## ---- eval = FALSE------------------------------------------------------------
#  install.packages('simmr')

## ---- message=FALSE-----------------------------------------------------------
library(simmr)

## ---- eval = FALSE------------------------------------------------------------
#  system.file("extdata", "geese_data.xls", package = "simmr")

## ---- echo = FALSE------------------------------------------------------------
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)

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

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

## ----fig.align = 'center',fig.width = 7,fig.height = 5------------------------
plot(geese_simmr, group = 1:8)

## ---- results = 'hide', message = FALSE---------------------------------------
geese_simmr_out = simmr_mcmc(geese_simmr)
summary(geese_simmr_out, type = 'diagnostics',
        group = 1)

## ----fig.align = 'center',fig.width = 7,fig.height = 5------------------------
posterior_predictive(geese_simmr_out, group = 5)

## ----fig.align = 'center',fig.width = 7,fig.height = 5------------------------
prior_viz(geese_simmr_out)

## ----fig.align = 'center',fig.width = 7,fig.height = 5------------------------
plot(geese_simmr_out, type = 'histogram')

## ----fig.align = 'center',fig.width = 7,fig.height = 5------------------------
compare_groups(geese_simmr_out, groups = 1:4, 
               source_name = 'Enteromorpha')

