NEWS

macpan2 1.5.0

Repeated calls of an optimizer now start from the previous best parameter vector
No longer fit full covariance matrix in sdreports

No longer exporting nlist.
Removing in-place modifications to model specification objects in mp_tmb_insert and mp_tmb_update.

Define explicit state variable updates, with the choice of applying mp_euler, mp_rk4, or mp_euler_multinomial update methods, the latter generating process error.
New stochasticity engine functions rbinom and reulermultinom.
mp_tmb_fixef_cov function for getting the covariance matrix of fixed effects.
mp_trajectory_ensemble and mp_trajectory_sim functions for summarizing random variation in trajectories.
Unpacking assignment in the engine. This means that you can do things like c(x, y) ~ z, where the values in z are assigned to elements in x, y, etc... in row-major order.
to_name_pairs function for returning all pairwise dot-concatenations of the elements of a character vector without dots.
to_values function for extracting the column from a data frame with only a single numerical column and turning numeric matrices and arrays with dimnames into a flattened numeric vector with labels produced by appropriately dot-concatenating the dimnames.

New installation instructions for installing from r-universe.
New vignette: real_data.
Document to_name, to_names, to_labels, which handle naming of structured objects.
Document print function in the ?engine_functions.
simple_sims example in ?engine_functions now runs without error.
Help file examples for mp_tmb_insert and mp_tmb_update.
Readme/vignette examples better expose calls to library for the user.

simple_sims no longer returns outputs for the zeroth time-step.
Using last.par.best to finalize the TMB objective function following optimization.
group_sums now checks for bad group indexes.
rbind_lag now throws an error when lag > 1 because there are conceptual errors with this case. We will get back to this when we can to allow these important cases by adding an argument with initial conditions associated with negative time steps.

Streamlined installation via r-universe.
mp_tmb_calibrator and mp_tmb_optimize functions for calibration using a simple and restrictive trajectory matching model. Future releases will allow more functionality.
mp_tmb_coef and mp_tmbstan_coef for tables of statistical parameters used in calibration.
mp_trajectory_sd and mp_trajectory_ensemble for getting information about fitted trajectory uncertainty.
mp_tmb_update|insert functions for creating new model specs from existing ones.
Parameters specified as a data frame can now place default values in columns with any of the following names: "default", "Default", "value", "Value", "val", "Val"
mp_tmb_library can return a list of model specs with alternative_specs, if the model makes alternatives available.
time_var engine function is better than the old time_group, which required two expressions rather than one to do the same thing. time_group will remain but is softly deprecated.
Fixed effects extractor and formatter.
mp_default function for extracting spec and simulator defaults in long-format.
rbind_time allows integer vectors for subsetting times
options(macpan2_verbose = FALSE) will turn off the flood of information provided by TMB. Note that this only takes effect if set before creating a TMB simulator.

(in progress) Calibration vignette is updated to be a simpler quick-start, and previous advanced material is moved to an advanced vignette.
mp_tmb_model_spec documentation is filled out.
group_sums TMB engine function third argument updated from old pre-1.0.0 behaviour.

No more flows.csv, derivations.json files in the library, and instead tmb.R files.
No more Compartmental function, and instead mp_tmb_model_spec and mp_tmb_library.
{group|row|col}Sums are now called {group|row|col}_sums.
Final argument of group_sums used to be the length of the output vector, but now it is a vector of the desired output length.
TMBModel and associated classes (ExprList) are no longer exported, in favour of mp_... functions for doing similar things.
Sort simulation output by time step.

Constant integer vectors can now be passed to C++.
Integer vectors can be used to subset assignment matrices (i.e. integer subsetting on the left-hand-side).
mp_trajectory() function, which is roughly equivalent to model$report(..., .phases = "during").
New print function in the TMB engine.
No need to declare empty matrices when creating TMB model objects, and matrices that are derived are automatically detected.

Optimize C++ simulation history storage by avoiding unnecessary allocations
Use state and flow names in expression inserters
Chattier validity checking
Radial basis functions
New starter models (thanks @mayaearn and @Flynn-Primrose )
- macpan-base -- re-implementation of the McMaster group's COVID-19 model in macpan2
- ww -- wastewater model (doesn't yet have a readme)
- new readme for and clean up of previous models
Report what expression broke on the C++ side
Developer tools for switching between different C++ files and working directories
Package reference organization cleanup (thanks @bbolker )
Time-varying parameters vignette

Interface for optimization of TMB simulation objects
TMB simulation model updating with caching
Parameter transformations
Get initial values of matrices in TMB simulation objects
State and flow variable names can be used in expressions in some contexts
Example model indexing (thank you @bbolker!)
Engine function rbind_time defaults to row binding the full simulation history
Fix bug when the entire model has no inflows or no outflows
Fix bugs in symbolic R-side manipulation of expressions
Fix previously broken argument_dots option in model definition files (thank you @Flynn-Primrose )