View source: R/fit_dynamic_growth.R
fit_MCMC_growth  R Documentation 
The function fit_MCMC_growth()
has been superseded by the toplevel
function fit_growth()
, which provides a unified approach for growth modelling.
But, it can still fit a growth model to a data obtained under dynamic conditions using the onestep approach (MCMC algorithm).
fit_MCMC_growth(
fit_data,
env_conditions,
starting_point,
known_pars,
sec_model_names,
niter,
...,
check = TRUE,
formula = logN ~ time,
logbase_mu = logbase_logN,
logbase_logN = 10
)
fit_data 
Tibble with the data to use for model fit. It must contain a column with the elapsed time (named "time" by default) and another one with the decimal logarithm of the observed population size (named "logN" by default). Different column names can be specified using the "formula" argument. 
env_conditions 
Tibble with the (dynamic) environmental conditions during the experiment. It must have one column with the elapsed time (named "time" by default) and as many columns as required with the environmental conditions. A different column name can be specified using the "formula" argument, although it must be the same one as in "fit_data". Note that only those defined in "sec_model_names" will be considered for the model fit. 
starting_point 
A named vector of starting values for the model parameters.
Parameters for the primary model must be named in the usual way. Parameters for the
secondary model are named as 
known_pars 
A named vector of known model parameters (i.e. not fitted). They
must be named using the same convention as for 
sec_model_names 
A named character vector defining the secondary model for each
environmental factor. The names define the factor and the value the type of model.
Names must match columns in 
niter 
number of iterations of the MCMC algorithm. 
... 
Additional arguments passed to modFit. 
check 
Whether to check model parameters (TRUE by default). 
formula 
an object of class "formula" describing the x and y variables.

logbase_mu 
Base of the logarithm the growth rate is referred to. By default, the same as logbase_logN. See vignette about units for details. 
logbase_logN 
Base of the logarithm for the population size. By default, 10 (i.e. log10). See vignette about units for details. 
An instance of FitDynamicGrowthMCMC()
.
## We use the example data included in the package
data("example_dynamic_growth")
data("example_env_conditions")
## Definition of the secondary models
sec_model_names < c(temperature = "CPM", aw= "CPM")
## Any model parameter can be fixed
known_pars < list(Nmax = 1e4, # Primary model
N0 = 1e0, Q0 = 1e3, # Initial values of the primary model
mu_opt = 4, # mu_opt of the gamma model
temperature_n = 1, # Secondary model for temperature
aw_xmax = 1, aw_xmin = .9, aw_n = 1 # Secondary model for water activity
)
## We need starting values for the remaining parameters
my_start < list(temperature_xmin = 25, temperature_xopt = 35,
temperature_xmax = 40,
aw_xopt = .95)
## We can now call the fitting function
set.seed(12124) # Setting seed for repeatability
my_MCMC_fit < fit_MCMC_growth(example_dynamic_growth, example_env_conditions,
my_start, known_pars, sec_model_names, niter = 3000)
## Always check the MCMC chain!!
plot(my_MCMC_fit$fit_results)
## We can compare data against fitted curve
plot(my_MCMC_fit)
## Any environmental factor can be included using add_factor
plot(my_MCMC_fit, add_factor = "temperature",
label_y1 = "Count (log CFU/ml)", label_y2 = "Temperature (C)")
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