data.frame in long format by differencing the values for
a response within the interval.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.
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 = ".")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 data.frame containing the column from which the
growth rates are to be calculated.
A character giving the names of the columns in
data from which the growth rates are to be calculated.
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).
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.
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".
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.
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 "".
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.
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.
A character giving the suffix to be
appended to response to form the names of the columns
containing the calculated the growth rates.
A character giving the separator to use in
appending suffix.inteval to a growth rate. For no separator, set to
"".
Chris Brien
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.
byIndv4Intvl_GRsAvg, byIndv4Intvl_WaterUse, getTimesSubset, GrowthRates,
byIndv4Times_SplinesGRs
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")
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