simmr: quick start guide

Andrew Parnell

2019-07-03

Step 1: install simmr

Use:

install.packages('simmr')

then

library(simmr)

Step 2: load in the data

Some geese isotope data is included with this package. Find where it is with:

system.file("extdata", "geese_data.xls", package = "simmr")

Load into R with:

library(readxl)
path = system.file("extdata", "geese_data.xls", package = "simmr")
geese_data = lapply(excel_sheets(path), read_excel, path = path)

If you want to see what the original Excel sheet looks like you can run system(paste('open',path)).

We can now separate out the data into parts

targets = geese_data[[1]]
sources = geese_data[[2]]
TEFs = geese_data[[3]]
concdep = geese_data[[4]]

Step 3: load the data into simmr

geese_simmr = simmr_load(mixtures = as.matrix(targets[, 1:2]),
                         source_names = sources$Sources,
                         source_means = sources[,2:3],
                         source_sds = sources[,4:5],
                         correction_means = TEFs[,2:3],
                         correction_sds = TEFs[,4:5],
                         concentration_means = concdep[,2:3],
                         group = as.factor(paste('Day', targets$Time)))

Step 4: plot the data

plot(geese_simmr, group = 1:8)

Step 5: run through simmr and check convergence

geese_simmr_out = simmr_mcmc(geese_simmr)
summary(geese_simmr_out, type = 'diagnostics',
        group = 1)

Check that the model fitted well:

posterior_predictive(geese_simmr_out, group = 5)
## Compiling model graph
##    Resolving undeclared variables
##    Allocating nodes
## Graph information:
##    Observed stochastic nodes: 40
##    Unobserved stochastic nodes: 46
##    Total graph size: 190
## 
## Initializing model

Step 6: look at the output

Look at the influence of the prior:

prior_viz(geese_simmr_out)

Look at the histogram of the dietary proportions:

plot(geese_simmr_out, type = 'histogram')

compare_groups(geese_simmr_out, groups = 1:4, 
               source_name = 'Enteromorpha')
## Most popular orderings are as follows:
##                                     Probability
## Day 428 > Day 124 > Day 398 > Day 1      0.2131
## Day 428 > Day 398 > Day 124 > Day 1      0.1681
## Day 428 > Day 124 > Day 1 > Day 398      0.1561
## Day 428 > Day 398 > Day 1 > Day 124      0.1261
## Day 428 > Day 1 > Day 124 > Day 398      0.0856
## Day 428 > Day 1 > Day 398 > Day 124      0.0742
## Day 124 > Day 428 > Day 398 > Day 1      0.0444
## Day 124 > Day 428 > Day 1 > Day 398      0.0344
## Day 398 > Day 428 > Day 124 > Day 1      0.0261
## Day 398 > Day 428 > Day 1 > Day 124      0.0158
## Day 398 > Day 124 > Day 428 > Day 1      0.0119
## Day 124 > Day 398 > Day 428 > Day 1      0.0111
## Day 1 > Day 428 > Day 124 > Day 398      0.0058
## Day 124 > Day 1 > Day 428 > Day 398      0.0047
## Day 398 > Day 1 > Day 428 > Day 124      0.0047
## Day 1 > Day 428 > Day 398 > Day 124      0.0042
## Day 1 > Day 124 > Day 428 > Day 398      0.0031
## Day 1 > Day 398 > Day 428 > Day 124      0.0025
## Day 124 > Day 398 > Day 1 > Day 428      0.0022
## Day 398 > Day 124 > Day 1 > Day 428      0.0017
## Day 124 > Day 1 > Day 398 > Day 428      0.0014
## Day 398 > Day 1 > Day 124 > Day 428      0.0014
## Day 1 > Day 124 > Day 398 > Day 428      0.0008
## Day 1 > Day 398 > Day 124 > Day 428      0.0006

For the many more options available to run and analyse output, see the main vignette via vignette('simmr')