NEWS

---

biotmle 1.37.1

• Removal of the 'superheat' dependency, which has been archived on CRAN. The heatmap drawn by 'heatmap_ic()' is now built directly with 'ggplot2'.
• 'heatmap_ic()' gains a 'row_dendrogram' argument, which restores the row dendrogram previously available through 'superheat'. Biomarkers are ordered by hierarchical clustering whether or not the dendrogram is drawn, so this argument affects only the display. It defaults to 'FALSE', matching the default of the 'superheat' argument it replaces. Drawing the dendrogram introduces dependencies on 'ggdendro' and 'patchwork'.
• 'heatmap_ic()' now returns a 'ggplot' object, which can be stored and further modified in place, rather than drawing to the active graphics device as a side effect.
• ‘heatmap_ic()' gains a 'scale' argument controlling whether each biomarker’s contributions are standardized across observations before plotting; this replaces the argument of the same name previously forwarded to 'superheat'.
• Arguments passed to 'heatmap_ic()' via '...' are now forwarded to 'ggplot2::geom_tile()' rather than to 'superheat::superheat()'. Calls that relied on 'superheat'-specific arguments (e.g., 'left.label', 'clustering.method', 'row.dendrogram') must be updated.

biotmle 1.18.0

• No significant updates; these version numbers reflect the automatic version increments applied by Bioconductor at each release cycle.

biotmle 1.17.0

• Removal of 'future' and 'doFuture' for simplification of parallelization. All control of parallel computation now done through 'BiocParallel'.

biotmle 1.16.0

• No significant updates.

biotmle 1.15.0

• No significant updates.

biotmle 1.14.0

• No significant updates.

biotmle 1.13.0

• No significant updates.

biotmle 1.12.0

• No significant updates.

biotmle 1.11.0

• Change of estimation backend from the 'tmle' package to the 'drtmle' package.
• Removal of option to have repeated subjects since unsupported in new backend.
• Adds argument 'bppar_debug' to facilitate debugging around parallelization.

biotmle 1.10.0

• No significant updates.

biotmle 1.8.0

• No significant updates.

biotmle 1.6.0

• No significant updates.

biotmle 1.4.0

• An updated release of this package for Bioconductor 3.7, released April 2018.
• This release primarily implements minor changes, including the use of colors in the plots produced by the visualization methods.

biotmle 1.3.0

• An updated release of this package for Bioconductor 3.6, released in October 2017.
• An option for applying this methodology to next-generation sequencing data has been added, based on the popular "voom" transform of the limma R package.
• Facilities for parallelized computation have been completely re-implemented: current routines favor a combination of future and BiocParallel.
• The method for estimating biomarkers based on an observed outcome has been removed (temporarily). Inference based on this method requires re-thinking.
• A full suite of unit tests have been added, covering most package functions.

biotmle 1.0.0

• The first release of this package was made as part of Bioconductor 3.5, in 2016. The biotmle R package provides routines for statistical methodology first described in the technical manuscript [1] and the software paper [2]: 1. Nima S. Hejazi, Sara Kherad-Pajouh, Mark J. van der Laan, Alan E. Hubbard. Variance stabilization of targeted sstimators of causal parameters in high-dimensional settings. https://arxiv.org/abs/1710.05451 2. Nima S. Hejazi, Weixin Cai, Alan E. Hubbard. biotmle: Targeted Learning for Biomarker Discovery. The Journal of Open Source Software, 2(15), 2017. https://dx.doi.org/10.21105/joss.00295