Package: growthPheno 2.1.26

growthPheno: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits

Assists in the plotting and functional smoothing of traits measured over time and the extraction of features from these traits, implementing the SET (Smoothing and Extraction of Traits) method described in Brien et al. (2020) Plant Methods, 16. Smoothing of growth trends for individual plants using natural cubic smoothing splines or P-splines is available for removing transient effects and segmented smoothing is available to deal with discontinuities in growth trends. There are graphical tools for assessing the adequacy of trait smoothing, both when using this and other packages, such as those that fit nonlinear growth models. A range of per-unit (plant, pot, plot) growth traits or features can be extracted from the data, including single time points, interval growth rates and other growth statistics, such as maximum growth or days to maximum growth. The package also has tools adapted to inputting data from high-throughput phenotyping facilities, such from a Lemna-Tec Scananalyzer 3D (see <https://www.youtube.com/watch?v=MRAF_mAEa7E/> for more information). The package 'growthPheno' can also be installed from <http://chris.brien.name/rpackages/>.

Authors:Chris Brien [aut, cre]

growthPheno_2.1.26.tar.gz
growthPheno_2.1.26.zip(r-4.5)growthPheno_2.1.26.zip(r-4.4)growthPheno_2.1.26.zip(r-4.3)
growthPheno_2.1.26.tgz(r-4.4-any)growthPheno_2.1.26.tgz(r-4.3-any)
growthPheno_2.1.26.tar.gz(r-4.5-noble)growthPheno_2.1.26.tar.gz(r-4.4-noble)
growthPheno_2.1.26.tgz(r-4.4-emscripten)growthPheno_2.1.26.tgz(r-4.3-emscripten)
growthPheno.pdf |growthPheno.html✨
growthPheno/json (API)

# Install 'growthPheno' in R:
install.packages('growthPheno', repos = c('https://briencj.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/briencj/growthpheno/issues

Datasets:
  • RicePrepped.dat - Prepped data from an experiment to investigate a rice germplasm panel.
  • RiceRaw.dat - Data for an experiment to investigate a rice germplasm panel
  • cart.dat - A small data set to use in function examples
  • cart.dat - A small data set to use in function examples
  • longi.dat - A small data set to use in function examples
  • raw.dat - A small data set to use in function examples
  • tomato.dat - Longitudinal data for an experiment to investigate tomato response to mycorrhizal fungi and zinc

On CRAN:

6.49 score 6 stars 38 scripts 374 downloads 3 mentions 67 exports 137 dependencies

Last updated 4 months agofrom:8707c78e2c. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 07 2024
R-4.5-winOKNov 07 2024
R-4.5-linuxOKNov 07 2024
R-4.4-winOKNov 07 2024
R-4.4-macOKNov 07 2024
R-4.3-winOKNov 07 2024
R-4.3-macOKNov 07 2024

Exports:AGRdiffanomanomPlotargs4chosen_plotargs4chosen_smoothargs4devnboxes_plotargs4meddevn_plotargs4profile_plotargs4smoothingas.smooths.framebyIndv_ValueCalcbyIndv4Intvl_GRsAvgbyIndv4Intvl_GRsDiffbyIndv4Intvl_ValueCalcbyIndv4Intvl_WaterUsebyIndv4Times_GRsDiffbyIndv4Times_SplinesGRscalcLaggedcalcTimescorrPlotcumulatedesignFactorsfitSplinegetDatesgetTimesSubsetimagetimesPlotimportExcelintervalGRaverageintervalGRdiffintervalPVAintervalPVA.data.frameintervalValueCalculateintervalWUIis.smooths.framelongiPlotlongitudinalPrimePGRplotAnomplotCorrmatrixplotDeviationsBoxesplotImagetimesplotLongitudinalplotMedianDeviationsplotProfilesplotSmoothsComparisonplotSmoothsDevnBoxplotsplotSmoothsMedianDevnsprepImageDataprobeDFprobeSmoothingprobeSmoothsPVAPVA.data.framePVA.matrixrcontribrcontrib.data.framercontrib.matrixRGRdiffsmoothSplinesplitContGRdiffsplitSplinessplitValueCalculatetraitExtractFeaturestraitSmoothtwoLevelOpcreatevalidSmoothsFrameWUI

