Description Usage Arguments Value Note Author(s) Examples
Wrapper function to build the IPM corresponding to every level of the discrete covariate, and return a list of these.
1 2 3 4 5 6 7 8 9 | sampleSequentialIPMs(dataf, nBigMatrix = 10, minSize = -2,
maxSize = 10,
integrateType = "midpoint", correction = "none",
explSurv = surv ~ size + size2 + covariate,
explGrow = sizeNext ~ size + size2 + covariate,
regType = "constantVar",
explFec = fec ~size, Family="gaussian",
Transform = "none",
fecConstants = data.frame(NA))
|
dataf |
a dataframe with columns ‘size’, ‘sizeNext’, 'surv', 'fec', 'covariate', 'covariatel'; and 'age' indicating which individuals are seedlings for identifying the mean and variance in seedling size. |
nBigMatrix |
number of bins in size. |
minSize |
minimum size. |
maxSize |
maximum size. |
integrateType |
integration type. |
correction |
correction for unintentional eviction (individuals move outside the size range of the IPM). This correction redistributes individuals so that column sums of the IPM match expected survival for that column. |
explSurv |
Formula and explanatory variables used in the survival model. |
explGrow |
explanatory variables used in the growth model. |
regType |
Formula and regression Type for growth (normal density function, truncated, etc). |
explFec |
explanatory variables used in the fecundity. |
Family |
a character vector containing the names of the families to be used for the glms, e.g., binomial, poisson, etc. Again, these must appear in the order defined by the list of formula |
Transform |
a character vector containing the names of the transforms to be used for the response variables, e.g., log, sqrt, -1, etc. Again, these must appear in the order defined by the list of formula |
fecConstants |
data.frame of constant multipliers for the fecundity model. |
list of matrices corresponding to covariates, in order.
Formerly makeListIPMs(). makeListIPMs() is no longer supported but has been hidden (.makeListIPMs()) and can be accessed for backward compatibility.
Cory Merow, C. Jessica E. Metcalf, Sean M. McMahon, Roberto Salguero-Gomez, Eelke Jongejans.
1 2 | dff <- generateData()
IPMlist <- sampleSequentialIPMs(dff, Transform="log")
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