# Analysis of Puya raimondii germination trials on a temperature gradient # Accompanying the following publication: # Nicola C. Steer, Paul M. Ramsay & Miguel Franco # nlstimedist: An R package for the biologically meaningful quantification of # unimodal phenology distributions # Methods in Ecology and Evolution library(nlstimedist) library(nlstools) library(ggplot2) Puya <- read.csv("PuyaGermination.csv", header = TRUE, sep = ",") ## T8.4 Puya1.1 <- timedist(Puya, x = "x", y = "T8.4", r = 0.04, c = 0.5, t = 40) Puya1.1 summary(Puya1.1, correlation = TRUE, symbolic.cor = FALSE) confint2(Puya1.1) Puya1.1$m$rss() Puya1.1$m$getMoments() tdPercentiles(Puya1.1, n = 0.01) tdPercentiles(Puya1.1, n = seq(0.1, 0.9, 0.1)) ## T9.3 Puya1.2 <- timedist(Puya, x = "x", y = "T9.3", r = 0.04, c = 0.5, t = 33) Puya1.2 summary(Puya1.2, correlation = TRUE, symbolic.cor = FALSE) Puya1.2$m$rss() ## T12.5 Puya1.3 <- timedist(Puya, x = "x", y = "T12.5", r = 0.03, c = 0.5, t = 28) Puya1.3 summary(Puya1.3, correlation = TRUE, symbolic.cor = FALSE) Puya1.3$m$rss() ## T13.8 Puya1.4 <- timedist(Puya, x = "x", y = "T13.8", r = 0.04, c = 0.5, t = 25) Puya1.4 summary(Puya1.4, correlation = TRUE, symbolic.cor = FALSE) Puya1.4$m$rss() ## T14.7 Puya1.5 <- timedist(Puya, x = "x", y = "T14.7", r = 0.03, c = 0.5, t = 27) Puya1.5 summary(Puya1.5, correlation = TRUE, symbolic.cor = FALSE) Puya1.5$m$rss() ## T16.7 Puya1.6 <- timedist(Puya, x = "x", y = "T16.7", r = 0.03, c = 0.5, t = 15) Puya1.6 summary(Puya1.6, correlation = TRUE, symbolic.cor = FALSE) Puya1.6$m$rss() ## T17.6 Puya1.7 <- timedist(Puya, x = "x", y = "T17.6", r = 0.05, c = 0.5, t = 14) Puya1.7 summary(Puya1.7, correlation = TRUE, symbolic.cor = FALSE) Puya1.7$m$rss() ## T19.5 Puya1.8 <- timedist(Puya, x = "x", y = "T19.5", r = 0.05, c = 0.5, t = 16) Puya1.8 summary(Puya1.8, correlation = TRUE, symbolic.cor = FALSE) Puya1.8$m$rss() ## T20 Puya1.9 <- timedist(Puya, x = "x", y = "T20", r = 0.04, c = 0.5, t = 18) Puya1.9 summary(Puya1.9, correlation = TRUE, symbolic.cor = FALSE) Puya1.9$m$rss() ## T21.7 Puya2.1 <- timedist(Puya, x = "x", y = "T21.7", r = 0.03, c = 0.5, t = 25) Puya2.1 summary(Puya2.1, correlation = TRUE, symbolic.cor = FALSE) Puya2.1$m$rss() ## T22.4 Puya2.2 <- timedist(Puya, x = "x", y = "T22.4", r = 0.03, c = 0.5, t = 30) Puya2.2 summary(Puya2.2, correlation = TRUE, symbolic.cor = FALSE) Puya2.2$m$rss() ## T23.7 Puya2.3 <- timedist(Puya, x = "x", y = "T23.7", r = 0.03, c = 0.5, t = 40) Puya2.3 summary(Puya2.3, correlation = TRUE, symbolic.cor = FALSE) Puya2.3$m$rss() ## PDF Plot tdPdfPlot(Puya1.1, Puya1.2, Puya1.3, Puya1.4, Puya1.5, Puya1.6, Puya1.7, Puya1.8, Puya1.9, Puya2.1, Puya2.2, Puya2.3, S = c(0.74, 0.78, 0.81, 0.82, 0.80, 0.74, 0.79, 0.80, 0.78, 0.73, 0.72, 0.44), xVals = seq(0, 60, 0.001)) ## CDF Plot tdCdfPlot(Puya1.1, Puya1.2, Puya1.3, Puya1.4, Puya1.5, Puya1.6, Puya1.7, Puya1.8, Puya1.9, Puya2.1, Puya2.2, Puya2.3, S = c(0.74, 0.78, 0.81, 0.82, 0.80, 0.74, 0.79, 0.80, 0.78, 0.73, 0.72, 0.44), xVals = seq(0, 60, 0.001))