Dependencies:abindashbackportsbase64encbitopsbootbroombslibcachemcarcarDatacellrangercheckmatecliclustercolorspacecorrplotcowplotcpp11crayondaedata.tableDerivdigestdoBydotCall64dplyrevaluatefansifarverfastmapfdsfieldsFNNfontawesomeforcatsforeignFormulafsgenericsGGallyggplot2ggpubrggrepelggsciggsignifggstatsgluegridExtragtablehdrcdehighrHmischmshtmlTablehtmltoolshtmlwidgetsisobandJOPSjquerylibjsonlitekernlabKernSmoothknitrkslabelinglatticelifecyclelme4locfitmagrittrmapsMASSMatrixMatrixModelsmclustmemoisemgcvmicrobenchmarkmimeminqamodelrmulticoolmunsellmvtnormnlmenloptrnnetnumDerivpatchworkpbkrtestpcaPPpillarpkgconfigplyrpolynompracmaprettyunitsprogresspurrrquantregR6rainbowrappdirsRColorBrewerRcppRcppEigenRCurlreadxlrematchreshaperlangrmarkdownrpartrstatixrstudioapisassscalesSemiParspamSparseMSpATSstringistringrsurvivaltibbletidyrtidyselecttinytextryCatchLogutf8vctrsviridisviridisLitewithrxfunyaml

growthPheno-manual

Rendered fromgrowthPheno-manual.pdf.asisusingR.rsp::asison Nov 07 2024.

Last update: 2020-07-11
Started: 2020-07-11

Rice: an example illustrating the first five steps for Smoothing and Extracting Traits (SET)

Rendered fromRice.pdf.asisusingR.rsp::asison Nov 07 2024.

Last update: 2020-07-11
Started: 2020-07-11

Tomato: an example of the Smoothing and Extraction of Traits (SET) process

Rendered fromTomato.pdf.asisusingR.rsp::asison Nov 07 2024.

