{ "_id": "6a197b68acfb0bcc41df5cda", "Package": "growthPheno", "Version": "3.1.18", "Date": "2025-10-19", "Title": "Functional Analysis of Phenotypic Growth Data to Smooth and\nExtract Traits", "Authors@R": "person(\"Chris\",\"Brien\", role = c(\"aut\",\"cre\"),\ncomment = c(ORCID = \"0000-0003-0581-1817\"),\nemail = \"chris.brien@adelaide.edu.au\")", "VignetteBuilder": "R.rsp", "Description": "Assists in the plotting and functional smoothing of traits\nmeasured over time and the extraction of features from these\ntraits, implementing the SET (Smoothing and Extraction of\nTraits) method described in Brien et al. (2020) Plant Methods,\n16. Smoothing of growth trends for individual plants using\nnatural cubic smoothing splines or P-splines is available for\nremoving transient effects and segmented smoothing is available\nto deal with discontinuities in growth trends. There are\ngraphical tools for assessing the adequacy of trait smoothing,\nboth when using this and other packages, such as those that fit\nnonlinear growth models. A range of per-unit (plant, pot, plot)\ngrowth traits or features can be extracted from the data,\nincluding single time points, interval growth rates and other\ngrowth statistics, such as maximum growth or days to maximum\ngrowth. The package also has tools adapted to inputting data\nfrom high-throughput phenotyping facilities, such from a\nLemna-Tec Scananalyzer 3D (see\n for more\ninformation). The package 'growthPheno' can also be installed\nfrom .", "License": "GPL (>=2)", "URL": "http://chris.brien.name/", "BugReports": "https://github.com/briencj/growthPheno/issues", "RoxygenNote": "5.0.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 10:23:22 UTC", "User": "root" }, "Author": "Chris Brien [aut, cre]\n()", "Maintainer": "Chris Brien ", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev", "Repository": "https://briencj.r-universe.dev", "Date/Publication": "2025-10-19 07:56:57 UTC", "RemoteUrl": "https://github.com/briencj/growthpheno", "RemoteRef": "HEAD", "RemoteSha": "2296fbdd2fd103fdff09681576f39f7d6eb173ce", "MD5sum": "8a8cd2ef3eb711342a1769e4fb945939", "_user": "briencj", "_type": "src", "_file": "growthPheno_3.1.18.tar.gz", "_fileid": "4e63ebfb70ba05ea11b83ded713e29fadb23a1bb651890f1d9e57787b342611b", "_filesize": 4686706, "_sha256": "4e63ebfb70ba05ea11b83ded713e29fadb23a1bb651890f1d9e57787b342611b", "_created": 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"Position", "DAP", "Snapshot.ID.Tag", "cDAP", "DAP.diffs", "cPosn", "Block", "Cart", "AMF", "Zn", "Treatments", "Weight.After", "Water.Amount", "WU", "PSA" ], "rows": 1120, "table": true, "tojson": true } ], "_help": [ { "page": "growthPheno-pkg", "title": "Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits", "topics": [ "growthPheno-package", "growthPheno" ] }, { "page": "anom", "title": "Tests if any values in a vector are anomalous in being outside specified limits", "topics": [ "anom" ] }, { "page": "args4chosen_plot", "title": "Creates a 'list' of the values for the options of profile plots for the chosen smooth", "topics": [ "args4chosen_plot" ] }, { "page": "args4chosen_smooth", "title": "Creates a 'list' of the values for the smoothing parameters for which a smooth is to be extracted", "topics": [ "args4chosen_smooth" ] }, { "page": "args4devnboxes_plot", "title": "Creates a 'list' of the values for the options of profile plots for comparing smooths", "topics": [ "args4devnboxes_plot" ] }, { "page": "args4meddevn_plot", "title": "Creates a 'list' of the values for the options of median deviations plots for smooths", "topics": [ "args4meddevn_plot" ] }, { "page": "args4profile_plot", "title": "Creates a 'list' of the values for the options of profile plots for comparing smooths", "topics": [ "args4profile_plot" ] }, { "page": "args4smoothing", "title": "Creates a 'list' of the values for the smoothing parameters to be passed to a smoothing function", "topics": [ "args4smoothing" ] }, { "page": "as.smooths.frame", "title": "Forms a 'smooths.frame' from a 'data.frame', ensuring that the correct columns are present.", "topics": [ "as.smooths.frame" ] }, { "page": "byIndv_ValueCalc", "title": "Calculates a single value that is a function of an individual's values for a response.", "topics": [ "byIndv_ValueCalc" ] }, { "page": "byIndv4Intvl_GRsAvg", "title": "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.", "topics": [ "byIndv4Intvl_GRsAvg" ] }, { "page": "byIndv4Intvl_GRsDiff", "title": "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.", "topics": [ "byIndv4Intvl_GRsDiff" ] }, { "page": "byIndv4Intvl_ValueCalc", "title": "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.", "topics": [ "byIndv4Intvl_ValueCalc" ] }, { "page": "byIndv4Intvl_WaterUse", "title": "Calculates water use traits (WU, WUR, WUI) over