In cboettig/earlywarning: Detection of Early Warning Signals for Catastrophic Bifurcations

ro warning=FALSE, message=FALSE, comment=NA, tidy=FALSE, cache=TRUE, verbose=TRUE, refresh="ready", dev='Cairo_pdf', fig.width=6, fig.height=5, fig.path="./" or

``` {r cache=FALSE} library(ggplot2) pdf.options(pointsize=8) theme_bw()

``` {r replicate_crashes, fig.width=12, fig.height=10}
library(data.table)
library(reshape2)
library(earlywarning)
load("zoom.rda")
ggplot(subset(zoom, value>250 & reps %in% levels(zoom$reps)[1:9])) + 
  geom_line(aes(time, value)) +
  facet_wrap(~reps, scales="free") +
  theme_bw()

```r dt <- data.table(subset(zoom, value>250)) var <- dt[, warningtrend(data.frame(time=time, value=value), window_var), by=reps]$V1 acor <- dt[, warningtrend(data.frame(time=time, value=value), window_autocorr), by=reps]$V1 dat <- melt(data.frame(Variance=var, Autocorrelation=acor))

load("nullzoom3.rda") nulldt <- data.table(nullzoom) nullvar <- nulldt[, warningtrend(data.frame(time=time, value=value), window_var), by=reps]$V1 nullacor <- nulldt[, warningtrend(data.frame(time=time, value=value), window_autocorr), by=reps]$V1 nulldat <- melt(data.frame(Variance=nullvar, Autocorrelation=nullacor))

``` {r indicators}
ggplot(dat) + 
  geom_histogram(aes(value, y=..density..), binwidth=0.2, alpha=.5) +
  facet_wrap(~variable) + xlim(c(-1, 1)) + 
  geom_density(data=nulldat, aes(value), bw=0.2) + theme_bw()

``` {r }

ggplot(dat) + geom_line(aes(time, value, group=reps), alpha=.01)

````

cboettig/earlywarning documentation built on May 13, 2019, 2:07 p.m.