Usage
runSimpleModel(dataf, chosenSize, minSize = c(), maxSize = c(),
nBigMatrix = 500, do.plot = TRUE, is.log = TRUE,
integrateType = "midpoint", correction="none")
Arguments
dataf
a dataframe with columns size, sizeNext (which is continuous stage in the next time step), and surv, at a minimum.
chosenSize
the target size for which passage time estimates are desired.
minSize
minimum size for the IPM, defaults to a vector of length zero, in which case, it is estimated as either 0.5*min(dataf$size,na.rm = TRUE) if the minimum size is positive, or 1.5*min(dataf$size, na.rm = TRUE) if the minimum size is negative (e.g., reflectin
maxSize
minimum size for the IPM, defaults to a vector of length zero, in which case, it is estimated as 1.5*max(dataf$size, na.rm = TRUE).
nBigMatrix
number of bins used in the IPM.
do.plot
boolean describing whether plots should be produced.
is.log
boolean describing whether continuous stage is on a log scale or not (for plotting).
integrateType
integration type, defaults to "midpoint" (which uses probability density function); other option is "cumul" (which uses the cumulative density function).
correction
correction type, defaults to "none"; option is "constant" which will multiply every column of the IPM by a constant sufficient to adjust values to those predicted for survival at that stage.