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| Original file line number | Diff line number | Diff line change |
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| @@ -1,51 +1,42 @@ | ||
| # analysis.R | ||
| # custom functions for calling all the analysis and plot functions on a dataset | ||
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| analysis <- function(data, cpu, nboot, freq){ | ||
| m <- fit_models(data, "LSN") | ||
| sampling <- sampling_freq(m$const, m$timedep, cpu=cpu, nboot=nboot, | ||
| sample_effort=freq, length.original=length(m$X)) | ||
| taus <- bootstrap_tau(m$X, m$const, m$timedep, cpu=cpu, nboot=nboot) | ||
| mc <- montecarlotest(m$const, m$timedep, cpu=cpu, nboot=nboot) | ||
| list(m=m, taus=taus, mc=mc, sampling=sampling, data=data, freq=freq) | ||
| } | ||
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| compare_roc_curves <- function(taus, mc, legend=TRUE, ...){ | ||
| mc <- remove_unconverged(mc) | ||
| taus <- reformat_tau_dists(taus) | ||
| auc1 <- roc_curve(taus[[1]], ...) | ||
| auc2 <- roc_curve(taus[[2]], add=TRUE, col=2, ...) | ||
| auc3 <- roc_curve(taus[[3]], add=TRUE, col=3, ...) | ||
| auc4 <- roc_curve(mc, add=TRUE, col=4, ...) | ||
| if(legend) | ||
| legend("bottomright", c(paste("Var: ", round(auc1,3)), | ||
| paste("Acor:", round(auc2, 3)), | ||
| paste("Skew:", round(auc3,3)), | ||
| paste("Lik: ", round(auc4,3))), | ||
| col=c(1,2,3,4), lty=1, cex=1, lwd=2) | ||
| } | ||
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| plot_roc_curves <- function(objects, legend=TRUE, ...){ | ||
| plot_roc_curves <- function(objects, legend=TRUE, cex.legend=1, ...){ | ||
| # objects a list in which entry contains a fit object with null and | ||
| # test dists for all the indicators. | ||
| stats <- which_statistic(objects) | ||
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| auc <- numeric(length(objects)) # store area under curve | ||
| legend_txt <- character(length(objects)) # AUC will go in legend | ||
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| auc[1] <- roc_curve(objects[[1]], lwd=2, col=1, ...) | ||
| legend_txt[1] <- paste("AUC =",round(auc[1],2)) | ||
| legend_txt[1] <- paste(stats[1], ", ", round(auc[1],2), sep="") | ||
| for(i in 2:length(objects)){ | ||
| auc[i] <- roc_curve(objects[[i]], lwd=2, col=i, add=TRUE, ...) | ||
| legend_txt[i] <- paste("AUC =",round(auc[i],2)) | ||
| legend_txt[i] <- paste(stats[i], ", ", round(auc[i],2),sep="") | ||
| } | ||
| legend("bottomright",legend_txt, col=c(1:length(objects)), lty=1, lwd=3) | ||
| legend("bottomright",legend_txt, col=c(1:length(objects)), | ||
| lty=1, lwd=3, cex=cex.legend) | ||
| } | ||
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| plot_dists <- function(objects, ...){ | ||
| n <- length(objects) | ||
| stats <- which_statistic(objects) | ||
| par(mfrow=c(1,n), mar=c(6,6,4,2)) | ||
| for(i in 1:n){ | ||
| plot(objects[[i]], xlab=stats[i], ...) | ||
| } | ||
| } | ||
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| which_statistic <- function(objects){ | ||
| sapply(objects, function(x){ | ||
| if(is(x, "pow")) | ||
| "log(Lik Ratio)" | ||
| else if(is(x, "tau_dist_montecarlo")) | ||
| gsub("^(.{7}).*", "\\1",x$signal) ## TRUNCATE name to 7 chars | ||
| }) | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,52 @@ | ||
| # ibm_stable_analysis.R | ||
| rm(list=ls()) | ||
| require(warningsignals) | ||
| require(socialR) | ||
| script <- "ibm_analysis.R" | ||
| gitaddr <- gitcommit(script) | ||
| tags="warningsignals, stochpop" | ||
| tweet_errors(script, tags=tags) | ||
| on.exit(system("git push")) | ||
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| cpu <- 4 | ||
| nboot <- 500 | ||
| freq <- c(25, 50, 100, 200, 500) | ||
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| source("analysis.R") | ||
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| ## The analyses -- slow! | ||
| data(ibms) | ||
| m <- fit_models(ibm_stable, "LSN") | ||
| sampling <- sampling_freq(m$const, m$timedep, cpu=cpu, nboot=nboot, | ||
| sample_effort=freq) | ||
| taus <- reformat_tau_dists(bootstrap_tau(m$X, m$const, m$timedep, | ||
| cpu=cpu, nboot=nboot)) | ||
| mc <- remove_unconverged(montecarlotest(m$const, m$timedep, | ||
| cpu=cpu, nboot=nboot)) | ||
| indicator_sampling <- indicator_sampling_freq(m, cpu, nboot, | ||
| sample_effort=freq) | ||
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| ### Plot methods | ||
| ## Original plot | ||
| png("ibm_stable_roc.png"); plot_roc_curves(c(list(mc), taus)); dev.off() | ||
| upload("ibm_stable_roc.png", script=script, gitaddr=gitaddr, tags=tags) | ||
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| for(i in 1:length(freq)){ | ||
| input <- c(sampling[i], indicator_sampling[[i]]) | ||
| file <- paste("ibm_stable_", freq[i], ".png", sep="") | ||
| png(file); | ||
| plot_roc_curves(input, cex.axis=2, cex.lab=2); | ||
| dev.off() | ||
| upload(file, script=script, gitaddr=gitaddr, tags=tags) | ||
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| file <- paste("dist_ibm_stable_", freq[i], ".png", sep="") | ||
| png(file, width=480*length(input)) | ||
| plot_dists(input, cex.axis=3, cex.lab=3.5); | ||
| dev.off() | ||
| upload(file, script=script, gitaddr=gitaddr, tags=tags) | ||
| } | ||
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