NEWS

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SITH 1.2.0

The main feature of this update is the ability to simulate tumors under targeted therapy.

New functionality:

• Several new parameters to simulateTumor() have been added. After max_pop is reached, therapy is applied and all non-resistants cells die. Then the tumor grows to recurrent_size. To control the probability that a new mutation confers treatment resistance, use the resistance_prob parameter.
• When plotting the tumor, the colors are now chosen so that grey is neutral and cells with similar genotypes have similar colors.

SITH 1.1.0 (2021-01-05)

This update introduces new functionality for the tumor growth simulator.

New functionality:

• A new parameter to simulateTumor() has been added. This allows the user to specify a custom disease model for more control over the kinds of mutations that can occur. See vignette for more details.
• Coverage has been added to bulkSample() and randomBulkSamples() to better simulate real sequencing data.

Changes to existing functionality:

• The alleles data frame which was returned by simulateTumor() has been renamed to genotypes to be biologically correct.

Bug fixes:

• In visualizeTumor, there was an issue where suggested package rgl was not being used conditionally.

Internal changes:

• The C++ code has been completely refactored for organization.

SITH 1.0.1 (2020-07-02)

This patch contains bug fixes. In addition, the dependence on R 4.0.0 is switched to 3.6.0, so that users on the old release can use the package.

Bug fixes:

• An ambiguous call to the overloaded pow() in "post_processing.h" causes a compilation error on Solaris.

SITH 1.0.0 (2020-07-01)

Initial submission to CRAN.