R: Extract features, that are single-valued for each individual,...

traitExtractFeatures {growthPheno}

R Documentation

Extract features, that are single-valued for each individual, from traits observed over time.

Description

Extract one or more sets of features from traits observed over time, the result being traits that have a single value for each individual. The sets of features are:

single times – the value for each individual for a single time. (uses getTimesSubset)
growth rates for a time interval – the average growth rate (AGR and/or RGR) over a time interval for each individual. (uses byIndv4Intvl_GRsDiff or byIndv4Intvl_GRsAvg)
water use traits for a time interval – the total water use (WU), the water use rate (WUR) and the water use index (WUI) over a time interval for each individual. (uses byIndv4Intvl_WaterUse)
growth rates for the imaging period overall – the average growth rate (AGR and/or RGR) over the whole imaging period for each individual. (uses byIndv4Intvl_GRsDiff or byIndv4Intvl_GRsAvg)
water use traits for the imaging period overall – the total water use (WU), the water use rate (WUR) and the water use index (WUI) for the whole imaging period for each individual. (uses byIndv4Intvl_WaterUse)
totals for the imaging period overall – the total over the whole imaging period of a trait for each individual. (uses byIndv4Intvl_ValueCalc)
maximum for the imaging period overall – the maximum value over the whole imaging period, and the time at which it occurred, for each individual. (uses byIndv4Intvl_ValueCalc)

The Tomato vignette illustrates the use of traitSmooth and traitExtractFeatures to carry out the SET procedure for the example presented in Brien et al. (2020). Use vignette("Tomato", package = "growthPheno") to access it.

Usage

traitExtractFeatures(data, individuals = "Snapshot.ID.Tag", times = "DAP", 
                     starts.intvl = NULL, stops.intvl = NULL, 
                     suffices.intvl = NULL, 
                     responses4intvl.rates = NULL, 
                     growth.rates = NULL, 
                     growth.rates.method = "differences", 
                     suffices.growth.rates = NULL, 
                     water.use4intvl.traits = NULL, 
                     responses4water = NULL, 
                     water.trait.types = c("WU", "WUR", "WUI"), 
                     suffix.water.rate = "R", suffix.water.index = "I", 
                     responses4singletimes = NULL, times.single = NULL, 
                     responses4overall.rates = NULL, 
                     water.use4overall.water = NULL, 
                     responses4overall.water = NULL, 
                     responses4overall.totals = NULL, 
                     responses4overall.max = NULL, 
                     intvl.overall = NULL, suffix.overall = NULL, 
                     sep.times.intvl = "to", sep.suffix.times = ".", 
                     sep.growth.rates = ".", sep.water.traits = "", 
                     mergedata = NULL, ...)

