growthPheno-pkg

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growthPheno

growthPheno

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Keywords
package, hplot, manip
Index

For an overview of the use of these functions and an example see below.

(i) Data

exampleData

A small data set to use in function examples.
RiceRaw.dat Data for an experiment to investigate a rice
germplasm panel.
tomato.dat Longitudinal data for an experiment to investigate
tomato response to mycorrhizal fungi and zinc.
(ii) Data frame manipulation

designFactors

Adds the factors and covariates for a blocked,
split-plot design. getTimesSubset
Forms a subset of 'responses' in 'data' that
contains their values for the nominated times. importExcel
Imports an Excel imaging file and allows some
renaming of variables. longitudinalPrime
Selects a set variables to be retained in a
data frame of longitudinal data. twoLevelOpcreate
Creates a data.frame formed by applying, for
each response, abinary operation to the values of
two different treatments.
(iii) Plots

plotAnom

Identifies anomalous individuals and produces
longitudinal plots without them and with just them.
plotCorrmatrix Calculates and plots correlation matrices for a
set of responses.
plotDeviationsBoxes Produces boxplots of the deviations of the observed
values from the smoothed values over values of x.
plotImagetimes Plots the time within an interval versus the interval.
For example, the hour of the day carts are imaged
against the days after planting (or some other
number of days after an event).
plotLongitudinal Plots longitudinal data for a set of indiividuals
plotMedianDeviations Calculates and plots the median of the deviations
of the smoothed values from the observed values.
probeSmoothing Compares, for a set of specified values of df and
different smoothing methods, a response and the smooths
of it, possibly along with growth rates calculated
from the smooths.
(iii) Smoothing

fitSpline

Produce the fits from a natural cubic smoothing
spline applied to a response in a 'data.frame',
and growth rates can be computed using derivatives. splitSplines
Adds the fits, and optionally growth rates computed
from derivatives, after fitting natural cubic
smoothing splines to subsets of a response to a
'data.frame'.
(iv) Growth rate and WUI calculation

fitSpline

Produce the fits from a natural cubic smoothing
spline applied to a response in a 'data.frame',
and growth rates can be computed using derivatives.
GrowthRates Calculates growth rates (AGR, PGR, RGRdiff)
between pairs of values in a vector.
intervalGRaverage Calculates the growth rates for a specified
time interval by taking weighted averages of
growth rates for times within the interval.
intervalGRdiff Calculates the growth rates for a specified
time interval.
splitContGRdiff Adds the growth rates calculated continuously
over time for subsets of a response to a
'data.frame'.
splitSplines Adds the fits, and optionally growth rates computed
from derivatives, after fitting natural cubic
smoothing splines to subsets of a response to a
'data.frame'.
WUI Calculates the Water Use Index (WUI).
intervalWUI Calculates water use indices (WUI) over a
specified time interval to a data.frame.
(v) General calculations

anom

Tests if any values in a vector are anomalous
in being outside specified limits. calcLagged
Replaces the values in a vector with the result
of applying an operation to it and a lagged value. calcTimes
Calculates for a set of times, the time intervals
after an origin time and the position of each
within a time interval cumulate
Calculates the cumulative sum, ignoring the
first element if exclude.1st is TRUE. intervalValueCalculate
Calculates a single value that is a function of
an individual's values for a response over a
specified time interval. splitValueCalculate
Calculates a single value that is a function of
an individual's values for a response.
(vi) Principal variates analysis (PV A)

intervalPVA

Selects a subset of variables observed within a
specified time interval using PVA.
PVA Selects a subset of variables using PVA.
rcontrib Computes a measure of how correlated each
variable in a set is with the other variable,
conditional on a nominated subset of them.

Overview

This package can be used to analyse growth data using splines to follow the time trend and then to extract traits for further analysis. There are tools that aid in choosing the degree of smoothing and the selection of traits. There are also functions for importing and orgainizing the data that are generally applicable, although they do have defaults that make them particularly adapted to data from a high-throughput phenotyping facility based on a Lemna-Tec Scananalyzer 3D system.

