Plot Data
---------

Enjoy this brief demonstration of the plot data module

### First we simulate some data and estimate means and standard deviations

    # 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)

### Plot the data as repeated measures

<figure>
<img src="../inst/extdata/data/ProjectAllData-Mean-StagesOfCheese-Plot01-1528465133.png" alt="plot1" width="800" /><figcaption>plot1</figcaption>
</figure>

### Lets add some noise

    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)

### Plot the noise as repeated measures

<figure>
<img src="../inst/extdata/data/ProjectAllData-Mean-StagesOfCheese-Plot01-1528466639.png" alt="plot2" width="800" /><figcaption>plot2</figcaption>
</figure>

### Let’s add a group

    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)

### Plot the split data

<figure>
<img src="../inst/extdata/data/ProjectAllData-Mean-StagesOfCheese-Plot01-1528467502.png" alt="plot3" width="800" /><figcaption>plot3</figcaption>
</figure>