Arguments

`data`	A `data.frame` containing the columns specified by `individuals`, `times`, the various `responses` arguments and the `water.use argument`.
`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 identifying the intervals and, if a `factor` or `character`, the values should be numerics stored as characters.
`starts.intvl`	A `numeric` giving the times, in terms of values in `times`, that are the initial times for a set of intervals for which `growth.rates` and `water.use` traits are to be obtained. These times may also be used to obtain values for single-time traits (see `responses4singletimes`).
`stops.intvl`	A `numeric` giving the times, in terms of values in `times`, that are the end times for a set of intervals for which `growth.rates` and `water.use` traits are to be obtained. These times may also be used to obtain values for single-time traits (see `responses4singletimes`).
`suffices.intvl`	A `character` giving the suffices for intervals specified using `starts.intvl` and `stops.intvl`. If `NULL`, the suffices are automatically generated using `starts.intvl`, `stops.intvl` and `sep.times.intvl`.
`responses4intvl.rates`	A `character` specifying the names of the columns containing responses for which growth rates are to be obtained for the intervals specified by `starts.intvl` and `stops.intvl`. For `growth.rates.method` set to `differences`, the growth rates will be computed from the column of the `response` values whose name is listed in `responses4intvl.rates`. For `growth.rates.method` set to `derivatives`, the growth rates will be computed from a column with the growth rates computed for each time. The name of the column should be a `response` listed in `responses4intvl.rates` to which is appended an element of `suffices.growth.rates`.
`growth.rates.method`	A `character` specifying the method to use in calculating the growth rates over an interval for the responses specified by `responses4intvl.rates`. The two possibilities are `"differences"` and `"ratesaverages"`. For `differences`, the growth rate for an interval is computed by taking differences between the values of a response for pairs of `times`. For `ratesaverage`, the growth rate for an interval is computed by taking weighted averages of growth rates for times within the interval. That is, `differences` operates on the response and `ratesaverage` operates on the growth rates previously calculated from the response, so that the appropriate one of these must be in `data`. The `ratesaverage` option is most appropriate when the growth rates are calculated using the derivatives of a fitted curve. Note that, for responses for which the AGR has been calculated using differences, both methods will give the same result, but the `differences` option will be more efficient than `ratesaverages`.
`growth.rates`	A `character` specifying which growth rates are to be obtained for the intervals specified by `starts.intvl` and `stops.intvl`. It should contain one of both of `"AGR"` and `"RGR"`.
`suffices.growth.rates`	A `character` giving the suffices appended to `responses4intvl.rates` in constructung the column names for the storing the growth rates specified by `growth.rates`. If `suffices.growth.rates` is `NULL`, then `"AGR"` and `"RGR"` will be used.
`water.use4intvl.traits`	A `character` giving the names of the columns in `data` that contain the water use values that are to be used in computing the water use traits (WU, WUR, WUI) for the intervals specified by `starts.intvl` and `stops.intvl`. If there is only one column name, then the `WUI` will be calculated using this name for all column names in `responses4water`. If there are several column names in `water.use4intvl.traits`, then there must be either one or the same number of names in `responses4water`. If both have same number of names, then the two lists of column names will be processed in parallel, so that a single `WUI` will be produced for each pair of `responses4water` and `water.use4intvl.traits` values.
`responses4water`	A `character` giving the names of the columns in `data` that are to provide the numerator in calculating a `WUI` for the intervals specified using `starts.intvl` and `stops.intvl`. The denominator will be the values in the columns in `data` whose names are those given by `water.use4intvl.traits`. If there is only one column name in `responses4water`, then the `WUI` will be calculated using this name for all column names in `responses4water`. If there are several column names in `responses4water`, then there must be either one or the same number of names in `water.use4intvl.traits`. If both have same number of names, then the two lists of column names will be processed in parallel, so that a single `WUI` will be produced for each pair of `responses4water` and `water.use4intvl.traits` values. See the `Value` section for a description of how `responses4water` is incorporated into the names constructed for the water use traits.
