GrowthFit: GrowthFit class

Description

The GrowthFit class contains a growth model fitted to data under static or dynamic conditions. Its constructor is fit_growth().

It is a subclass of list with the items:

environment: type of environment as in fit_growth()
algorithm: type of algorithm as in fit_growth()
data: data used for model fitting
start: initial guess of the model parameters
known: fixed model parameters
primary_model: a character describing the primary model
fit_results: an instance of modFit or modMCMC with the results of the fit
best_prediction: Instance of GrowthPrediction with the best growth fit
sec_models: a named vector with the secondary models assigned for each environmental factor. NULL for environment="constant"
env_conditions: a tibble with the environmental conditions used for model fitting. NULL for environment="constant"
niter: number of iterations of the Markov chain. NULL if algorithm != "MCMC"
logbase_mu: base of the logarithm for the definition of parameter mu (check the relevant vignette)
logbase_logN: base of the logarithm for the definition of the population size (check the relevant vignette)

Usage

# S3 method for GrowthFit
print(x, ...)
# S3 method for GrowthFit
coef(object, ...)
# S3 method for GrowthFit
summary(object, ...)
# S3 method for GrowthFit
predict(object, times = NULL, env_conditions = NULL, ...)
# S3 method for GrowthFit
residuals(object, ...)
# S3 method for GrowthFit
vcov(object, ...)
# S3 method for GrowthFit
deviance(object, ...)
# S3 method for GrowthFit
fitted(object, ...)
# S3 method for GrowthFit
logLik(object, ...)
# S3 method for GrowthFit
AIC(object, ..., k = 2)
# S3 method for GrowthFit
plot(
  x,
  y = NULL,
  ...,
  add_factor = NULL,
  line_col = "black",
  line_size = 1,
  line_type = 1,
  point_col = "black",
  point_size = 3,
  point_shape = 16,
  ylims = NULL,
  label_y1 = NULL,
  label_y2 = add_factor,
  label_x = "time",
  line_col2 = "black",
  line_size2 = 1,
  line_type2 = "dashed"
)
# S3 method for GrowthFit
predictMCMC(
  model,
  times,
  env_conditions,
  niter,
  newpars = NULL,
  formula = . ~ time
)

Value

An instance of MCMCgrowth.

Arguments

x: The object of class GrowthFit to plot.
...: ignored.
object: an instance of GrowthFit
times: Numeric vector of storage times for the predictions.
env_conditions: Tibble with the (dynamic) environmental conditions during the experiment. It must have one column named 'time' with the storage time and as many columns as required with the environmental conditions.
k: penalty for the parameters (k=2 by default)
y: ignored
add_factor: whether to plot also one environmental factor. If NULL (default), no environmental factor is plotted. If set to one character string that matches one entry of x$env_conditions, that condition is plotted in the secondary axis. Ignored if environment="constant"
line_col: Aesthetic parameter to change the colour of the line geom in the plot, see: ggplot2::geom_line()
line_size: Aesthetic parameter to change the thickness of the line geom in the plot, see: ggplot2::geom_line()
line_type: Aesthetic parameter to change the type of the line geom in the plot, takes numbers (1-6) or strings ("solid") see: ggplot2::geom_line()
point_col: Aesthetic parameter to change the colour of the point geom, see: ggplot2::geom_point()
point_size: Aesthetic parameter to change the size of the point geom, see: ggplot2::geom_point()
point_shape: Aesthetic parameter to change the shape of the point geom, see: ggplot2::geom_point()
ylims: A two dimensional vector with the limits of the primary y-axis. NULL by default
label_y1: Label of the primary y-axis.
label_y2: Label of the secondary y-axis. Ignored if environment="constant"
label_x: Label of the x-axis
line_col2: Same as lin_col, but for the environmental factor. Ignored if environment="constant"
line_size2: Same as line_size, but for the environmental factor. Ignored if environment="constant"
line_type2: Same as lin_type, but for the environmental factor. Ignored if environment="constant"
model: An instance of GrowthFit
niter: Number of iterations.
newpars: A named list defining new values for the some model parameters. The name must be the identifier of a model already included in the model. These parameters do not include variation, so defining a new value for a fitted parameters "fixes" it. NULL by default (no new parameters).
formula: A formula stating the column named defining the elapsed time in env_conditions. By default, . ~ time.

Methods (by generic)

print(GrowthFit): print of the model
coef(GrowthFit): vector of fitted model parameters.
summary(GrowthFit): statistical summary of the fit.
predict(GrowthFit): vector of model predictions.
residuals(GrowthFit): vector of model residuals.
vcov(GrowthFit): variance-covariance matrix of the model, estimated as 1/(0.5*Hessian) for regression and as the variance-covariance of the draws for MCMC
deviance(GrowthFit): deviance of the model.
fitted(GrowthFit): vector of fitted values.
logLik(GrowthFit): loglikelihood of the model
AIC(GrowthFit): Akaike Information Criterion
plot(GrowthFit): compares the fitted model against the data.
predictMCMC(GrowthFit): prediction including parameter uncertainty