a specified time interval for each individual in a 'data.frame' in long format.", "topics": [ "byIndv4Intvl_WaterUse" ] }, { "page": "byIndv4Times_GRsDiff", "title": "Adds to a 'data.frame', the growth rates calculated for consecutive times for individuals in the 'data.frame' in long format by differencing response values.", "topics": [ "byIndv4Times_GRsDiff" ] }, { "page": "byIndv4Times_periodicRates", "title": "Adds the necessary 'times' and rates values to a 'data.frame' to make a set of periodic, or equally spaced, rates.", "topics": [ "byIndv4Times_periodicRates" ] }, { "page": "byIndv4Times_SplinesGRs", "title": "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.", "topics": [ "byIndv4Times_SplinesGRs" ] }, { "page": "byIndv4Times_WaterUse", "title": "Adds to a 'data.frame', water use traits calculated for consecutive times for individuals in the 'data.frame' in long format.", "topics": [ "byIndv4Times_WaterUse" ] }, { "page": "calcLagged", "title": "Replaces the values in a vector with the result of applying an operation to it and a lagged value", "topics": [ "calcLagged" ] }, { "page": "calcTimes", "title": "Calculates for a set of times, the time intervals after an origin time and the position of each within a time interval", "topics": [ "calcTimes" ] }, { "page": "cumulate", "title": "Calculates the cumulative sum, ignoring the first element if exclude.1st is TRUE", "topics": [ "cumulate" ] }, { "page": "designFactors", "title": "Adds the factors and covariates for a blocked, split-unit design", "topics": [ "designFactors" ] }, { "page": "exampleData", "title": "A small data set to use in function examples", "topics": [ "exampleData", "indv.dat", "longi.dat", "raw.dat" ] }, { "page": "getTimesSubset", "title": "Forms a subset of 'responses' in 'data' that contains their values for the nominated times", "topics": [ "getTimesSubset" ] }, { "page": "growthPheno-deprecated", "title": "Deprecated Functions in the Package growthPheno", "topics": [ "anomPlot", "corrPlot", "fitSpline", "getDates", "growthPheno-deprecated", "imagetimesPlot", "intervalGRaverage", "intervalGRdiff", "intervalValueCalculate", "intervalWUI", "longiPlot", "longitudinalPrime", "plotLongitudinal", "plotMedianDeviations", "probeDF", "probeSmoothing", "splitContGRdiff", "splitSplines", "splitValueCalculate" ] }, { "page": "GrowthRates", "title": "Calculates growth rates (AGR, PGR, RGRdiff) between pairs of values in a vector", "topics": [ "AGRdiff", "GrowthRates", "PGR", "RGRdiff" ] }, { "page": "importExcel", "title": "Imports an Excel imaging file and allows some renaming of variables", "topics": [ "importExcel" ] }, { "page": "intervalPVA.data.frame", "title": "Selects a subset of variables using Principal Variable Analysis (PVA), based on the observed values within a specified time interval", "topics": [ "intervalPVA", "intervalPVA.data.frame" ] }, { "page": "is.smooths.frame", "title": "Tests whether an object is of class smooths.frame", "topics": [ "is.smooths.frame" ] }, { "page": "plotAnom", "title": "Identifies anomalous individuals and produces profile plots without them and with just them", "topics": [ "plotAnom" ] }, { "page": "plotCorrmatrix", "title": "Calculates and plots correlation matrices for a set of responses", "topics": [ "plotCorrmatrix" ] }, { "page": "plotDeviationsBoxes", "title": "Produces boxplots of the deviations of the observed values from the smoothed values over values of x.", "topics": [ "plotDeviationsBoxes" ] }, { "page": "plotImagetimes", "title": "Plots the position of a time within an interval against the interval for image", "topics": [ "plotImagetimes" ] }, { "page": "plotProfiles", "title": "Produces profile plots of longitudinal data for a set of individuals", "topics": [ "plotProfiles" ] }, { "page": "plotSmoothsComparison", "title": "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.", "topics": [ "plotSmoothsComparison" ] }, { "page": "plotSmoothsDevnBoxplots", "title": "Produces boxplots for several sets of deviations of the smoothed values from a response, possibly along with growth rates.", "topics": [ "plotSmoothsDevnBoxplots" ] }, { "page": "plotSmoothsMedianDevns", "title": "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.", "topics": [ "plotSmoothsMedianDevns" ] }, { "page": "prepImageData", "title": "Prepares raw imaging data for further processing", "topics": [ "prepImageData" ] }, { "page": "probeSmooths", "title": "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.", "topics": [ "probeSmooths" ] }, { "page": "PVA", "title": "Selects a subset of variables using Principal Variable Analysis (PVA)", "topics": [ "PVA" ] }, { "page": "PVA.data.frame", "title": "Selects a subset of variables stored in a data.frame using Principal Variable 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