pcvr package - RDocumentation

Learn R Programming

pcvr

R functions for use with plantCV output

Installation

A stable version of pcvr can be installed from CRAN

install.packages("pcvr")
library(pcvr)

Alternatively, the development version of pcvr can be installed using remotes/devtools install_github as shown below. Note that the default behavior in devtools/remotes is to only install true dependencies. Several functions in pcvr use specific packages that would otherwise not be needed for most work, notably the brms supporting functions. To install suggested packages (see DESCRIPTION file) add dependencies=T to the install_github function call.

devtools::install_github("danforthcenter/pcvr", build_vignettes=T) # to install without building vignettes set the build_vignettes argument to F or exclude it.
library(pcvr)

Usage

Please see the bellwether vignette for a general introduction to pcvr. In the future we expect to have more vignettes and to specialize each to some degree.

vignette("bellwether", package="pcvr")
# or 
browseVignettes("pcvr")

Feedback

Please report bugs and make feature requests with issues in this repository.

Copy Link

Version

Install

install.packages('pcvr')

Monthly Downloads

520

Version

1.2.0

License

GPL-2

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/danforthcenter/pcvr

Homepage

https://plantcv.org/

Maintainer

Josh Sumner

Last Published

April 16th, 2025

Functions in pcvr (1.2.0)

Time conversion and plotting for bellwether data

Function to visualize brms survival models specified using growthSS.

Read in lemnatech watering data from metadata.json files

Remove outliers from bellwether data using cook's distance

Function to visualize hypotheses tested on brms models similar to those made using growthSS outputs.

Function to help fulfill elements of the Bayesian Analysis Reporting Guidelines.

cumulativePheno

Reduce phenotypes in longitudinal data to cumulative sums of phenotypes.

conjugate-class

Class conjugate for output from the pcvr::conjugate function.

Ease of use nlme wrapper function for fitting growth models specified by growthSS

distributionPlot

Function for plotting iterations of posterior distributions

fitGrowthmgcvgam

Ease of use mgcv wrapper function for fitting gams specified by growthSS

Bayesian testing using conjugate priors and method of moments for single or multi value traits.

Ease of use wrapper function for fitting various growth models specified by growthSS

Ease of use lm wrapper function for fitting growth models specified by mvSS

fitGrowthflexsurv

Ease of use wrapper function for fitting growth models specified by growthSS

Variance partitioning using Full Random Effects Models

Ease of use brms wrapper function for fitting growth models specified by growthSS

fitGrowthsurvreg

Ease of use wrapper function for fitting growth models specified by growthSS

fitGrowthnlrqgam

Ease of use rq wrapper function for fitting gams specified by growthSS

fitGrowthnlmegam

Ease of use lme wrapper function for fitting gams specified by growthSS

Ease of use nls wrapper function for fitting growth models specified by growthSS

flexsurvregPlot

Function to visualize flexsurv::flexsurvreg models fit by fitGrowth.

Ease of use nlrq wrapper function for fitting growth models specified by growthSS

Ease of use rq wrapper function for fitting models specified by mvSS

fitGrowthnlsgam

Ease of use lm wrapper function for fitting gams specified by growthSS

Function to visualize models made by fitGrowth.

Growth data simulating function

Ease of use growth model helper function.

Function to visualize common quantreg::nlrq growth models.

Helper function for visualizing differences in GAMs fit with mgcv::gam

Function to visualize common stats::nls growth models.

Function to visualize common nlme::nlme growth models.

Class pcvrss for models specified in pcvr.

Visualizing igraph networks

Multi Value Trait simulating function

Plot a conjugate object.

Ease of use multi-value trait model helper function.

Multi Value Trait Aggregation function

Function to run a PCA, plot and optionally return the data with PCA coordinates and pca object

Earth Mover's Distance between spectral histograms

print.pcvrsssummary

Print a pcvrsssummary object.

Summarize a pcvrss object.

summary.conjugate

Summarize a conjugate object.

Print a pcvrss object.

Plot Variable Influence on Projection

Function to visualize quantreg::rq general additive growth models.

Function to visualize survival::survreg models fit by fitGrowth.

Check priors used in ease of use brms functions

Calculate pseudo water use efficiency from phenotype and watering data

Hypothesis testing for fitGrowth models.

Make Joyplots for multi value trait plantCV data

Read in plantCV csv from bellwether phenotyper style experiments analyzed with plantCV versions <4.

Run Partial Least Squares Regression on spectral data

Default theme for ggplots made by pcvr functions.

relativeTolerance

Calculate relative tolerance of some phenotype(s) relative to control

Read in plantCV csv output in wide or long format

print.conjugate

Print a conjugate object.

print.conjugatesummary

Print a conjugatesummary object.

Network analysis of a distance matrix

Helper function to check groups in data.

Function to visualize brms models similar to those made using growthSS outputs.

subset helper function for use reading in large data, called in pcv.sub.read

Combine Draws From brms Models