NEWS.md
In IxPopDyMod: Framework for Tick Population and Infection Modeling

IxPopDyMod 0.3.0

Rewrote config(), breaking the components of a config object out into a hierarchy of (new) S3 objects: predictors, life_cycle, parameters, predictor_spec, transition_function, and transition. This has numerous advantages, including the ability for users to build up individual components of a config with validation from the new classes, rather than constructing the entire config object in one step. This update means users need to modify any existing config objects to fit the new schema. The most significant changes are:
Life cycles are represented with the life_cycle class, which contains a list of transition objects. Previously, this data was represented in the transitions and parameters attributes of a config.
Modified the mechanism for passing functions to transitions to compute transition probability or duration. These functions are now wrapped in a class, transition_function. Previously, configs contained strings with the name of functions to get() from the environment; now we pass the transition_functions themselves. This removes the model's dependence on the global R environment, improving reproducibility.
Using predictor_spec and parameters, passing parameter and predictor values to transition_functions is now done more explicitly.
Updated the example configs to conform to the new schema.
Removed several pieces of non-core functionality that we think are better handled by users. This refocuses the package on its core purpose: configuring and running tick population models.
Removed read_config() and write_config(), which provided the ability to serialize and deserialize configs. These functions were not sufficient to comprehensively serialize all configs for reproducible model results. Now, the package only handles in-memory objects.
Removed run_all_configs() and the related parallel package dependency. This function was just a thin wrapper over a call to lapply or a parallel apply operation.
Removed graph_lifecycle() for visualizing the flow between life stages, and the dependency on the package igraph. Instead, life_cycle includes a print method with useful information on the flow between life stages.
Removed vary_param() and vary_many_params().
Removed the graphing functions graph_population_each_group() and graph_population_overall_trend(). These functions were intended as an easy way to visualize model results, but they did not handle all cases, since model output can be highly variable. We now recommend users write their own code, e.g. with ggplot2, to visualize results.
Removed three columns from the data frame output from run(): age_group, process and infected. These columns were populated based on the assumption that life stage names were structured as a three-character string like <process><infected><age_group>, and used downstream in the graphing functions. Now, users are completely free to name life stages as they wish.
Added annual_growth_rate(), for determining the annual factor by which population changes. Results from the growth_rate() function can be sensitive to the specific time period being modeled -- this aims to be a more universally applicable alternative.
Refactored growth_rate() to use base R.

IxPopDyMod 0.2.0

Added new configs to the package.
ogden2005, which replicates an existing deer tick population model by Ogden et al. (2005).
winter_tick, based on literature on the winter tick and used as an example of the package's flexibility for studying different tick species.
host_example_config, infect_example_config, and temp_example_config, which are used as examples of package use. Added examples with these configs to the readme.
Generalized config() to take a single predictors argument, instead of separate weather and host_comm arguments. This simplifies the config() structure, and allows using other types of data as a predictor for transitions.
write_config() arguments are updated to reflect this change.
Some internal functions are updated to support this change.
Added snow_cover_fun() transition function which is used in the winter_tick model configuration.
Fixed write_config() to write steps and initial population as integers rather than decimal numbers.