NEWS

simlandr 0.4.0 (2025-02-12)

Added simulation helper functions sim_SDE() and multi_init_simulation() for simulating stochastic differential equations (SDEs) and multiple initial conditions, respectively.
Added as.mcmc.list() method for lists of simulation outputs. The added simulation functions also have the option to return the output as an mcmc or mcmc.list object, so that they can be used with coda functions.
The landscape estimation functions now get a new parameter weight_var to specify the variable that contains the weight of each sample point. This may be useful if user applies importance sampling.
Added vignettes and more examples.

Removed unused parameter Umax from the documentation of make_kernel_dist() (an internal function).

Further improved documentation, function, and class names, and cleaned unnecessary exported functions. Removed some deprecated functions.
Made the parameter names of the landscape functions more consistent; used better default values for landscape functions.
For single simulation landscape functions, added make_*d_single() alias.
Removed some default values for barrier calculation functions (they are often not suitable and can be misleading).
Added print(), summary() and plot() methods for several classes.
Replaced get_geom() with a method of the autolayer() generic function from ggplot2. get_geom() is now deprecated.
Replaced get_barrier_height() with a method of the summary() generic function. get_barrier_height() is now deprecated.
Renamed hash_big.matrix class to hash_big_matrix for consistent use of dots; renamed related functions accordingly.
Added coda::cumuplot() as a possible option for check_conv().
For barrier_batch objects, renamed the column b to barrier to avoid possible conflicts.
Removed some unnecessary messages.
Added some examples to README.
Updated the vignette: updated some function, object, and parameter names; removed some references that we are now questioning.
Bug fix: Parameter vg in make_barrier_grid_2d() and make_barrier_grid_3d() was changed to ag and the class of this parameter was changed from var_grid (deprecated) to arg_grid.

Renamed var and par in batch simulation functions to arg (argument) and ele (element).
Adjusted the algorithm of calculating minimal energy paths (previously "minimal elevation paths").
Added an non-gradient example function sim_fun_nongrad(); renamed sim_fun_test2() to sim_fun_grad().
Added title for the color bar in plot_ly based plots; used theme_bw() throughout all ggplot2 based plots.
Improved some documentation; included a new vignette.

Improved the manual.
Added sim_fun_test2 function for testing.
Added ... for batch_simulation().
Added border for white dots in the geom of calculate_barrier_2d() and calculate_barrier_2d_batch().