Data suitable for use with this package consists of columns of data obtained from a set of units (pots, carts or plots) over time. There should be a unique identifier for each unit, which by default is Snapshot.ID.Tag, and variable giving the Days after Planting for each measurement, by default Time.after.Planting..d.. In some cases, it is expected that there will be a column labelled Snapshot.Time.Stamp, which reflects the imaging time from which a particular data value was obtained. For imaging data, the carts/pots may be arranged in a grid of Lanes \(\times\) Positions.

Al-Tamimi et al. (2016) describe a seven-step process to produce phenotypic traits from imaging measurements, a subset of which may be applicable to any longitudinal data set. Some minor modifications of this process has resulted in the following eight-step process:

  1. Import the data: Use importExcel to import the raw data from the Excel file (xlsx or csv). This step should also involve any editing of the data needed to take account of mishaps during the data collection and the need to remove faulty data (produces raw.dat). Generally, data can be removed by replacing only values for responses with missing values (NA) for carts whose data is to be removed, leaving the identifying information intact.

  2. Organize the data: Use longitudinalPrime to select a subset of the imaging variables produced by the Lemna Tec Scanalyzer and, if the design is a blocked, split-plot design, use designFactors to add covariates and factors that might be used in the analysis (produces the data frame longi.prime.dat).

  3. Form derived longitudinal traits Add derived responses that result in a value for each observation: use splitContGRdiff to obtain continuous growth rates i.e. a growth rate for each time of observation, except the first; WUI to produce continuous Water Use Indices (WUI) and cumulate to produce cumulative responses. (Produces the data frame longi.dat.)

  4. Exploratory analysis: Use splitSplines to fit splines, using say direct smoothing and an arbitrary value of 5 for the df, to smooth the longitudinal trends in the primary traits and calculate continuous growth rates from the smoothed response (added to the data frame longi.dat). There are two options for calculating continuous smoothed growth rates: (i) by differencing --- use splitContGRdiff; (ii) from the first derivatives of the splines --- in splitSplines include 1 in the deriv argument, include "AGR" in suffices.deriv and set the RGR to say "RGR".Produce plots of the unsmoothed and smoothed longitudinal data using plotLongitudinal.

  5. Choose the smoothing.method and df: Use probeSmoothing to compare the smooths for a number of values of df and for different smoothing.methods. If necessary, re-run splitSplines with a revised value of df, replacing replace the initial smoothed primary traits and derived tratis in longi.dat; replot using plotLongitudinal.

  6. Clean the data: Check for anomalies in the data, perhaps employing plotAnom. Decide if excluding data is justified. To exclude data, consider whether it is better, especially for the analysis stage, if only the values of the responses are removed by setting them to missing (NA), rather than removing complete rows of the data.

  7. Extract per-cart traits: These are traits for which there is a single value for each cart, pot or plot (by default, identified by the Snapshot.ID.Tag). (produces the data frame cart.dat)

    1. Initialize a cart data.frame with the factors and covariates for a single observation from all carts. This can be done by subsetting longi.dat so that there is one entry for each cart.

    2. Use getTimesSubset to add traits at specific times to the cart data.frame, often the first and last day of imaging for each Snapshot.ID.Tag. The times need to be selected so that there is one and only one observation for each cart. Also form traits, such as growth rates over the whole imaging period, based on these values

    3. Based on the longitudinal plots, decide on the intervals for which growth rates and WUIs are to be calculated. The growth rates for intervals are calculated from the continuous growth rates, using intervalGRdiff, if the continuous growth rates were calculated by differencing, or intervalGRaverage, if they were calculated from first derivatives. To calculate WUIs for intervals, use intervalWUI, The interval growth rates and WUIs are added to the cart data.frame.

  8. (Optional) There is also the possibility that, for experiments investigating salinity, the Shoot Ion Independent Tolerance (SIIT) index can be calculated using twoLevelOpcreate.

The vignette Rice illustrates this process. Use `vignette("Rice", package = "growthPheno") to access the vignette.

References

Al-Tamimi, N, Brien, C.J., Oakey, H., Berger, B., Saade, S., Ho, Y. S., Schmockel, S. M., Tester, M. and Negrao, S. (2016) New salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping. Nature Communications, 7, 13342.

See Also

dae

Aliases
  • growthPheno-pkg
  • growthPheno
Documentation reproduced from package growthPheno, version 1.0-13, License: GPL (>= 2)

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