`water.trait.types`	A `character` listing the trait types to compute and return. It should be some combination of `WU`, `WUR` and `WUI`. See Details in `byIndv4Intvl_WaterUse` for how each is calculated.
`suffix.water.rate`	A `character` giving the label to be appended to the value of `water.use4intvl.traits` to form the name of the WUR.
`suffix.water.index`	A `character` giving the label to be appended to the value of `water.use4intvl.traits` to form the name of the WUI.
`responses4singletimes`	A `character` specifying the names of the columns containing `responses` for which a column of the values is to be formed for each response for each of the times values specified in `times.single`. If `times.single` is `NULL`, then the unique values in the combined `starts.intvl` and `stops.intvl` will be used.
`times.single`	A `numeric` giving the times of imaging, for each of which, the values of each `responses4singletimes` will be stored in a column of the resulting `data.frame`. If `NULL`, then the unique values in the combined `starts.intvl` and `stops.intvl` will be used.
`responses4overall.rates`	A `character` specifying the names of the columns containing responses for which growth rates are to be obtained for the whole imaging period i.e. the interval specified by `intvl.overall`. The settings of `growth.rates.method`, `growth.rates`, `suffices.growth.rates`, `sep.growth.rates`, `suffix.overall` and `intvl.overall` will be used in producing the growth rates. See `responses4intvl.rates` for more information about how these arguments are used.
`water.use4overall.water`	A `logical` indicating whether the overall water.traits are to be obtained. The settings of `water.trait.types`, `suffix.water.rate`, `suffix.water.index`, `sep.water.traits`, `suffix.overall` and `intvl.overall` will be used in producing the overall water traits. See `water.use4intvl.traits` for more information about how these arguments are used.
`responses4overall.water`	A `character` giving the names of the columns in `data` that are to provide the numerator in calculating a `WUI` for the interval corresponding to the whole imaging period. See `response.water` for further details. See `responses4water` for more information about how this argument is processed.
`responses4overall.totals`	A `character` specifying the names of the columns containing responses for which a column of the values is to be formed by summing the response for each individual over the whole of the imaging period.
`responses4overall.max`	A `character` specifying the names of the columns containing responses for which columns of the values are to be formed for the maximum of the response for each individual over the whole of the imaging period and the `times` value at which the maximum occurred.
`intvl.overall`	A `numeric` giving the starts and stop times of imaging. If `NULL`, the start time will be the minimum of `starts.intvl` and the stop time will be the maximum of `stops.intvl`.
`suffix.overall`	A `character` giving the suffix to be appended to the names of traits that apply to the whole imagng period. It applies to `overall.growth.rates`, `water.use4overall.water`, `responses4overall.water` and `responses4overall.totals`. If `NULL`, then nothing will be added.
`sep.times.intvl`	A `character` giving the separator to use in combining a `starts.intvl` with a `stops.intvl` in constructing the suffix to be appended to an interval trait. If set to `NULL` and there is only one value for each of `starts.intvl` and `stops.intvl`, then no suffix will be added; otherwise `sep.times.intvl` set to `NULL` will result in an error.
`sep.suffix.times`	A `character` giving the separator to use in appending a suffix for times to a trait. For no separator, set to `""`.
`sep.growth.rates`	A `character` giving the character(s) to be used to separate the `suffices.growth.rates` value from the `responses4intvl.rates` values in constructing the name for a new rate. It is also used for separating `responses4water` values from the `suffix.water.index`. For no separator, set to `""`.
`sep.water.traits`	A `character` giving the character(s) to be used to separate the `suffix.rate` and `suffix.index` values from the `response` value in constructing the name for a new rate/index. The default of `""` results in no separator.
`mergedata`	A `data.frame` containing a column with the name given in `individuals` and for which there is only one row for each value given in this column. In general, it will be that the number of rows in `mergedata` is equal to the number of unique values in the column in `data` labelled by the value of `individuals`, but this is not mandatory. If `mergedata` is not `NULL`, the values extracted by `traitExtractFeatures` will be `merge`d with it.
`...`	allows passing of arguments to other functions; not used at present.

