byIndv4Intvl_GRsAvg {growthPheno}

Calculates the growth rates for a specified time interval for individuals in a data.frame in long format by taking weighted averages of growth rates for times within the interval.

Description

Using previously calculated growth rates over time, calculates the Absolute Growth Rates for a specified interval using the weighted averages of AGRs for each time point in the interval (AGR) and the Relative Growth Rates for a specified interval using the weighted geometric means of RGRs for each time point in the interval (RGR).

Usage

byIndv4Intvl_GRsAvg(data, responses, 
                    individuals = "Snapshot.ID.Tag", times = "DAP", 
                    which.rates = c("AGR","RGR"), 
                    suffices.rates=c("AGR","RGR"), sep.rates = ".",
                    start.time, end.time, 
                    suffix.interval, sep.suffix.interval = ".", 
                    sep.levels=".", na.rm=FALSE)

Arguments

data

A data.frame containing the columns from which the growth rates are to be calculated.

responses

A character giving the names of the responses for which there are columns in data that contain the growth rates that are to be averaged. The names of the growth rates should have either AGR or RGR appended to the responses names.

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 averaged to obtain growth rates for an interval. It should be a combination of one or more of "AGR" and "RGR".

suffices.rates

A character giving the suffices to be appended to response to form the names of the columns containing the calculated the growth rates and in which growth rates are to be stored. Their elements will be matched with those 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.suffices.rates 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 "".

sep.levels

A character giving the separator to use when the levels of individuals are combined. This is needed to avoid using a character that occurs in a factor to delimit levels when the levels of individuals are combined to identify subsets.

na.rm

A logical indicating whether NA values should be stripped before the calculation of weighted means proceeds.

Details

The AGR for an interval is calculated as the weighted mean of the AGRs for times within the interval. The RGR is calculated as the weighted geometric mean of the RGRs for times within the interval; in fact the exponential is taken of the weighted means of the logs of the RGRs. The weights are obtained from the times. They are taken as the sum of half the time subintervals before and after each time, except for the end points; the end points are taken to be the subintervals at the start and end of the interval.

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

See Also

byIndv4Intvl_GRsDiff, byIndv4Intvl_WaterUse, splitValueCalculate, getTimesSubset,
GrowthRates, byIndv4Times_SplinesGRs, splitContGRdiff

Examples

data(exampleData)
longi.dat <- byIndv4Times_SplinesGRs(data = longi.dat, 
                                     response="PSA", response.smoothed = "sPSA", 
                                     individuals = "Snapshot.ID.Tag", 
                                     times = "DAP", 
                                     df = 4, 
                                     rates.method = "deriv", 
                                     which.rates = c("AGR", "RGR"), 
                                     suffices.rates = c("AGRdv", "RGRdv"))
sPSA.GR <- byIndv4Intvl_GRsAvg(data = longi.dat, 
                               response="sPSA", times = "DAP", 
                               which.rates = c("AGR","RGR"), 
                               suffices.rates = c("AGRdv","RGRdv"), 
                               start.time = 31, end.time = 35, 
                               suffix.interval = "31to35")