growthPheno v1.0-22
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Plotting, Smoothing and Growth Trait Extraction for Longitudinal Data
Assists in producing longitudinal or profile plots of measured
traits. These allow checks to be made for anomalous data and growth patterns
in the data to be explored. Smoothing of growth trends for individual plants
using smoothing splines is available for removing transient effects. There
are tools for diagnosing the adequacy of trait smoothing, either using this
package or other packages, such as those that fit nonlinear growth models.
A range of per-unit (pot, plant, plot) growth traits can be extracted from
longitudinal data, including single time-point smoothed trait values and
their growth rates, interval growth rates and other growth statistics, such
as maximum growth. The package is particularly suited to preparing data from
high-throughput phenotyping facilities, such as imaging data from a Lemna-Tec Scananalyzer
(see <https://www.lemnatec.com/products/conveyor-scanalyzer/> for more
information). The package 'growthPheno' can also be installed from
<http://chris.brien.name/rpackages/>.
Functions in growthPheno
| Name | Description | |
| exampleData | A small data set to use in function examples | |
| designFactors | Adds the factors and covariates for a blocked, split-plot design | |
| 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 | |
| intervalGRaverage | Calculates the growth rates for a specified time interval by taking weighted averages of growth rates for times within the interval | |
| importExcel | Imports an Excel imaging file and allows some renaming of variables | |
| GrowthRates | Calculates growth rates (AGR, PGR, RGRdiff) between pairs of values in a vector | |
| PVA | Selects a subset of variables using Principal Variable Analysis (PVA) | |
| cumulate | Calculates the cumulative sum, ignoring the first element if exclude.1st is TRUE | |
| growthPheno-deprecated | Deprecated Functions in the Package asremlPlus | |
| plotMedianDeviations | Calculates and plots the median of the deviations of the smoothed values from the observed values. | |
| calcTimes | Calculates for a set of times, the time intervals after an origin time and the position of each within a time interval | |
| RiceRaw.dat | Data for an experiment to investigate a rice germplasm panel | |
| growthPheno-pkg | growthPheno | |
| WUI | Calculates the Water Use Index (WUI) | |
| probeDF | Compares, for a set of specified values of df, a response and the smooths of it, possibly along with growth rates calculated from the smooths | |
| 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 | |
| plotImagetimes | Plots the position of a time within an interval against the interval for each cart | |
| getTimesSubset | Forms a subset of responses in data that contains their values for the nominated times | |
| intervalGRdiff | Calculates the growth rates for a specified time interval | |
| plotLongitudinal | Plots longitudinal data for a set of indiividuals | |
| 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 | |
| intervalWUI | Calculates water use indices (WUI) over a specified time interval to a data.frame | |
| twoLevelOpcreate | Creates a data.frame formed by applying, for each response, a binary operation to the paired values of two different treatments | |
| intervalPVA | Selects a subset of variables observed within a specified time interval using Principal Variable Analysis (PVA) | |
| intervalValueCalculate | Calculates a single value that is a function of an individual's values for a response over a specified time interval | |
| rcontrib | Computes a measure of how correlated each variable in a set is with the other variable, conditional on a nominated subset of them | |
| longitudinalPrime | Selects a set variables to be retained in a data frame of longitudinal data | |
| splitContGRdiff | Adds the growth rates calculated continuously over time for subsets of a response to a data.frame | |
| plotCorrmatrix | Calculates and plots correlation matrices for a set of responses | |
| 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 | |
| plotDeviationsBoxes | Produces boxplots of the deviations of the observed values from the smoothed values over values of x. | |
| splitValueCalculate | Calculates a single value that is a function of an individual's values for a response | |
| tomato.dat | Longitudinal data for an experiment to investigate tomato response to mycorrhizal fungi and zinc | |
| plotAnom | Identifies anomalous individuals and produces longitudinal plots without them and with just them | |
| No Results! | ||
Vignettes of growthPheno
| Name | ||
| Rice.pdf.asis | ||
| Tomato.pdf.asis | ||
| growthPheno-manual.pdf.asis | ||
| No Results! | ||
Last month downloads
Details
| Date | 2020-03-17 |
| VignetteBuilder | R.rsp |
| License | GPL (>= 2) |
| URL | http://chris.brien.name |
| RoxygenNote | 5.0.1 |
| NeedsCompilation | no |
| Packaged | 2020-03-17 07:21:52 UTC; briencj |
| Repository | CRAN |
| Date/Publication | 2020-03-18 06:10:02 UTC |
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