# growthPheno v1.0-21

Monthly downloads

## 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 | |

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 | |

intervalValueCalculate | Calculates a single value that is a function of an individual's values for a response over a specified time interval | |

importExcel | Imports an Excel imaging file and allows some renaming of variables | |

intervalGRdiff | Calculates the growth rates for a specified time interval | |

getTimesSubset | Forms a subset of responses in data that contains their values for the nominated times | |

growthPheno-deprecated | Deprecated Functions in the Package asremlPlus | |

intervalWUI | Calculates water use indices (WUI) over a specified time interval to a data.frame | |

growthPheno-pkg | growthPheno | |

longitudinalPrime | Selects a set variables to be retained in a data frame of longitudinal data | |

plotAnom | Identifies anomalous individuals and produces longitudinal plots without them and with just them | |

plotLongitudinal | Plots longitudinal data for a set of indiividuals | |

plotImagetimes | Plots the position of a time within an interval against the interval for each cart | |

intervalGRaverage | Calculates the growth rates for a specified time interval by taking weighted averages of growth rates for times within the interval | |

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

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 | |

intervalPVA | Selects a subset of variables observed within a specified time interval using Principal Variable Analysis (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 | |

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. | |

plotMedianDeviations | Calculates and plots the median of the deviations of the smoothed values from the observed values. | |

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 | |

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 | |

cumulate | Calculates the cumulative sum, ignoring the first element if exclude.1st is TRUE | |

calcTimes | Calculates for a set of times, the time intervals after an origin time and the position of each within a time interval | |

anom | Tests if any values in a vector are anomalous in being outside specified limits | |

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) | |

designFactors | Adds the factors and covariates for a blocked, split-plot design | |

RiceRaw.dat | Data for an experiment to investigate a rice germplasm panel | |

WUI | Calculates the Water Use Index (WUI) | |

calcLagged | Replaces the values in a vector with the result of applying an operation to it and a lagged value | |

No Results! |

## Vignettes of growthPheno

Name | ||

Rice.pdf.asis | ||

growthPheno-manual.pdf.asis | ||

No Results! |

## Last month downloads

## Details

Date | 2020-01-12 |

VignetteBuilder | R.rsp |

License | GPL (>= 2) |

URL | http://chris.brien.name |

RoxygenNote | 5.0.1 |

NeedsCompilation | no |

Packaged | 2020-01-12 08:29:47 UTC; briencj |

Repository | CRAN |

Date/Publication | 2020-01-12 14:40:06 UTC |

#### Include our badge in your README

```
[![Rdoc](http://www.rdocumentation.org/badges/version/growthPheno)](http://www.rdocumentation.org/packages/growthPheno)
```