Changelog • TreeMineR

TreeMineR (development version)

Fixed Monte Carlo P-value calculation in TreeMineR(). Simulated maximum log-likelihood ratios (LLRs) equal to the observed LLR are now counted as at least as extreme as the observed value (>= instead of >), as required for a valid Monte Carlo P-value. Previously, ties were excluded, which inflated the family-wise type-I error rate, particularly for sparse count data with many possible ties (#9).
Fixed calc_llr() so that nodes in which every individual is exposed (or every individual is unexposed) no longer get an undefined (NaN) log-likelihood ratio. Such nodes were previously dropped from both the simulated reference distribution and the reported results, which could bias P-values (#9).
Added a check to TreeMineR() which now throws an error if p is not greater than 0 and smaller than 1. p = 0 or p = 1 made the log-likelihood ratio degenerate (Inf) for all nodes containing exposed, respectively unexposed, individuals.

CRAN release: 2026-02-27

Fixed issue in the example dataset: The example dataset included individuals with non-constant exposure status, i.e., individuals who were at the same time exposed and unexposed. This should not be allowed. The example dataset has been updated accordingly.
Added a check to the TreeMineR function which now throws an error if exposure status is not constant within ids.

CRAN release: 2025-04-05

CRAN release: 2024-08-27

Added option to TreeMineR() for returning the test distribution of LLRs used for calculating the P-values.
Fixed issues with the ATC tree included in the package. The previous version of the tree did only include ATC codes with a depth of at least 5 levels. The updated version includes also codes with a lower depth, e.g., A02AH, which only has a depth of 4 levels.

CRAN release: 2024-04-02