Plant Phenotyping and Bayesian Statistics

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Documentation for package ‘pcvr’ version 1.1.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

awkHelper	subset helper function for use reading in large data, called in pcv.sub.read
barg	Function to help fulfill elements of the Bayesian Analysis Reporting Guidelines.
brmPlot	Function to visualize brms models similar to those made using growthSS outputs.
brmSurvPlot	Function to visualize brms survival models specified using growthSS.
brmViolin	Function to visualize hypotheses tested on brms models similar to those made using growthSS outputs.
bw.outliers	Remove outliers from bellwether data using cook's distance
bw.time	Time conversion and plotting for bellwether data
bw.water	Read in lemnatech watering data from metadata.json files
checkGroups	Helper function to check groups in data.
combineDraws	Combine Draws From brms Models
conjugate	Bayesian testing using conjugate priors and method of moments for single or multi value traits.
cumulativePheno	Reduce phenotypes in longitudinal data to cumulative sums of phenotypes.
distributionPlot	Function for plotting iterations of posterior distributions
fitGrowth	Ease of use wrapper function for fitting various growth models specified by growthSS
fitGrowthbrms	Ease of use brms wrapper function for fitting growth models specified by 'growthSS'
fitGrowthbrmsgam	Ease of use brms wrapper function for fitting growth models specified by 'growthSS'
fitGrowthflexsurv	Ease of use wrapper function for fitting growth models specified by 'growthSS'
fitGrowthlm	Ease of use lm wrapper function for fitting growth models specified by 'mvSS'
fitGrowthmgcvgam	Ease of use mgcv wrapper function for fitting gams specified by 'growthSS'
fitGrowthnlme	Ease of use nlme wrapper function for fitting growth models specified by 'growthSS'
fitGrowthnlmegam	Ease of use lme wrapper function for fitting gams specified by 'growthSS'
fitGrowthnlrq	Ease of use nlrq wrapper function for fitting growth models specified by 'growthSS'
fitGrowthnlrqgam	Ease of use rq wrapper function for fitting gams specified by 'growthSS'
fitGrowthnls	Ease of use nls wrapper function for fitting growth models specified by 'growthSS'
fitGrowthnlsgam	Ease of use lm wrapper function for fitting gams specified by 'growthSS'
fitGrowthrq	Ease of use rq wrapper function for fitting models specified by 'mvSS'
fitGrowthsurvreg	Ease of use wrapper function for fitting growth models specified by 'growthSS'
flexsurvregPlot	Function to visualize 'flexsurv::flexsurvreg' models fit by 'fitGrowth'.
frem	Variance partitioning using Full Random Effects Models
gamPlot	Function to visualize common 'stats::nls' growth models.
gam_diff	Helper function for visualizing differences in GAMs fit with 'mgcv::gam'
growthPlot	Function to visualize models made by fitGrowth.
growthSim	Growth data simulating function
growthSS	Ease of use growth model helper function.
lmPlot	Function to visualize common 'stats::nls' growth models.
mvSim	Multi Value Trait simulating function
mvSS	Ease of use multi-value trait model helper function.
mv_ag	Multi Value Trait Aggregation function
net.plot	Visualizing igraph networks
nlmePlot	Function to visualize common 'nlme::nlme' growth models.
nlrqPlot	Function to visualize common 'quantreg::nlrq' growth models.
nlsPlot	Function to visualize common 'stats::nls' growth models.
pcadf	Function to run a PCA, plot and optionally return the data with PCA coordinates and pca object
pcv.emd	Earth Mover's Distance between spectral histograms
pcv.euc	Earth Mover's Distance between spectral histograms
pcv.joyplot	Make Joyplots for multi value trait plantCV data
pcv.net	Network analysis of a distance matrix
pcv.plsr	Run Partial Least Squares Regression on spectral data
pcvrss	Class 'pcvrss' for models specified in 'pcvr'.
pcvrss-class	Class 'pcvrss' for models specified in 'pcvr'.
pcv_theme	Default theme for ggplots made by pcvr functions.
plotPrior	Check priors used in ease of use brms functions
plotVIP	Plot Variable Influence on Projection
print.pcvrss	Print a 'pcvrss' object.
print.pcvrsssummary	Print a 'pcvrsssummary' object.
pwue	Calculate pseudo water use efficiency from phenotype and watering data
read.pcv	Read in plantCV csv output in wide or long format
read.pcv.3	Read in plantCV csv from bellwether phenotyper style experiments analyzed with plantCV versions <4.
relativeTolerance	Calculate relative tolerance of some phenotype(s) relative to control
rqPlot	Function to visualize 'quantreg::rq' general additive growth models.
summary.pcvrss	Summarize a 'pcvrss' object.
survregPlot	Function to visualize 'survival::survreg' models fit by 'fitGrowth'.
testGrowth	Hypothesis testing for fitGrowth models.