NEWS.md

In phillipnicol/SITH: A Spatial Model of Intra-Tumor Heterogeneity

Version 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.

Version 1.1.0 January 3, 2021

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.

Version 1.0.1 July 1, 2020

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.

Version 1.0.0 June 29, 2020

Initial submission to CRAN.

phillipnicol/SITH documentation built on April 4, 2024, 8:10 p.m.