R: Calculates the growth rates for a specified time interval for...

byIndv4Intvl_GRsDiff {growthPheno}

R Documentation

Calculates the growth rates for a specified time interval for individuals in a `data.frame` in long format by differencing the values for a response within the interval.

Description

Using the values of the responses, calculates the specified combination of the Absolute Growth Rates using differences (AGR), the Proportionate Growth Rates (PGR) and Relative Growth Rates using log differences (RGR) between two nominated time points.

Usage

byIndv4Intvl_GRsDiff(data, responses, 
                     individuals = "Snapshot.ID.Tag", times = "DAP", 
                     which.rates = c("AGR","PGR","RGR"), 
                     suffices.rates=NULL, sep.rates = ".", 
                     start.time, end.time, 
                     suffix.interval, sep.suffix.interval = ".")

Arguments

`data`	A `data.frame` containing the column from which the growth rates are to be calculated.
`responses`	A `character` giving the names of the columns in `data` from which the growth rates are to be calculated.
`individuals`	A `character` giving the name of the `factor` that defines the subsets of the `data` for which each subset corresponds to the `response` values for an individual (e.g. plant, pot, cart, plot or unit).
`times`	A `character` giving the name of the column in `data` containing the times at which the data was collected, either as a `numeric`, `factor`, or `character`. It will be used in calculating growth rates and, if a `factor` or `character`, the values should be numerics stored as characters.
`which.rates`	A `character` giving the growth rates that are to be calculated. It should be a combination of one or more of `"AGR"`, `"PGR"` and `"RGR"`.
`suffices.rates`	A `character` giving the characters to be appended to the names of the responses in constructing the names of the columns containing the calculated growth rates. The order of the suffices in `suffices.rates` should correspond to the order of the elements of `which.rates`.
`sep.rates`	A `character` giving the character(s) to be used to separate the `suffices.rates` value from a `response` value in constructing the name for a new rate. For no separator, set to `""`.
`start.time`	A `numeric` giving the times, in terms of values in `times`, that will give a single value for each `Snapshot.ID.Tag` and that will be taken as the observation at the start of the interval for which the growth rate is to be calculated.
`end.time`	A `numeric` giving the times, in terms of values `times`, that will give a single value for each `Snapshot.ID.Tag` and that will be taken as the observation at the end of the interval for which the growth rate is to be calculated.
`suffix.interval`	A `character` giving the suffix to be appended to `response` to form the names of the columns containing the calculated the growth rates.
`sep.suffix.interval`	A `character` giving the separator to use in appending `suffix.inteval` to a growth rate. For no separator, set to `""`.

Details

The AGR is calculated as the difference between the values of response at the end.time and start.time divided by the difference between end.time and start.time. The PGR is calculated as the ratio of response at the end.time to that at start.time and the ratio raised to the power of the reciprocal of the difference between end.time and start.time. The RGR is calculated as the log of the PGR and so is equal to the difference between the logarithms of response at the end.time and start.time divided by the difference between end.time and start.time.

Value

A data.frame with the growth rates. The name of each column is the concatenation of (i) one of responses, (ii) one of AGR, PGR or RGR, or the appropriate element of suffices.rates, and (iii) suffix.interval, the three components being separated by full stops.

Author(s)

Chris Brien

Examples

data(exampleData)
sPSA.GR <- byIndv4Intvl_GRsDiff(data = longi.dat, 
                                responses = "sPSA", times = "DAP", 
                                which.rates = c("AGR","RGR"), 
                                start.time = 31, end.time = 35,
                                suffix.interval = "31to35")

[Package growthPheno version 2.1.25 Index]

Calculates the growth rates for a specified time interval for individuals in a data.frame in long format by differencing the values for a response within the interval.