data.frame, the growth rates for individuals calculated
continuously over time by differencing response values.Uses AGRdiff, PGR and
RGRdiff to calculate growth rates continuously
over time for the response by differencing pairs of pairs
of response values and
stores the results in data. The subsets are those values
with the same levels combinations of the factors listed in
individuals.
Note: this function is soft deprecated and may be removed in
future versions.
Use byIndv4Times_GRsDiff.
splitContGRdiff(data, responses,
individuals = "Snapshot.ID.Tag", INDICES = NULL,
which.rates = c("AGR","PGR","RGR"), suffices.rates=NULL,
times.factor = "Days", avail.times.diffs = FALSE,
ntimes2span = 2)A data.frame containing data to which has been
added 9i) a column for the differences between the times,
if it is not already in data, and (ii) columns with growth rates.
The name of the column for times differences will be the
times with ".diffs" appended. The name for each of the
growth-rate columns will be either the value of response with
one of ".AGR", ".PGR" or "RGR", or the
corresponding value from suffices.rates appended. Each growth
rate will be positioned at observation
ceiling(ntimes2span + 1) / 2 relative to the two times from
which the growth rate is calculated.
A data.frame containing the columns for which
growth rates are to be calculated.
A character giving the names of the columns in
data for which growth rates are to be calculated.
A character giving the name(s) of the
factor(s) that define the subsets of response
that correspond to the response values for an individual
(e.g. plant, pot, cart, plot or unit) for which growth rates are
to be calculated continuously. If the columns corresponding to
individuals are not factor(s) then they will
be coerced to factor(s). The subsets are formed using
split.
A pseudonym for individuals.
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 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 logical indicating whether there is an
appropriate column of times diffserences that can be used as
the denominator in computing the growth rates. If TRUE, it will
be assumed that the name of the column is the value of times
with .diffs appended. If FALSE, a column, whose
column name will be the value of times with .diffs
appended, will be formed and saved in the result, overwriting any
existing columns with the constructed name in data. It will
be calculated using the values of times in data.
A numeric giving the number of values in
times to span in calculating growth rates by differencing.
Each growth rate is calculated as the difference in the values of
one of the responses for pairs of times values that
are spanned by ntimes2span times values divided by
the difference between this pair of times values. For
ntimes2span set to 2, a growth rate is the
difference between consecutive pairs of values of one of the
responses divided by the difference between consecutive
pairs of times values.
A character giving the characters to be
appended to the names of the responses to provide 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. If NULL, the values
of which.rates are used.
Chris Brien
fitSpline, splitSplines
data(exampleData)
longi.dat <- splitContGRdiff(data = longi.dat,
response="sPSA", times.factor = "DAP",
individuals = "Snapshot.ID.Tag",
which.rates=c("AGR", "RGR"),
avail.times.diffs = TRUE)
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