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).
intervalGRaverage(responses, individuals = "Snapshot.ID.Tag",
which.rates = c("AGR","RGR"), suffices.rates=c("AGR","RGR"),
start.time, end.time, times.factor = "Days", suffix.interval,
data, sep=".", na.rm=TRUE)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.
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.
A character giving the name(s) of the
factor(s) that define the subsets of the data
for which each subset corresponds to the responses
for an individual.
A character giving the growth rates that are
to be averaged to obtain growth rates for an interval.
It should be a combination "AGR" and "RGR".
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.
A numeric giving the times,
in terms of levels of times.factor, 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.
A numeric giving the times,
in terms of levels of times.factor, 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.
A character giving the name of the column in
data containing the factor for times at which the data was
collected. Its levels will be used in calculating growth rates and
should be numeric values stored as characters.
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.
A data.frame containing the columns from which the
growth rates are to be calculated.
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.
A logical indicating whether NA values should be
stripped before the calculation of weighted means proceeds.
Chris Brien
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.factor. 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.
intervalGRdiff, intervalWUI, splitValueCalculate, getDates, GrowthRates, splitSplines, splitContGRdiff
data(exampleData)
longi.dat <- splitSplines(longi.dat, response="Area", x="xDays",
INDICES = "Snapshot.ID.Tag",
df = 4, deriv=1, suffices.deriv="AGRdv", RGR="RGRdv")
Area.smooth.GR <- intervalGRaverage("Area.smooth", which.rates = c("AGR","RGR"),
suffices.rates = c("AGRdv","RGRdv"),
start.time = 31, end.time = 35,
suffix.interval = "31to35",
data = longi.dat)
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