NEWS.md

In rdinnager/slimr: Create, Run and Post-Process 'SLiM' Population Genetics Forward Simulations

slimr (development version)

slimr 0.4.0

• Updated slimr to be fully compatible with SLiM v4.1 updates
• Changed SLIM_HOME environmental variable to SLIMR_PATH, which now should be set with the full path to the SLiM executable, not just the directory containing it
• Updated slim_setup() function which now provides cross-platform automatic installation using conda via the reticulate package. Now it should not be necessary for users to manually install SLiM any more
• Simplified slim_run() API and temporarily removed ability to use R callbacks (the plan is to eventually replace this functionality with a new 'slimr verb' function)
• Added new 'slimr verb' r_message(). r_message() can be called in a slim_block() to print a message to the R console while the SLiM simulation is running. This is useful for debugging and monitoring progress of a simulation.
• slim_run() with progress = TRUE now produces a progress bar for any simulation (previously it only worked if you created output with r_output()) and is much more efficient (produces less overhead)
• slim_script_render_dots() function added. It works just like slim_script_render(), but accepts values to be filled in a templated slimr_script as named arguments. For example slim_script_render_dots(x, mut_rate = c(1e-6, 1e-7)) will render the slimr_script called x with mut_rate set to 1e-6 and 1e-7. This can sometimes be less verbose than using a list or data frame to fill in a templated slimr_script, especially useful when you simply want to test different values quickly.

slimr 0.3.0

• Added slim_auto() function to automatically insert r_template() and r_inline() statement in useful places in a slimr_script, based on computational graph analysis
• Added as_slimr_code() function, which is similar to as_slimr_script(), which converts SLiM code as a character vector into a slimr_script object, but as_slimr_code() returns the code necessary to create the slimr_script instead. this allows copy and pasting the text into the R console or IDE so that it can be subsequently edited and modified.
• Added vignette showing how to create a multispecies model in slimr, and documented the multispecies feature in the documentation for slim_block()

slimr 0.2.1

• allow user to manually set SLiM executable directory with SLIM_HOME environmental variable

slimr 0.2.0

• all SLiM callbacks now supported
• slimr now fully supports SLiM versions 4.0 and greater, including support for multispecies models (though these have been extensively tested yet) and are currently undocumented
• slimr verbs are now prefixed with r_ (e.g. r_output, r_inline, r_template). The old version slimr_ prefixed version are still available for backwards compatibility, but should be considered soft-deprecated

slimr 0.1.0

• SLiM Classes available for help with autocomplete now have nested class objects (e.g. sim$subpopulations references a Subpopulation object, so you can then autocomplete sim$subpopulations$individuals, for example)
• $ accessor can now be used in place of SLiM's . operator. (previously user's always had to use %.% to represent .)
• slimr now replaces any <- assignment operators in SLiM code with =.

slimr 0.0.0.9001

• slim_run() function runs a slimr_script in SLiM and collects results
• slimr 'verbs' implemented (slimr_template(), slimr_inline(), and slimr_output()). These can be used inside SLiM coding block to powerful effect!
• slim_block() creates blocks of SLiM code, and slim_script() puts them together into scripts.
• Package functional

slimr 0.0.0.9000

• Added a NEWS.md file to track changes to the package.

rdinnager/slimr documentation built on March 5, 2025, 12:24 a.m.