Value

A data.frame that contains an individuals column and a column for each extracted trait, in addition to any columns in mergedata. The number of rows in the data.frame will equal the number of unique element of the individuals column in data, except when there are extra values in the individuals column in data. If the latter applies, then the number of rows will equal the number of unique values in the combined individuals columns from mergedata and data.

The names of the columns produced by the function are constructed as follows:

single times – A name for a single-time trait is formed by appending a full stop to an element of responses4singletimes, followed by the value of times at which the values were observed.
growth rates for a time interval – The name for an interval growth rate is constructed by concatenating the relevant element of responses4intvl.rates, growth.rates and a suffix for the time interval, each separated by a full stop. The interval suffix is formed by joining its starts.intvl and stops.intvl values, separating them by the value of sep.times.intvl.
growth rates for the whole imaging period – The name for an interval growth rate is constructed by concatenating the relevant element of responses4intvl.rates, growth.rates and suffix.overall, each separated by a full stop.
water use traits for a time interval – Construction of the names for the three water traits begins with the value of water.use4intvl.traits. The rate (WUR) has either R or the value of suffix.water.rate added to the value of water.use4intvl.traits. Similarly the index (WUI) has either I or the value of suffix.water.index added to it. The WUI also has the element of responses4water used in calculating the WUI prefixed to its name. All three water use traits have a suffix for the interval appended to their names. This suffix is contructed by joining its starts.intvl and stops.intvl, separated by the value of sep.times.intvl.
water use traits for the whole imaging period – Construction of the names for the three water traits begins with the value of water.use4intvl.traits. The rate (WUR) has either R or the value of suffix.water.rate added to the value of water.use4intvl.traits. Similarly the index (WUI) has either I or the value of suffix.water.index added to it. The WUI also has the element of responses4water used in calculating the WUI prefixed to its name. All three water use traits have suffix.overall appended to their names.
the total for the whole of imaging period – The name for whole-of-imaging total is formed by combining an element ofresponses4overall.totals with suffix.overall, separating them by a full stop.
maximum for the whole of imaging period – The name of the column with the maximum values will be the result of concatenating the responses4overall.max, "max" and suffix.overall, each separated by a full stop. The name of the column with the value of times at which the maximum occurred will be the result of concatenating the responses4overall.max, "max" and the value of times, each separated by a full stop.

The data.frame is returned invisibly.

Author(s)

Chris Brien

References

Brien, C., Jewell, N., Garnett, T., Watts-Williams, S. J., & Berger, B. (2020). Smoothing and extraction of traits in the growth analysis of noninvasive phenotypic data. Plant Methods, 16, 36. doi:10.1186/s13007-020-00577-6.

Examples

 #Load dat
 data(tomato.dat)

 #Define DAP constants 
 DAP.endpts   <- c(18,22,27,33,39,43,51)
 nDAP.endpts <- length(DAP.endpts)
 DAP.starts <- DAP.endpts[-nDAP.endpts]
 DAP.stops   <- DAP.endpts[-1]
 DAP.segs <- list(c(DAP.endpts[1]-1, 39), 
                   c(40, DAP.endpts[nDAP.endpts]))
 #Add PSA rates and smooth PSA, also producing sPSA rates
 tom.dat <- byIndv4Times_SplinesGRs(data = tomato.dat, 
                                    response = "PSA", response.smoothed = "sPSA", 
                                    times = "DAP", rates.method = "differences", 
                                    smoothing.method = "log", 
                                    spline.type = "PS", lambda = 1, 
                                    smoothing.segments = DAP.segs)
  
 #Smooth WU
 tom.dat <- byIndv4Times_SplinesGRs(data = tom.dat, 
                                    response = "WU", response.smoothed = "sWU",
                                    rates.method = "none", 
                                    times = "DAP", 
                                    smoothing.method = "direct", 
                                    spline.type = "PS", lambda = 10^(-0.5), 
                                    smoothing.segments = DAP.segs)
 
 #Extract single-valued traits for each individual
 indv.cols <- c("Snapshot.ID.Tag", "Lane", "Position", "Block", "Cart", "AMF", "Zn")
 indv.dat <- subset(tom.dat, subset = DAP == DAP.endpts[1], 
                    select = indv.cols)
 indv.dat <- traitExtractFeatures(data = tom.dat, 
                                  starts.intvl = DAP.starts, stops.intvl = DAP.stops, 
                                  responses4singletimes = "sPSA", 
                                  responses4intvl.rates = "sPSA", 
                                  growth.rates = c("AGR", "RGR"), 
                                  water.use4intvl.traits = "sWU", 
                                  responses4water = "sPSA", 
                                  responses4overall.totals = "sWU",
                                  responses4overall.max = "sPSA.AGR",
                                  mergedata = indv.dat)

[Package growthPheno version 2.1.25 Index]