Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## -----------------------------------------------------------------------------
realistic_stomach_data_path <- system.file("extdata", "realistic_stomach_data.csv",
package = "EcoDiet")
realistic_stomach_data <- read.csv(realistic_stomach_data_path)
knitr::kable(realistic_stomach_data)
## -----------------------------------------------------------------------------
realistic_biotracer_data_path <- system.file("extdata", "realistic_biotracer_data.csv",
package = "EcoDiet")
realistic_biotracer_data <- read.csv(realistic_biotracer_data_path)
knitr::kable(realistic_biotracer_data[c(1:3, 31:33, 61:63), ])
## ---- fig.height = 5, fig.width = 8-------------------------------------------
library(EcoDiet)
plot_data(biotracer_data = realistic_biotracer_data,
stomach_data = realistic_stomach_data)
## -----------------------------------------------------------------------------
literature_configuration <- FALSE
data <- preprocess_data(biotracer_data = realistic_biotracer_data,
trophic_discrimination_factor = c(0.8, 3.4),
literature_configuration = literature_configuration,
stomach_data = realistic_stomach_data)
## ---- fig.height = 5, fig.width = 8-------------------------------------------
plot_prior(data, literature_configuration)
## ---- fig.height = 5, fig.width = 8-------------------------------------------
plot_prior(data, literature_configuration, pred = "Pout")
## -----------------------------------------------------------------------------
filename <- "mymodel.txt"
write_model(file.name = filename, literature_configuration = literature_configuration, print.model = F)
mcmc_output <- run_model(filename, data, run_param="test")
## ---- eval = FALSE------------------------------------------------------------
# mcmc_output <- run_model(filename, data, run_param="normal", parallelize = T)
## ---- eval = FALSE------------------------------------------------------------
# plot_results(mcmc_output, data)
## ---- eval = FALSE------------------------------------------------------------
# plot_results(mcmc_output, data, pred = "Pout")
## ---- eval = FALSE------------------------------------------------------------
# plot_results(mcmc_output, data, pred = "Pout",
# variable = "PI", prey = c("Bivalves", "Worms"))
## -----------------------------------------------------------------------------
literature_configuration <- TRUE
## -----------------------------------------------------------------------------
realistic_literature_diets_path <- system.file("extdata", "realistic_literature_diets.csv",
package = "EcoDiet")
realistic_literature_diets <- read.csv(realistic_literature_diets_path)
knitr::kable(realistic_literature_diets)
## -----------------------------------------------------------------------------
data <- preprocess_data(biotracer_data = realistic_biotracer_data,
trophic_discrimination_factor = c(0.8, 3.4),
literature_configuration = literature_configuration,
stomach_data = realistic_stomach_data,
literature_diets = realistic_literature_diets,
nb_literature = 12,
literature_slope = 0.5)
## ---- fig.height = 5, fig.width = 8-------------------------------------------
plot_prior(data, literature_configuration)
## ---- fig.height = 5, fig.width = 8-------------------------------------------
plot_prior(data, literature_configuration, pred = "Pout")
## -----------------------------------------------------------------------------
filename <- "mymodel_literature.txt"
write_model(file.name = filename, literature_configuration = literature_configuration, print.model = F)
mcmc_output <- run_model(filename, data, run_param="test")
## ---- eval = FALSE------------------------------------------------------------
# mcmc_output <- run_model(filename, data, run_param=list(nb_iter=100000, nb_burnin=50000, nb_thin=50, nb_adapt=50000), parallelize = T)
## ---- eval = FALSE------------------------------------------------------------
# plot_results(mcmc_output, data)
## ---- eval = FALSE------------------------------------------------------------
# plot_results(mcmc_output, data, pred = "Pout")
## ---- eval = FALSE------------------------------------------------------------
# plot_results(mcmc_output, data, pred = "Pout", save = TRUE, save_path = ".")
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.