Test for of variances of the entire collection (EC) and core set (CS) for quantitative traits by Levene's test (Levene 1960) .
Arguments
- data
The data as a data frame object. The data frame should possess one row per individual and columns with the individual names and multiple trait/character data.
- names
Name of column with the individual names as a character string.
- quantitative
Name of columns with the quantitative traits as a character vector.
- selected
Character vector with the names of individuals selected in core collection and present in the
namescolumn.
Value
A data frame with the following columns
- Trait
The quantitative trait.
- EC_V
The variance of the EC.
- CS_V
The variance of the CS.
- EC_CV
The coefficient of variance of the EC.
- CS_CV
The coefficient of variance of the CS.
- Levene_Fvalue
The test statistic.
- Levene_pvalue
The p value for the test statistic.
- Levene_significance
The significance of the test statistic (*: p \(\leq\) 0.01; **: p \(\leq\) 0.05; ns: p \( > \) 0.05).
References
Levene H (1960). “Robust tests for equality of variances.” In Olkin I, Ghurye SG, Hoeffding W, Madow WG, Mann HB (eds.), Contribution to Probability and Statistics: Essays in Honor of Harold Hotelling, 278–292. Stanford University Press, Palo Alto, CA.
Examples
data("cassava_CC")
data("cassava_EC")
ec <- cbind(genotypes = rownames(cassava_EC), cassava_EC)
ec$genotypes <- as.character(ec$genotypes)
rownames(ec) <- NULL
core <- rownames(cassava_CC)
quant <- c("NMSR", "TTRN", "TFWSR", "TTRW", "TFWSS", "TTSW", "TTPW", "AVPW",
"ARSR", "SRDM")
qual <- c("CUAL", "LNGS", "PTLC", "DSTA", "LFRT", "LBTEF", "CBTR", "NMLB",
"ANGB", "CUAL9M", "LVC9M", "TNPR9M", "PL9M", "STRP", "STRC",
"PSTR")
ec[, qual] <- lapply(ec[, qual],
function(x) factor(as.factor(x)))
levene.evaluate.core(data = ec, names = "genotypes",
quantitative = quant, selected = core)
#> Trait EC_V CS_V EC_CV CS_CV Levene_Fvalue Levene_pvalue
#> 1 NMSR 59.087307 66.982464 0.6557556 0.7513439 0.08138887 7.754559e-01
#> 2 TTRN 3.650995 5.168937 0.4957973 0.5784099 4.48085067 3.440983e-02
#> 3 TFWSR 20.545565 37.050176 0.8349124 0.9588343 9.73620667 1.834623e-03
#> 4 TTRW 2.745559 8.185938 0.8730338 1.0929363 32.17078669 1.635197e-08
#> 5 TFWSS 34.723261 52.465146 0.8487110 0.9348325 5.47834742 1.935920e-02
#> 6 TTSW 4.008444 9.527677 0.8385793 1.0057366 20.99595381 4.910026e-06
#> 7 TTPW 95.800602 158.740945 0.7911214 0.8937898 8.23203952 4.162436e-03
#> 8 AVPW 11.312159 29.789173 0.7848312 0.9597393 32.84901670 1.160456e-08
#> 9 ARSR 5.082044 3.862988 1.2132652 1.1545293 0.37336766 5.412494e-01
#> 10 SRDM 25.329950 18.184402 0.1332473 0.1130209 5.02652477 2.508002e-02
#> Levene_significance
#> 1 ns
#> 2 *
#> 3 **
#> 4 **
#> 5 *
#> 6 **
#> 7 **
#> 8 **
#> 9 ns
#> 10 *