twoLevelOpcreate: Creates a data.frame formed by applying, for each response, a...

In growthPheno: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits

Creates a data.frame formed by applying, for each response, a binary operation to the paired values of two different treatments

Description

Takes pairs of values for a set of responses indexed by a two-level treatment.factor and calculates, for each of pair, the result of applying a binary operation to their values for the two levels of the treatment.factor. The level of the treatment.factor designated the control will be on the right of the binary operator and the value for the other level will be on the left.

Usage

twoLevelOpcreate(data, responses, treatment.factor = "Treatment.1", 
                 suffices.treatment = c("Cont","Salt"), control = 1, 
                 columns.suffixed = NULL, 
                 operations = "/", suffices.results="OST", 
                 columns.retained = c("Snapshot.ID.Tag","Smarthouse","Lane", 
                                      "Zone","cZone","SHZone","ZLane",
                                      "ZMainunit","cMainPosn", "Genotype.ID"),
                 by = c("Smarthouse","Zone","ZMainunit"))

Arguments

data	A data.frame containing the columns specified by treatment.factor, columns.retained and responses.
responses	A character giving the names of the columns in data that contain the responses to which the binary operations are to be applied.
treatment.factor	A factor with two levels corresponding to what is to be designated the control and treated observations .
suffices.treatment	A character giving the characters to be appended to the names of the responses and columns.suffixed in constructing the names of the columns containing the responses and columns.suffixed for each level of the treatment.factor. The order of the suffices in suffices.treatment should correspond to the order of the levels of treatment.factor.
control	A numeric, equal to either 1 or 2, that specifies the level of treatment.factor that is the control treatment. The value for the control level will be on the right of the binary operator.
columns.suffixed	A character giving the names of the columns.retained in data that are to be have the values for each treatment retained and whose names are to be suffixed using suffices.treatment. Generally, this is done when columns.retained has different values for different levels of the treatment.factor.
operations	A character giving the binary operations to perform on the values for the two different levels of the treatment.factor. It should be either of length one, in which case the same operation will be performed for all columns specified in response.GR, or equal in length to response.GR so its elements correspond to those of response.GR.
suffices.results	A character giving the characters to be appended to the names of the responses in constructing the names of the columns containing the results of applying the operations. The order of the suffices in suffices.results should correspond to the order of the operators in operations.
columns.retained	A character giving the names of the columns in data that are to be retained in the data.frame being created. These are usually factors that index the results of applying the operations and that might be used subsequently.
by	A character giving the names of the columns in data whose combinations will be unique for the observation for each treatment. It is used by merge when combining the values of the two treatments in separate columns in the data.frame to be returned.

Value

A data.frame containing the following columns and the values of the :

1. those from data nominated in columns.retained;

2. those containing the treated values of the columns whose names are specified in responses; the treated values are those having the other level of treatment.factor to that specified by control;

3. those containing the control values of the columns whose names are specified in responses; the control values are those having the level of treatment.factor specified by control;

4. those containing the values calculated using the binary operations; the names of these columns will be constructed from responses by appending suffices.results to them.

Author(s)

Chris Brien

Examples

data(exampleData)
responses <- c("sPSA.AGR","sPSA.RGR")
cols.retained <-  c("Snapshot.ID.Tag","Smarthouse","Lane","Position",
                    "DAP","Snapshot.Time.Stamp", "Hour", "xDAP",
                    "Zone","cZone","SHZone","ZLane","ZMainunit",
                    "cMainPosn", "Genotype.ID")
longi.SIIT.dat <- 
  twoLevelOpcreate(data = longi.dat, responses = responses, 
                   suffices.treatment=c("C","S"),
                   operations = c("-", "/"), 
                   suffices.results = c("diff", "SIIT"), 
                   columns.retained = cols.retained, 
                   by = c("Smarthouse","Zone","ZMainunit","DAP"))
longi.SIIT.dat <- with(longi.SIIT.dat, 
                            longi.SIIT.dat[order(Smarthouse,Zone,ZMainunit,DAP),])

growthPheno documentation built on June 8, 2025, 12:51 p.m.