Nothing
## ----echo=FALSE---------------------------------------------------------------
library(chillR)
## -----------------------------------------------------------------------------
library(chillR)
library(ggplot2)
data(KA_weather)
data(KA_bloom)
hourtemps <- stack_hourly_temps(KA_weather, latitude=50.4)
## -----------------------------------------------------------------------------
yc <- 40
zc <- 190
iSeason <- genSeason(hourtemps, years=c(2009))
res <- PhenoFlex(temp=hourtemps$hourtemps$Temp[iSeason[[1]]],
times=c(1: length(hourtemps$hourtemps$Temp[iSeason[[1]]])),
zc=zc, stopatzc=TRUE, yc=yc, basic_output=FALSE)
## ----fig.width = 6, fig.height=4, fig.cap="Chill accumulation over time. The dashed line respresents $y_c$, the critical amount of chill units for ecodormancy to be broken."----
DBreakDay <- res$bloomindex
seasontemps<-hourtemps$hourtemps[iSeason[[1]],]
seasontemps[,"x"]<-res$x
seasontemps[,"y"]<-res$y
seasontemps[,"z"]<-res$z
seasontemps<-add_date(seasontemps)
ggplot(data=seasontemps[1:DBreakDay,],aes(x=Date,y=y)) +
geom_line(col="blue",lwd=1.5) +
theme_bw(base_size=20) +
geom_hline(yintercept=yc,lty=2) +
labs(title="Chill (y) accumulation")
## ----fig.width = 6, fig.height=4, fig.cap="Heat accumulation over time. The dashed line respresents the $z_c$, the critical amount of heat units for ecodormancy to be broken."----
ggplot(data=seasontemps[1:DBreakDay,],aes(x=Date,y=z)) +
geom_line(col="red",lwd=1.5) +
theme_bw(base_size=20) +
geom_hline(yintercept=zc,lty=2) +
labs(title="Heat (z) accumulation")
## -----------------------------------------------------------------------------
SeasonList <- genSeasonList(hourtemps$hourtemps, years=c(2003:2008))
## -----------------------------------------------------------------------------
par <- c(40, 190, 0.5, 25, 3372.8, 9900.3, 6319.5, 5.939917e13, 4, 36, 4, 1.60)
upper <- c(41, 200, 1.0, 30, 4000.0, 10000.0, 7000.0, 6.e13, 10, 40, 10, 50.00)
lower <- c(38, 180, 0.1, 0 , 3000.0, 9000.0, 6000.0, 5.e13, 0, 0, 0, 0.05)
## -----------------------------------------------------------------------------
Fit_res <- phenologyFitter(par.guess=par,
modelfn = PhenoFlex_GDHwrapper,
bloomJDays=KA_bloom$pheno[which(KA_bloom$Year %in% c(2003:2008))],
SeasonList=SeasonList, lower=lower, upper=upper,
control=list(smooth=FALSE, verbose=FALSE, maxit=10,
nb.stop.improvement=5))
## ----eval=FALSE---------------------------------------------------------------
# control=list(smooth=FALSE, verbose=TRUE, maxit=1000,
# nb.stop.improvement=250)
## ----eval=FALSE---------------------------------------------------------------
# modelfn=StepChill_Wrapper
## ----comment=""---------------------------------------------------------------
summary(Fit_res)
## ----fig.width = 6, fig.height=4----------------------------------------------
plot(Fit_res)
## -----------------------------------------------------------------------------
Fit_res.boot <- bootstrap.phenologyFit(Fit_res, boot.R=10,
control=list(smooth=FALSE, verbose=TRUE, maxit=10,
nb.stop.improvement=5),
lower=lower, upper=upper, seed=1726354)
## ----comment=""---------------------------------------------------------------
summary(Fit_res.boot)
## ----fig.width = 6, fig.height=4----------------------------------------------
plot(Fit_res.boot)
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