From ae13a2e7f373f697cdfb6acb7ae042d6e27d8967 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 24 Mar 2017 15:22:07 +0100 Subject: Add pkgdown docu, change package build directory --- docs/reference/drplot.html | 268 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 268 insertions(+) create mode 100644 docs/reference/drplot.html (limited to 'docs/reference/drplot.html') diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html new file mode 100644 index 0000000..eff1338 --- /dev/null +++ b/docs/reference/drplot.html @@ -0,0 +1,268 @@ + + + + + + + + +Plot dose-response models — drplot • drfit + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Plot dose-response models

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Produce graphics of dose-response data and dose-response relationships + either combined or separately, for one or more substances.

+ + + 
drplot(drresults, data, dtype, alpha, ctype, path,
+     fileprefix, overlay, xlim, ylim, xlab, ylab, axes, frame.plot, postscript,
+     pdf, png, bw, pointsize, colors, ltys, pchs, devoff, lpos)
+ +

Arguments

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drresults

A data frame as returned from drfit.

data

A data frame as returned from drdata. The data frame has to + contain at least a factor called "substance", a vector called "unit" + containing the unit used for the dose, a column "response" with the + response values of the test system normalized between 0 and 1, a column + "dose" with the numeric dose values and a factor called "dosefactor" + containing the dose as a factor.

dtype

A string describing if the raw data should be plotted ("raw"), or an error + bar should be constructed from the standard deviations of the responses at + each dose level ("std", default value) or from the confidence intervals + ("conf"). If you don't want to see the data, set it to "none".

alpha

The confidence level, defaulting to 0.95, only used if dtype "conf" has been + chosen.

ctype

This argument decides if horizontal lines are drawn to show the scatter of + the control values (dose = 0), if there are more than three of them. + Defaults to "none", further allowed values are "std" and "conf" for + displaying the standard deviation of the controls or the confidence + interval for the mean of the controls.

path

The path where graphic files should be put if any are produced. Defaults + to "./" i.e. the current working directory of R.

fileprefix

A string which will form the beginning of each filename, if graphic files + are created. Defaults to "drplot".

overlay

If TRUE, all output will be put into one graph, otherwise a separate graph + will be created for each substance.

xlim

The plot limits (min,max) on the dose axis.

ylim

The plot limits (min,max) on the response axis.

xlab

The axis title for the x axis. Defaults to "Concentration in" unit.

ylab

The axis title for the y axis. Defaults to "Normalized response".

axes

Specifies if axes should be drawn. Default is TRUE, as in + plot.default

frame.plot

Specifies if the plot should be framed. Default is TRUE, as in + plot.default

postscript

If TRUE, (a) postscript graph(s) will be created. Otherwise, and if + the pdf and png arguments are also FALSE, graphics will be + displayed with a screen graphics device.

pdf

If TRUE, (a) pdf graph(s) will be created. Otherwise, and if + the postscript, and png arguments are also FALSE, graphics will be + displayed with a screen graphics device.

png

If TRUE, (a) png graph(s) will be created. Otherwise, and if the + postscript and pdf arguments are also FALSE, graphics will be displayed + with a screen graphics device.

bw

A boolean deciding if the plots will be black and white or not. Default + is TRUE.

pointsize

The pointsize used for pdf, png and postscript graphics.

colors

This is a vector of colors, defaulting to 1:8, used for plotting the data.

ltys

This is a vector of line types for the dose-response models, defaulting to 1:8.

pchs

This is a vector of character types for the data. The default uses built-in + characters 1:n with n being the number of substances for which data are plotted + for overlays, or always 1 when no overlay plot is generated.

lpos

An optional argument defaulting to "topright" specifying the position + of the legend by being passed to the legend function. See the help for the + legend function for all possiblities.

devoff

If set to FALSE, the device will not be closed after creation of an overlay + pdf, png or postscript graph, so texts and other elements can + be added.

+ +

Value

+ +

+
results

You will get plots of data and/or the fitted dose-response curves, on the + screen and/or as postscript/pdf/png files, depending on the parameters.

+ + +

Note

+ +

There is a demo for each dataset that can be accessed by + demo(dataset)

+ + +

Examples

+ 
data(antifoul)
+r <- drfit(antifoul)
#> 
+#> TBT: Fitting data...
#> Waiting for profiling to be done...
#> 
+#> Zn Pyrithion: Fitting data...
#> Waiting for profiling to be done...
## Not run: drplot(r,antifoul)
+
+ +
+ + +
+ + + -- cgit v1.2.1