simmr
Use:
install.packages("simmr")
then
library(simmr)
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:
if (!requireNamespace("readxl", quietly = TRUE)) { stop("readxl needed for this vignette to work. Please install it.", call. = FALSE ) }
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]]
Note that if you don't have TEFs or concentration dependence you can set these all to the value 0 or just leave them blank in the step below.
simmr
geese_simmr <- simmr_load( mixtures = 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)) )
plot(geese_simmr, group = 1:8)
simmr
and check convergencegeese_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)
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" )
For the many more options available to run and analyse output, see the main vignette via vignette('simmr')
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.