detectSingleOutMaize: detectSingleOutMaize

In statgenHTP: High Throughput Phenotyping (HTP) Data Analysis

detectSingleOutMaize

Description

Function to detect plant outliers in a temporal lattice experiment on Maize which can be extended to other experiment types. The criteria needs three phenotypes (ex for maize: the estimated biomass, plant height and phyllocron)

plants are identified as "small outlier plant"

if for biomass AND phyllocron res_i < \mu_{res} - qnorm(threshold) * sd_{res}

plants are identified as "big outlier plant"

if for biomass AND plant height res_i > \mu_{res} + qnorm(threshold) * sd_{res}

Usage

detectSingleOutMaize(
  TP,
  timeBeforeTrt,
  trait1 = "Biomass",
  trait2 = "PlantHeight",
  trait3 = "phyllocron",
  thr = 0.95
)

Arguments

TP	An object of class TP.
timeBeforeTrt	A character or numeric value indicating the date just before treatment in the experiment. When using a character string to reference a time point, the value has to be an exact match to one of the existing timePoints. When using a number it will be matched by its number ("timeNumber") in the timePoints attribute of the TP object.
trait1	A character vector indicating the first trait to model in TP.
trait2	A character vector indicating the second trait to model in TP.
trait3	A character vector indicating the third trait to model in TP.
thr	A numeric value indicating the threshold.

Value

A list with three data.frames, modDat containing the data used for fitting the models, smallPlants containing the plants identified as small plants and bigPlants containing the plants identified as big plants.

See Also

Other functions for detecting outliers for single observations: detectSingleOut(), plot.singleOut(), removeSingleOut()

Examples

## Create a TP object containing the data from the PhenoArch.
phenoTParch <- createTimePoints(dat = PhenoarchDat1,
                                experimentName = "Phenoarch",
                                genotype = "Genotype",
                                timePoint = "Date",
                                plotId = "pos",
                                rowNum = "Row",
                                colNum = "Col")
singleOutMaize <- detectSingleOutMaize(phenoTParch,
                                       timeBeforeTrt = "2017-04-27",
                                       trait1 = "Biomass",
                                       trait2 = "PlantHeight",
                                       trait3 = "phyllocron",
                                       thr = 0.95)

statgenHTP documentation built on April 14, 2023, 9:12 a.m.