Changes in version 1.37.1 o Removal of the `superheat` dependency, which has been archived on CRAN. The heatmap drawn by `heatmap_ic()` is now built directly with `ggplot2`. o `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`. o `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. o `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`. o 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. Changes in version 1.18.0 o No significant updates; these version numbers reflect the automatic version increments applied by Bioconductor at each release cycle. Changes in version 1.17.0 o Removal of `future` and `doFuture` for simplification of parallelization. All control of parallel computation now done through `BiocParallel`. Changes in version 1.16.0 o No significant updates. Changes in version 1.15.0 o No significant updates. Changes in version 1.14.0 o No significant updates. Changes in version 1.13.0 o No significant updates. Changes in version 1.12.0 o No significant updates. Changes in version 1.11.0 o Change of estimation backend from the `tmle` package to the `drtmle` package. o Removal of option to have repeated subjects since unsupported in new backend. o Adds argument `bppar_debug` to facilitate debugging around parallelization. Changes in version 1.10.0 o No significant updates. Changes in version 1.8.0 o No significant updates. Changes in version 1.6.0 o No significant updates. Changes in version 1.4.0 o An updated release of this package for Bioconductor 3.7, released April 2018. o This release primarily implements minor changes, including the use of colors in the plots produced by the visualization methods. Changes in version 1.3.0 o An updated release of this package for Bioconductor 3.6, released in October 2017. o 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. o Facilities for parallelized computation have been completely re-implemented: current routines favor a combination of future and BiocParallel. o The method for estimating biomarkers based on an observed outcome has been removed (temporarily). Inference based on this method requires re-thinking. o A full suite of unit tests have been added, covering most package functions. Changes in version 1.0.0 o 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