Last update: 2020-07-11
Started: 2020-07-11

Readme and manuals

Help Manual

Help pageTopics
Functional Analysis of Phenotypic Growth Data to Smooth and Extract TraitsgrowthPheno-package growthPheno
Tests if any values in a vector are anomalous in being outside specified limitsanom
Creates a 'list' of the values for the options of profile plots for the chosen smoothargs4chosen_plot
Creates a 'list' of the values for the smoothing parameters for which a smooth is to be extractedargs4chosen_smooth
Creates a 'list' of the values for the options of profile plots for comparing smoothsargs4devnboxes_plot
Creates a 'list' of the values for the options of median deviations plots for smoothsargs4meddevn_plot
Creates a 'list' of the values for the options of profile plots for comparing smoothsargs4profile_plot
Creates a 'list' of the values for the smoothing parameters to be passed to a smoothing functionargs4smoothing
Forms a 'smooths.frame' from a 'data.frame', ensuring that the correct columns are present.as.smooths.frame
Calculates a single value that is a function of an individual's values for a response.byIndv_ValueCalc
Calculates the growth rates for a specified time interval for individuals in a 'data.frame' in long format by taking weighted averages of growth rates for times within the interval.byIndv4Intvl_GRsAvg
Calculates the growth rates for a specified time interval for individuals in a 'data.frame' in long format by differencing the values for a response within the interval.byIndv4Intvl_GRsDiff
Calculates a single value that is a 'function' of the values of an individual for a response in a 'data.frame' in long format over a specified time interval.byIndv4Intvl_ValueCalc
Calculates, water use traits (WU, WUR, WUI) over a specified time interval for each individual in a 'data.frame' in long format.byIndv4Intvl_WaterUse
Adds, to a 'data.frame', the growth rates calculated for consecutive times for individuals in a 'data.frame' in long format by differencing response values.byIndv4Times_GRsDiff
For a response in a 'data.frame' in long format, computes, for a single set of smoothing parameters, smooths of the response, possibly along with growth rates calculated from the smooths.byIndv4Times_SplinesGRs
Replaces the values in a vector with the result of applying an operation to it and a lagged valuecalcLagged
Calculates for a set of times, the time intervals after an origin time and the position of each within a time intervalcalcTimes
Calculates the cumulative sum, ignoring the first element if exclude.1st is TRUEcumulate
Adds the factors and covariates for a blocked, split-unit designdesignFactors
A small data set to use in function examplescart.dat exampleData longi.dat raw.dat
Fits a spline to a 'response' in a 'data.frame', and growth rates can be computed using derivativesfitSpline
Forms a subset of 'responses' in 'data' that contains their values for the nominated timesgetTimesSubset
Deprecated Functions in the Package growthPhenoanomPlot corrPlot getDates growthPheno-deprecated imagetimesPlot longiPlot probeDF
Calculates growth rates (AGR, PGR, RGRdiff) between pairs of values in a vectorAGRdiff GrowthRates PGR RGRdiff
Imports an Excel imaging file and allows some renaming of variablesimportExcel
Calculates the growth rates for a specified time interval by taking weighted averages of growth rates for times within the intervalintervalGRaverage
Calculates the growth rates for a specified time intervalintervalGRdiff
Selects a subset of variables using Principal Variable Analysis (PVA), based on the observed values within a specified time intervalintervalPVA intervalPVA.data.frame
Calculates a single value that is a function of an individual's values for a response over a specified time intervalintervalValueCalculate
Calculates water use indices (WUI) over a specified time interval to a data.frameintervalWUI
Tests whether an object is of class smooths.frameis.smooths.frame
Selects a set variables to be retained in a data frame of longitudinal datalongitudinalPrime
Identifies anomalous individuals and produces profile plots without them and with just themplotAnom
Calculates and plots correlation matrices for a set of responsesplotCorrmatrix
Produces boxplots of the deviations of the observed values from the smoothed values over values of x.plotDeviationsBoxes
Plots the position of a time within an interval against the interval for each cartplotImagetimes
Produces profile plots of longitudinal data for a set of individualsplotLongitudinal
Calculates and plots the median of the deviations of the smoothed values from the observed values.plotMedianDeviations
Produces profile plots of longitudinal data for a set of individualsplotProfiles
Plots several sets of smoothed values for a response, possibly along with growth rates and optionally including the unsmoothed values, as well as deviations boxplots.plotSmoothsComparison
Produces boxplots for several sets of deviations of the smoothed values from a response, possibly along with growth rates.plotSmoothsDevnBoxplots
Calculates and plots the medians of the deviations from the observed values for several sets of smoothed values stored in a 'data.frame' in long format.plotSmoothsMedianDevns
Prepares raw imaging data for further processingprepImageData
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 smoothsprobeSmoothing
For a response in a 'data.frame' in long format, computes and compares, for sets of smoothing parameters, smooths of the response, possibly along with growth rates calculated from the smooths.probeSmooths
Selects a subset of variables using Principal Variable Analysis (PVA)PVA
Selects a subset of variables stored in a data.frame using Principal Variable Analysis (PVA)PVA.data.frame
Selects a subset of variables using Principal Variable Analysis (PVA) based on a correlation matrixPVA.matrix
Computes a measure of how correlated each variable in a set is with the other variable, conditional on a nominated subset of themrcontrib
Computes a measure of how correlated each variable in a set is with the other variable, conditional on a nominated subset of themrcontrib.data.frame
Computes a measure of how correlated each variable in a set is with the other variable, conditional on a nominated subset of themrcontrib.matrix
Prepped data from an experiment to investigate a rice germplasm panel.RicePrepped.dat
Data for an experiment to investigate a rice germplasm panelRiceRaw.dat
Description of a smooths.frame objectsmooths.frame smooths.frame-class
Fit a spline to smooth the relationship between a 'response' and an 'x' in a 'data.frame', optionally computing growth rates using derivatives.smoothSpline
Adds, to a 'data.frame', the growth rates for individuals calculated continuously over time by differencing response values.splitContGRdiff
Adds the fits, and optionally growth rates computed from derivatives, after fitting splines to a response for an individual stored in a 'data.frame' in long formatsplitSplines
Calculates a single value that is a function of an individual's values for a responsesplitValueCalculate
Longitudinal data for an experiment to investigate tomato response to mycorrhizal fungi and zinctomato.dat
Extract features, that are single-valued for each individual, from traits observed over time.traitExtractFeatures
Obtain smooths for a trait by fitting spline functions and, having compared several smooths, allows one of them to be chosen and returned in a 'data.frame'.traitSmooth
Creates a data.frame formed by applying, for each response, a binary operation to the paired values of two different treatmentstwoLevelOpcreate
Checks that an object is a valid 'smooths.frame'.validSmoothsFrame
Calculates the Water Use Index (WUI)WUI