Relative Frequency Adjustments

Compute and transform relative frequencies or accessions for a qualitative trait by the following methods (Balakrishnan and Suresh 2001) :

• Square root-proportion

• Log-frequency

Usage

prop.adj(x, method = c("none", "log", "sqrt"))

Arguments

x

Data of a qualitative trait for accessions in a collection as a vector of type factor.

method

The method for transformation. Either "none" for no transformation or "log" for log-frequency transformation or "sqrt" for square root-proportion transformation.

Value

The relative frequencies as a named numeric vector.

Details

If \(p_{i}\) is the relative frequency of the \(i\)th descriptive state for a qualitative trait in a collection, then the square root-proportion transformed relative \(q_{i}\) is computed as

\[q_{i} = \frac{\sqrt{p_{i}}}{\sum_{i=1}^{s}\sqrt{p_{i}}}\]

Where \(s\) is the number of possible descriptor states for the qualitative trait in the collection.

Similarly, the log-frequency transformed relative \(q_{i}\) is computed as \[q_{i} = \frac{\log{F_{i}}}{\sum_{i=1}^{s}\log{F_{i}}}\]

Where \(F_{i}\) is the absolute frequency of the \(i\)th descriptive state for a qualitative trait in a collection.

References

Balakrishnan R, Suresh KK (2001). “Strategies for developing core collections of safflower (Carthamus tinctorius L.) germplasm-part II. Using an information measure for obtaining a core sample with pre-determined diversity levels for several descriptors simultaneously.” Indian Journal of Plant Genetic Resources, 14(1), 32–42.

Examples

suppressPackageStartupMessages(library(EvaluateCore))

library(EvaluateCore)

# Get data from EvaluateCore

data("cassava_EC", package = "EvaluateCore")

# Data of 'Colour of unexpanded apical leaves' qualitative trait
CUAL <- as.factor(cassava_EC$CUAL)

# Raw relative frequencies
prop.adj(CUAL, method = "none")
#>   Dark green        Green Green purple  Light green       Purple 
#>  0.190617577  0.001187648  0.527909739  0.028503563  0.251781473 

# Square root-proportion transformed relative frequencies
prop.adj(CUAL, method = "sqrt")
#>   Dark green        Green Green purple  Light green       Purple 
#>   0.23369439   0.01844636   0.38890779   0.09036836   0.26858311 

# Square log-frequency transformed relative frequencies
prop.adj(CUAL, method = "log")
#>   Dark green        Green Green purple  Light green       Purple 
#>   0.24903071   0.02990846   0.29298449   0.16703765   0.26103869