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removed ratio, better rsi_calc, update for freq

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dr. M.S. (Matthijs) Berends
2018-08-24 11:08:20 +02:00
parent 0c0e538ef4
commit a100d07da6
13 changed files with 116 additions and 140 deletions
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6
man/g.test.Rd
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@ -110,11 +110,7 @@ If there are more than two categories and you want to find out which ones are si
# by a single gene with two co-dominant alleles, you would expect a 1:2:1
# ratio.
x <- c(772, 1611, 737)
E <- ratio(x, "1:2:1")
E
# 780 1560 780
x <- c(772, 1611, 737)#'
G <- g.test(x, p = c(1, 2, 1) / 4)
# G$p.value = 0.12574.

60
man/ratio.Rd
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@ -1,60 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/g.test.R
\name{ratio}
\alias{ratio}
\title{Transform vector to ratio}
\usage{
ratio(x, ratio)
}
\arguments{
\item{x}{vector of values}
\item{ratio}{vector with ratios of \code{x} and with same length (like \code{ratio = c(1, 2, 1)}) or a text with characters \code{":"}, \code{"-"} or \code{","} (like \code{ratio = "1:2:1"} or even \code{ratio = "1:2:1.25"})}
}
\description{
Transform vector to ratio
}
\examples{
# = EXAMPLE 1 =
# Shivrain et al. (2006) crossed clearfield rice (which are resistant
# to the herbicide imazethapyr) with red rice (which are susceptible to
# imazethapyr). They then crossed the hybrid offspring and examined the
# F2 generation, where they found 772 resistant plants, 1611 moderately
# resistant plants, and 737 susceptible plants. If resistance is controlled
# by a single gene with two co-dominant alleles, you would expect a 1:2:1
# ratio.
x <- c(772, 1611, 737)
E <- ratio(x, "1:2:1")
E
# 780 1560 780
G <- g.test(x, p = c(1, 2, 1) / 4)
# G$p.value = 0.12574.
# There is no significant difference from a 1:2:1 ratio.
# Meaning: resistance controlled by a single gene with two co-dominant
# alleles, is plausible.
# = EXAMPLE 2 =
# Red crossbills (Loxia curvirostra) have the tip of the upper bill either
# right or left of the lower bill, which helps them extract seeds from pine
# cones. Some have hypothesized that frequency-dependent selection would
# keep the number of right and left-billed birds at a 1:1 ratio. Groth (1992)
# observed 1752 right-billed and 1895 left-billed crossbills.
x <- c(1752, 1895)
g.test(x)
# p = 0.01787343
# There is a significant difference from a 1:1 ratio.
# Meaning: there are significantly more left-billed birds.
}
\references{
McDonald, J.H. 2014. \strong{Handbook of Biological Statistics (3rd ed.)}. Sparky House Publishing, Baltimore, Maryland.
}
\seealso{
\code{\link{g.test}}
}