inst/examples/fishcollapse.md

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

Warning Signals in Fish Collapse

• Author Carl Boettiger [e-mail]
• Date: 10 Nov 2011
• Description: an example trying to detect early warning signals in data from fisheries collapses

Set up markdown format and image uploads. [code lang='r'] render_wordpress() opts_knit$set(upload = TRUE) opts_knit$set(imgur.key = getOption("imgur")) [/code]

Load required libraries [code lang='r'] require(warningsignals) require(ggplot2) require(reshape2) [/code]

Load the data

[code lang='r'] scotia <- read.csv("../../data/rawdata/sau_scotia.csv") [/code]

Visualize data

[code lang='r'] dat_scotia <- melt(scotia, id = "Year") p_scotia <- ggplot(dat_scotia, aes(Year, value, fill = variable)) + geom_area() print(p_scotia) [/code] [flickr]6793294944[/flickr]

Compute some indicators

Define some indicators [code lang='r'] window_var <- function(X, windowsize = (length(X)/2)) { out <- sapply(0:(length(X) - windowsize), function(i) { var(X[(i + 1):(i + windowsize)]) }) c(rep(NA, length(X) - length(out)), out) }

window_autocorr <- function(X, windowsize = (length(X)/2)) { out <- sapply(0:(length(X) - windowsize), function(i) acf(X[(i + 1):(i + windowsize)], lag.max = 1, plot = F)$acf[2]) c(rep(NA, length(X) - length(out)), out) } [/code]

Reformat the data, uses data.table to perform computations over species [code lang='r'] require(data.table) fish <- data.table(subset(dat_scotia, Year < 1992)) tmp <- data.frame(species = fish$variable, Year = fish$Year, Stock = fish$value, variance = fish[, window_var(value), by = "variable"]$V1, acor = fish[, window_autocorr(value), by = "variable"]$V1)

dat <- melt(tmp, id = c("Year", "species")) [/code]

Cod are approaching a crash, but lobster are going strong, but both seem to show the same pattern. [code lang='r'] ggplot(subset(dat, species %in% c("Atlantic.cod"))) + geom_point(aes(Year, value)) + facet_grid(variable ~ species, scales = "free_y") [/code] [flickr]6793295294[/flickr][code lang='r'] ggplot(subset(dat, species %in% c("American.lobster"))) + geom_point(aes(Year, value)) + facet_grid(variable ~ species, scales = "free_y") [/code] [flickr]6793296188[/flickr]

Note the indicator patterns vary widly and rather arbitrarily among species [code lang='r'] dt <- data.table(dat_scotia) indicator <- data.frame(dt[, window_var(value), by = "variable"], Year = dat_scotia$Year) ggplot(indicator) + geom_line(aes(Year, V1)) + facet_wrap(~variable, scales = "free_y") [/code] [flickr]6793296484[/flickr]

cboettig/warningsignals documentation built on May 13, 2019, 2:12 p.m.