Implemented basic parameter checks for coupled models.
Implemented MCMC predictions for coupled models.
Implemented the serial dilution method.
biogrowth 1.0.7
fixed a bug in the calculation of vcov methods. The
variance was not properly scaled.
biogrowth 1.0.6
included the fit_coupled_growth() function with a novel
approach for the Baranyi-Ratkowsky model.
biogrowth 1.0.5
included additional secondary models (Aryani, Inhibitory and
Rosso_aw).
included additional primary models (Baranyi_noLag,
Baranyi_noStationary, Loglinear, Bilinear_lag,
Bilinear_stationary).
fixed the CRAN name of vignette 0.5.
made several fixes in the documentation with broken links to
external functions
biogrowth 1.0.4
included logbase_mu and logbase_logN to
predict_growth_uncertainty().
biogrowth 1.0.3
added the CITATION to the paper in the JSS.
biogrowth 1.0.2
included a new vignette describing the use of custom distributions
for forward uncertainty propagation.
biogrowth 1.0.1
included two new datasets: refrigeratorSpain and
greek_tractors.
biogrowth 1.0.0-3
upgraded the HTML documentation to the format of R version 4
biogrowth 1.0.0-2
fixed a bug in coef.GlobalGrowthComparison and
coef.GrowthComparison
biogrowth 1.0.0
added a biogrowth-package help page
updated the roxygen2 documentation to markdown style
implemented predict_growth as an overall function for growth
predictions
implemented fit_growth as an overall function for growth
fitting
implemented time_to_size as an overall function for calculating the
time to reach a given population size
included lifecycle badges for every exported function
renamed stochastic_growth to predict_growth_uncertainty
implemented functions to calculate guesses for primary and secondary
models
implemented functions to show initial guesses of growth models
implemented logLik and AIC calculations for model fits
implemented functions for model comparison/selection
reimplemented the predict method for global fits for something that
makes more sense (it now returns a vector)
fixed a bug in time_to_logcount for trilinear model. It was messing
up the calculation in the horizontal parts
included arguments logbase_mu and logbase_logN to deal with
different unit systems
created new vignettes with a more “chapter-like” style
updated the README file
biogrowth 0.2.3
Included print methods for every class.
biogrowth 0.2.2
Added an alias to the mod-Gompertz function so ??modGompertz or
??gompertz finds it
Added bounds for fit_multiple_growth in the vignette to avoid an
error message in CRAN on macOS.
biogrowth 0.2.1
Included a times argument to the predict methods of dynamic fitting
functions.
Changed the base of the log-parameter transformation to 10 in
predict_stochastic_growth.
Changed the scale of plot.FitSecondaryGrowth.
Include 2 new datasets: growth_pH_temperature and
conditions_pH_temperature.
Updated the labels of plot.FitSecondaryGrowth, so now it shows the
transformation explicityly.
Updated the example dataset conditions_pH_temperature to better show
the models.
Fixed a bug in the example for predict_stochastic_growth
biogrowth 0.2.0
Included the Richards and logistic growth models.
predict_isothermal_growth now accepts both named vectors or list as
arguments.
The model definition for predict_stochastic_growth has been
improved. Now they are defined in a single argument using a tibble which
includes expected values, standard deviations and scale where the normal
distribution is defined. This makes it easier to define (not so many
arguments) and way more flexible (specially when it comes to adding new
models).
Using a flexible unit system was giving more issues than it solved.
Especially when making the Baranyi model under dynamic and static
conditions equivalent. Set the unit system to log10 for population size
and ln(units)/[time] for the growth rate.
Set the default binwidth of plot.TimeDistribution to NULL
(geom_histogram picks it).
Added a new vignette about using predict_dynamic_growth() for static
conditions.
Improved parameter validation for fit_secondary_growth.
Several improvements in the main vignette (new arguments, new
functions, better descriptions…).
biogrowth 0.1.2
Documented S3 classes.
Implemented additional S3 methods for all the fitting classes (vcov,
deviance, predict, fitted, residuals, coef).
Now, the full Ratkowsky model can be fitted under dynamic
conditions. I had forgotten to add it in the helper.^
Bug fix in distribution_to_logcount. If the growth rate was 0 in one
of the simulations, approx would give an error. Added ties=“ordered” to
try and fix this.
Bug fix in fit_secondary_model. The function was returning NA for
the fitted parameters due to some error generating the output.
I got rid of the ugly warning messages in fit_secondary_model. They
were due to bind_cols trying to fix names.
Bug fix in plotting of dynamic predictions. The attribute for the
y-axis label was not really used.
Reduced iterations in the vignette to reduce compilation time.
biogrowth 0.1.1
Added a NEWS.md file to track changes to the
package.
Included the full Ratkowsky model.
Added the possibility to a single model to various curves with the
fit_multiple_growth and
fit_multiple_growth_MCMC functions.
Included a new vignette with advanced plotting options.
Implemented automatic checks about model parameters for primary
models.
Implemented automatic checks about model parameters for cardinal
fits.
Implemented S3 methods for residuals.
Included S3 plotting method for secondary fits.
Added new arguments to the S3 plotting methods with additional
aesthetic options.
Defined a range in the Zwietering secondary model to avoid
unreasonable results.
Updated vignette with new functions.
Small changes in function documentation and vignettes for better
clarity.