CHNOSZ (version 0.9-5)

anim.TCA: Functions to Make Animations

Description

Make animated stability diagrams by creating a series of PNG files.

Usage

anim.TCA(redox = list(O2 = c(-95, -60)), high.T = FALSE,
    nframes.in = 15, nframes.out = 20, nframes.anim = 140,
    pHlim = c(0,10), width = 768, height = 576)

Arguments

redox

list, redox variable and limits.

high.T

logical, overlay high-temperature diagram?

nframes.in

numeric, number of lead-in frames.

nframes.out

numeric, number of lead-out frames.

nframes.anim

numeric, number of frames to be animated.

pHlim

numeric, pH limits to use for animation.

width

numeric, width of plot device.

height

numeric, height of plot device.

Details

anim.TCA creates a series of PNG figures that can be converted into an animated diagram. The animation shows how a logaH2O - logfO2 activity diagram for various species involved in the tricarboxylic acid (TCA) cycle changes as a function of pH. Alternatively, set redox to list(H2=c(-20,0)) to draw a logaH2O - logaH2 diagram. The diagrams are made at 25 degrees C unless high.T is TRUE, in which case the high-temperature (100 degrees C) stability fields are also drawn. The function fails with an error if either a directory named png is not present in the Rworking directory, or if the directory exist but is not empty. A number of PNG files are created in the directory. nframes.in and nframes.out specify the number of lead-in (before the start of the animation) and lead-out frames (at the end of the animation). The number of frames to be used for the actual animation (as pH increases ranges between the values specified in pHlim) is given by nframes.anim. After making the PNG files, they are converted to an animated GIF using the convert tool from the ImageMagick software distribution (http://www.imagemagick.org), if it is available on the system.

Examples

# animate the stability diagram with a high-temperature overlay
  anim.TCA(high.T=TRUE)
  # to make an animation with fewer frames than the default
  anim.TCA(nframes.in=5,nframes.out=5,nframes.anim=20)
  # using H2 instead of O2
  anim.TCA(list(H2=c(-20,0)))