducibility", "Within-Lab Precision", "Repeatability"),
box.lty=0)
# repeatability precision profile with some beautifications
plot(mod8.rep, BG="darkgray",
Points=list(pch=17, cex=1.5, col="blue"), Line=list(col="blue"),
Grid=list(x=seq(0, 400, 50), y=seq(0, 100, 10), col="white"),
Xlabel=list(cex=1.5, text="CA19-9 [U/mL]", col="blue"),
Ylabel=list(cex=1.5, text="Repeatability on Variance-Scale", col="blue"),
Crit=list(text.col="white", text.font=2, cex=1.25))
VFP documentation built on Nov. 10, 2022, 5:12 p.m.
R Package Documentation
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| plot.VFP | R Documentation |
Plot VFP-Ojbects.
Description
Function takes an object of class 'VFP' and plots a fitted variance-function either on the original variance-scale ('type="vc"') or on the CV-scale ("cv"). The corresponding 100x(1-alpha)% confidencen interval around the variance-function can be plotted either as lines ('ci.type="lines') or as per default as CI-band.
Usage
## S3 method for class 'VFP'
plot(
x,
model.no = NULL,
type = c("vc", "sd", "cv"),
add = FALSE,
alpha = 0.05,
ci.col = "gray90",
ci.type = c("band", "lines", "none"),
dispersion = NULL,
browse = FALSE,
BG = "white",
Title = list(),
Xlabel = list(),
Ylabel = list(),
Line = list(),
Points = list(),
Grid = list(),
Crit = list(),
ylim = NULL,
xlim = NULL,
Prediction = NULL,
Pred.CI = NULL,
Model = TRUE,
CI.method = c("chisq", "t", "normal"),
use.log = FALSE,
Npred = 200,
...
)
Arguments
x |
(VFP) object as returned by function 'fit.vfp' |
model.no |
(integer) specifying which model to plot, must be one of the fitted models |
type |
(character) either "vc" to generate a plot on the original variance-scale or "cv" to plot it on the coefficient of variation scale, i.e. CV = 100*sqrt(VC)/Mean or "log" to plot after a variance stabilizing transformation. The latter will not work if 'Prediction' is specified!. |
add |
(logical) TRUE = the current (im)precision profile is added to an existing plot, FALSE = a new plot will be generated |
alpha |
(numeric) value specifying the 100x(1-alpha)% confidencen interval to be plotted around the function |
ci.col |
(character) string specifying a color used for the CI-region |
ci.type |
(character) either "band" to plto the CI as polygon, or "lines" to plot the CI-bounds as two separate line using color 'ci.col' |
dispersion |
(numeric) NULL = the dispersion parameter will be estimated, numeric value = the dispersion parameter will be used as specified |
browse |
(logical) TRUE = if multiple models were fitted, all will be displayed one after the other in increasing order of their respective AIC, mouse-klick on the plot triggers switch to the next model |
BG |
(character) string specifying a background color |
Title |
(list) passed to function |
Xlabel |
(list) passed to function |
Ylabel |
(list) passed to function |
Line |
(list) passed to function |
Points |
(list) passed to function |
Grid |
(list) passed to function |
Crit |
(list) passed to function |
ylim |
(numeric) vector of length two specifying plot-limits in Y-direction, if NULL these will be automatically determined |
xlim |
(numeric) vector of length two specifying plot-limits in X-direction, if NULL these will be automatically determined |
Prediction |
(list) with elements 'y' specifying values on VC-, SD- or CV-scale depending on
'type' for which predictions on the X-axis are requested or 'x' specifying mean-values
on the X-axis for which predictions on the Y-axis are requested; furthermore,
all graphical parameters accepted by function |
Pred.CI |
(list) with all parameters accepted by function |
Model |
(logical) TRUE = plots the fitted model as subtitle below the main title, FALSE = omits this |
CI.method |
