In aravind-j/viabilitymetrics: Seed Viability Calculations and Curve Fitting

out_type <- knitr::opts_knit$get("rmarkdown.pandoc.to")

switch(out_type,
    html = {cat("<p> ICAR-National Bureau of Plant Genetic Resources, New Delhi.</p>")},
    latex = cat("\\begin{center}
    ICAR-National Bureau of Plant Genetic Resources, New Delhi.

\\end{center}" )
)

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knitr::opts_chunk$set(
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\begin{wrapfigure}{r}{0.35\textwidth} \vspace{-20pt} \begin{center} \includegraphics[width=0.33\textwidth]{r system.file("extdata", "viabilitymetrics.png", package = "viabilitymetrics")} \end{center} \vspace{-20pt} \end{wrapfigure}

Overview

The package viabilitymetrics..............

\clearpage

Installation

The package can be installed using the following functions:

# Install from CRAN
install.packages('viabilitymetrics', dependencies=TRUE)

# Install development version from Github
devtools::install_github("aravind-j/viabilitymetrics")

Then the package can be loaded using the function

library(viabilitymetrics)

Viability constants

\rowcolors{2}{gray!25}{white} \renewcommand{\arraystretch}{1.3}

library(viabilitymetrics)
load("vc.rda")

vc$Species <- gsub("\\*", "&#42;", vc$Species)
vc$Species <- paste("*", vc$Species, "*", sep = "")
vc$Species <- gsub("×", "$\\\\times$", vc$Species)
vc$Species <- gsub("(\\*)(.+)(cvs.|spp.)(\\*)", "\\1\\2\\4\\3", vc$Species)
vc$Species <- gsub("(\\*)(.+)(cv.)(\\s.+)(\\*)", "\\1\\2\\5\\3\\4", vc$Species)
vc$Species <- gsub("(\\*)(.+)(\\s)(ssp.)(\\s)(.+)(\\*)",
                   "\\1\\2\\*\\3\\4\\5\\*\\6\\7", vc$Species)
vc$Species <- gsub("(&#42;)(\\*)", "\\2\\1", vc$Species)
vc$Species <- gsub("(\\()(.+)(\\))(\\*)", "\\4\\1\\2\\3", vc$Species)

# vc$Species <- gsub("(\\s)(subsp.)(\\s)", "\\1\\*\\2\\*\\3", vc$Species)
# vc$Species <- gsub("(\\s)(convar.)(\\s)", "\\1\\*\\2\\*\\3", vc$Species)
# vc$Species <- gsub("(\\s)(var.)(\\s)", "\\1\\*\\2\\*\\3", vc$Species)

ind <- grepl("*Cucurbita pepo subsp. pepo convar. pepo var. styriaca*",
             vc$Species)
vc[ind,]$Species <- "*Cucurbita pepo* subsp. *pepo* convar. *pepo* var. *styriaca*"



vc$Reference <- gsub("\\[|\\]", "", vc$Reference)

colnames(vc) <- c("Index", "Species", "K~E~", "C~W~", "C~H~", "C~Q~", "Reference")
pander::pander(vc, style = 'multiline', justify = c('left'),
               split.table = Inf, keep.line.breaks = TRUE,
               use.hyphening = FALSE, missing = "")

* Viability constants are derived from storage experiment at a single temperature. C~H~ and C~Q~ here are the universal temperature coefficients (0.0329 and 0.000478 respectively).

Citing viabilitymetrics

detach("package:viabilitymetrics", unload=TRUE)
suppressPackageStartupMessages(library(viabilitymetrics))
cit <- citation("viabilitymetrics")
# yr <- format(Sys.Date(), "%Y")
# cit[1]$year <- yr
# oc <- class(cit)
# 
# cit <- unclass(cit)
# attr(cit[[1]],"textVersion") <- gsub("\\(\\)",
#                                      paste("\\(", yr, "\\)", sep = ""),
#                                      attr(cit[[1]],"textVersion"))
# class(cit) <- oc
cit

Session Info

sessionInfo()

References

aravind-j/viabilitymetrics documentation built on May 15, 2021, 9:10 a.m.