Package: growthPheno 2.1.25
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:
growthPheno_2.1.25.tar.gz
growthPheno_2.1.25.tar.gz(r-4.5-noble)growthPheno_2.1.25.tar.gz(r-4.4-noble)
growthPheno_2.1.25.tgz(r-4.4-emscripten)growthPheno_2.1.25.tgz(r-4.3-emscripten)
growthPheno.pdf |growthPheno.html✨
growthPheno/json (API)
# Install 'growthPheno' in R: |
install.packages('growthPheno', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/briencj/growthpheno/issues
- 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
Last updated 2 months agofrom:a785ea5983. Checks:OK: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 24 2024 |
R-4.5-linux | OK | Aug 24 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:abindashbackportsbase64encbitbit64bitopsbootbroombroom.helpersbslibcachemcarcarDatacellrangercheckmateclicliprclustercolorspacecorrplotcowplotcpp11crayondaedata.tableDerivdigestdoBydotCall64dplyrevaluatefansifarverfastmapfdsfieldsFNNfontawesomeforcatsforeignFormulafsgenericsGGallyggplot2ggpubrggrepelggsciggsignifggstatsgluegridExtragtablehavenhdrcdehighrHmischmshtmlTablehtmltoolshtmlwidgetsisobandJOPSjquerylibjsonlitekernlabKernSmoothknitrkslabelinglabelledlatticelifecyclelme4locfitmagrittrmapsMASSMatrixMatrixModelsmclustmemoisemgcvmicrobenchmarkmimeminqamodelrmulticoolmunsellmvtnormnlmenloptrnnetnumDerivpatchworkpbkrtestpcaPPpillarpkgconfigplyrpolynompracmaprettyunitsprogresspurrrquantregR6rainbowrappdirsRColorBrewerRcppRcppEigenRCurlreadrreadxlrematchreshaperlangrmarkdownrpartrstatixrstudioapisassscalesSemiParspamSparseMSpATSstringistringrsurvivaltibbletidyrtidyselecttinytextryCatchLogtzdbutf8vctrsviridisviridisLitevroomwithrxfunyaml
growthPheno-manual
Rendered fromgrowthPheno-manual.pdf.asis
usingR.rsp::asis
on Aug 24 2024.Last update: 2019-05-14
Started: 2019-05-14
Rice: an example illustrating the first five steps for Smoothing and Extracting Traits (SET)
Rendered fromRice.pdf.asis
usingR.rsp::asis
on Aug 24 2024.Last update: 2020-07-09
Started: 2019-05-14
Tomato: an example of the Smoothing and Extraction of Traits (SET) process
Rendered fromTomato.pdf.asis
usingR.rsp::asis
on Aug 24 2024.Last update: 2020-03-18
Started: 2020-03-18