(character) one of "t", "normal", "chisq" specifying which CI-method to use for deriving confidence intervals |
use.log |
(logical) TRUE = X- and Y-axis will be log-transformed |
Npred |
(integer) specifying the number of data points used to plot the fitted model, the larger the smoother (maybe slower if too large) |
... |
additional parameters passed forward |
Value
(matrix) of predictions at user-specified X- or Y-coordinates is invisibly return in case Prediction is not NULL
Author(s)
Andre Schuetzemeister andre.schuetzeneister@roche.com
See Also
fit.vfp, predict.VFP, predictMean
Examples
library(VCA)
data(VCAdata1)
lst <- anovaVCA(y~(device+lot)/day/run, VCAdata1, by="sample")
mat <- getMat.VCA(lst) # automatically selects "total"
mat
res <- fit.vfp(model.no=1:10, Data=mat)
plot(res)
plot(res, type="cv")
plot(res, type="cv", ci.type="lines", ci.col="red",
Grid=list(col="wheat"), Points=list(pch=2, lwd=2, col="black"))
# same for repeatability
mat.err <- getMat.VCA(lst, "error")
res.err <- fit.vfp(1:10, Data=mat.err)
plot(res.err)
# add predictions to plot, e.g. functional sensitivity
plot(res.err, type="cv", xlim=c(0, 4), Prediction=10)
# variability at X-values are of interest
plot(res.err, type="cv", xlim=c(0, 4), Prediction=list(x=0.5))
# one can specify X- and Y-values in the "Prediction" list-argument
plot(res.err, type="cv", xlim=c(0, 4),
Prediction=list(x=c(0.25, 0.5), y=15))
#######################################################################
# another example using CA19_9 data from CLSI EP05-A3
data(CA19_9)
# fit reproducibility model to data
fits.CA19_9 <- anovaVCA(result~site/day, CA19_9, by="sample")
# fit within-laboratory-model treating site as fixed effect
fits.ip.CA19_9 <- anovaMM(result~site/(day), CA19_9, by="sample")
# the variability "between-site" is not part of "total"
fits.ip.CA19_9[[1]]
fits.CA19_9[[1]]
# extract repeatability
rep.CA19_9 <- getMat.VCA(fits.CA19_9, "error")
# extract reproducibility
repro.CA19_9 <- getMat.VCA(fits.CA19_9, "total")
# extract intermediate-precision (within-lab)
ip.CA19_9 <- getMat.VCA(fits.ip.CA19_9, "total")
# fit model (a+bX)^C (model 8) to all three matrices
mod8.repro <- fit.vfp(repro.CA19_9, 8)
mod8.ip <- fit.vfp(ip.CA19_9, 8)
mod8.rep <- fit.vfp(rep.CA19_9, 8)
# plot reproducibility precision profile first
# leave enough space in right margin for a legend
plot(mod8.repro, mar=c(5.1, 7, 4.1, 15),
type="cv", ci.type="none", Model=FALSE,
Line=list(col="blue", lwd=3),
Points=list(pch=15, col="blue", cex=1.5),
xlim=c(10, 450), ylim=c(0,10),
Xlabel=list(text="CA19-9, kU/L (LogScale) - 3 Patient Pools, 3 QC Materials",
cex=1.5), Title=NULL,
Ylabel=list(text="% CV", cex=1.5),
Grid=NULL, Crit=NULL, log="x")
# add intermediate precision profile
plot (mod8.ip, type="cv", add=TRUE, ci.type="none",
Points=list(pch=16, col="deepskyblue", cex=1.5),
Line=list(col="deepskyblue", lwd=3), log="x")
# add repeatability precision profile
plot(mod8.rep, type="cv", add=TRUE, ci.type="none",
Points=list(pch=17, col="darkorchid3", cex=1.5),
Line=list(col="darkorchid3", lwd=3), log="x")
# add legend to right margin
legend.rm( x="center", pch=15:17, col=c("blue", "deepskyblue", "darkorchid3"),
cex=1.5, legend=c("Reproducibility", "Within-Lab Precision", "Repeatability"),
box.lty=0)
# repeatability precision profile with some beautifications
plot(mod8.rep, BG="darkgray",
Points=list(pch=17, cex=1.5, col="blue"), Line=list(col="blue"),
Grid=list(x=seq(0, 400, 50), y=seq(0, 100, 10), col="white"),
Xlabel=list(cex=1.5, text="CA19-9 [U/mL]", col="blue"),
Ylabel=list(cex=1.5, text="Repeatability on Variance-Scale", col="blue"),
Crit=list(text.col="white", text.font=2, cex=1.25))
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