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knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
Enjoy this brief demonstration of the plot data module
# Create normal distributed data with mean = 0 and standard deviation = 1 Sigma <- matrix(0.25,3,3) diag(Sigma) <- 1 set.seed(100) data <- MASS::mvrnorm(n=1000,mu=c(0,5,10), Sigma=Sigma, empirical=TRUE) colnames(data) <- c("Before","During","After") mcmc <- bfw::bfw(project.data = data, y = "Before,During,After", saved.steps = 50000, jags.model = "mean", job.title = "Stages of Cheese", jags.seed = 100, silent = TRUE) # Print output round(mcmc$summary.MCMC,3) #> Mean Median Mode ESS HDIlo HDIhi n #> mu[1]: Before 0 0 0.002 51201 -0.062 0.063 1000 #> mu[2]: During 5 5 5.000 50000 4.939 5.064 1000 #> mu[3]: After 10 10 10.000 50000 9.938 10.062 1000 #> sigma[1]: Before 1 1 1.000 49354 0.958 1.046 1000 #> sigma[2]: During 1 1 1.000 50000 0.957 1.045 1000 #> sigma[3]: After 1 1 0.997 50000 0.957 1.045 1000 Plot <- bfw::PlotMean(mcmc, run.repeated = TRUE) ParsePlot(Plot)
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set.seed(101) noise <- apply(data,2, function (x) x + rbinom(length(x),1,0.7)) noise.mcmc <- bfw::bfw(project.data = noise, y = "Before,During,After", saved.steps = 50000, jags.model = "mean", job.title = "Stages of Cheese", jags.seed = 101, silent = TRUE) # Print output round(noise.mcmc$summary.MCMC,3) #> Mean Median Mode ESS HDIlo HDIhi n #> mu[1]: Before 0.713 0.713 0.713 50000 0.641 0.781 1000 #> mu[2]: During 5.686 5.686 5.690 48350 5.618 5.756 1000 #> mu[3]: After 10.686 10.686 10.685 50648 10.617 10.753 1000 #> sigma[1]: Before 1.120 1.119 1.116 50000 1.072 1.170 1000 #> sigma[2]: During 1.116 1.116 1.112 50000 1.068 1.166 1000 #> sigma[3]: After 1.101 1.100 1.097 49233 1.054 1.151 1000 Plot <- bfw::PlotMean(noise.mcmc, run.repeated = TRUE) ParsePlot(Plot)
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combined.data <- as.data.frame(rbind(cbind(data,"Y"), cbind(noise,"X") ), stringsAsFactors=FALSE) combined.data[,1:3] <- lapply(combined.data[,1:3] , as.numeric) combined.data[,4] <- as.factor(combined.data[,4]) colnames(combined.data) <- c(colnames(data), "Groups") combined.data <- bfw::bfw(project.data = combined.data, y = "Before,During,After", x = "Groups", job.title = "Stages of Cheese", saved.steps = 50000, jags.model = "mean", jags.seed = 102, silent = TRUE) # Print output round(combined.data$summary.MCMC[, 3:7],3) #> Mode ESS HDIlo HDIhi n #> mu[1]: Before 0.359 50000 0.309 0.407 2000 #> mu[2]: Before vs. Groups @ X 0.713 50000 0.641 0.779 1000 #> mu[3]: Before vs. Groups @ Y -0.002 50000 -0.063 0.062 1000 #> mu[4]: During 5.342 50000 5.293 5.391 2000 #> mu[5]: During vs. Groups @ X 5.683 49103 5.616 5.754 1000 #> mu[6]: During vs. Groups @ Y 4.998 50000 4.938 5.062 1000 #> mu[7]: After 10.344 50000 10.293 10.390 2000 #> mu[8]: After vs. Groups @ X 10.688 49245 10.618 10.754 1000 #> mu[9]: After vs. Groups @ Y 9.999 50000 9.938 10.063 1000 #> sigma[1]: Before 1.119 50000 1.086 1.155 2000 #> sigma[2]: Before vs. Groups @ X 1.119 48125 1.071 1.169 1000 #> sigma[3]: Before vs. Groups @ Y 0.998 50000 0.958 1.045 1000 #> sigma[4]: During 1.112 50000 1.079 1.148 2000 #> sigma[5]: During vs. Groups @ X 1.115 49356 1.068 1.165 1000 #> sigma[6]: During vs. Groups @ Y 0.999 50000 0.957 1.045 1000 #> sigma[7]: After 1.105 50000 1.072 1.140 2000 #> sigma[8]: After vs. Groups @ X 1.098 50000 1.054 1.150 1000 #> sigma[9]: After vs. Groups @ Y 1.000 50000 0.957 1.045 1000 # Let's also add some colors! Plot <- bfw::PlotMean(combined.data, run.split = TRUE, run.repeated = TRUE, monochrome = FALSE) ParsePlot(Plot)
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