# Plant Phenotyping and Bayesian Statistics

## Documentation for package ‘pcvr’ version 1.4.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

pcvr-package | Plant Phenotyping and Bayesian Statistics
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.
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.
conjugate-class | Class 'conjugate' for output from the 'pcvr::conjugate' function.
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.outliers | Remove outliers from bellwether data using cook's distance
pcv.plsr | Run Partial Least Squares Regression on spectral data
pcv.time | Time conversion and plotting for bellwether data
pcv.water | Read in lemnatech watering data from metadata.json files
pcvr | Plant Phenotyping and Bayesian Statistics
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.
plot.conjugate | Plot a 'conjugate' object.
plotPrior | Check priors used in ease of use brms functions
plotVIP | Plot Variable Influence on Projection
print.conjugate | Print a 'conjugate' object.
print.conjugatesummary | Print a 'conjugatesummary' object.
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.
statBrmsMod | possible that ss is not a pcvrss object for compatibility with other brms models if "df" is part of it then work with that otherwise use general data. NOTE ggplot2:::Stat$compute_layer can use the default from ggproto 'make plot within a given panel of the ggplot (a facet)' this is mostly the same as the default ggproto compute_panel function, but it takes more named args and passes them to compute_group and avoids warning about individual/time columns. 'make data out of model per a given aes-group, should only be 1 per panel' this is the heavily customized component which makes data for ribbons from the model and ss objects.
statNlsMod | leaving the same as statBrmsMod for now. NOTE I think this can stay the same from brms version 'make data out of model per a given aes-group, should only be 1 per panel' this is the heavily customized component which makes data for ribbons from the model and ss objects.
stat_brms_model | Show a model fit with pcvr in a ggplot layer
stat_growthss | Show a model fit with pcvr in a ggplot layer
stat_lme_model | Show a model fit with pcvr in a ggplot layer
stat_nlme_model | Show a model fit with pcvr in a ggplot layer
stat_nlrq_model | Show a model fit with pcvr in a ggplot layer
stat_nls_model | Show a model fit with pcvr in a ggplot layer
summary.conjugate | Summarize a 'conjugate' object.
summary.pcvrss | Summarize a 'pcvrss' object.
survregPlot | Function to visualize 'survival::survreg' models fit by 'fitGrowth'.
testGrowth | Hypothesis testing for fitGrowth models.