# Phenotypic selection analysis in R

February 24, 2011
By

(This article was first published on Recology, and kindly contributed to R-bloggers)

I have up to recently always done my phenotypic selection analyses in SAS. I finally got some code I think works to do everything SAS would do. Feedback much appreciated!

`########################Selection analyses#############################install.packages(c("car","reshape","ggplot2"))require(car)require(reshape)require(ggplot2) # Create data setdat <- data.frame(plant = seq(1,100,1), trait1 = rep(c(0.1,0.15,0.2,0.21,0.25,0.3,0.5,0.6,0.8,0.9,1,3,4,10,11,12,13,14,15,16), each = 5), trait2 = runif(100), fitness = rep(c(1,5,10,20,50), each = 20)) # Make relative fitness columndat_ <- cbind(dat, dat\$fitness/mean(dat\$fitness))names(dat_)[5] <- "relfitness" # Standardize traitsdat_ <- cbind(dat_[,-c(2:3)], rescaler(dat_[,c(2:3)],"sd")) ####Selection differentials and correlations among traits, cor.prob uses function in functions.R file################################################################################### Function for calculating correlation matrix, corrs below diagonal,####### and P-values above diagonal############################################################################cor.prob <- function(X, dfr = nrow(X) - 2) {         R <- cor(X)         above <- row(R) < col(R)         r2 <- R[above]^2         Fstat <- r2 * dfr / (1 - r2)         R[above] <- 1 - pf(Fstat, 1, dfr)         R}  # Get selection differentials and correlations among traits in one data framedat_seldiffs <- cov(dat_[,c(3:5)]) # calculates sel'n differentials using covdat_selcorrs <- cor.prob(dat_[,c(3:5)]) # use P-values above diagonal for significance of sel'n differentials in dat_seldiffsdat_seldiffs_selcorrs <- data.frame(dat_seldiffs, dat_selcorrs) # combine the two ##############################################################################Selection gradientsdat_selngrad <- lm(relfitness ~ trait1 * trait2, data = dat_)summary(dat_selngrad) # where "Estimate" is our sel'n gradient ####Check assumptionsshapiro.test(dat_selngrad\$residuals) # normality, bummer, non-normalhist(dat_selngrad\$residuals) # plot residualsvif(dat_selngrad) # check variance inflation factors (need package car), everything looks fineplot(dat_selngrad) # cycle through diagnostic plots ############################################################################# Plot dataggplot(dat_, aes(trait1, relfitness)) + geom_point() + geom_smooth(method = "lm") + labs(x="Trait 1",y="Relative fitness")ggsave("myplot.jpeg")`

Created by Pretty R at inside-R.org

Plot of relative fitness vs. trait 1 standardized

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