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NEWS

• Remove functions deprecated >2 years ago.
• Fix package level documentation.

• Bugfixes for R devel checks.
• Move orphan functions to utils.
• Deprecated many long superseded functions.
• Deprecated some no longer useful gene expression functions.
• New PDF template.

• Bugfixes for R 4.0.0 compatibility.

• Deprecated several functions in favor of tidyverse alternatives.
• Modified PDF template.

This is primarily a cleanup release. Several functions were included in the Tmisc package early on while packages such as janitor were in development. This release removes (note, removes, doesn’t deprecate) functions that were previously copied from other packages, introducing a few potentially breaking changes.

• Removed set_names() as this is exported from rlang.
• Removed beep(). Use the beepr package instead.
• Removed remove_empty_cols(), remove_empty_rows(), convert_to_NA() and clean_names(). Use remove_empty(), etc., from the janitor package instead.
• Removed unrowname(). Use magrittr::set_rownames() (loaded with tidyverse).

• Added an RMarkdown template.

• Add in to insert =. Optionally map the keyboard shortcut to Alt+- to insert = instead of the traditional <-.

• New functions %like% and %nlike% work like %in% and %nin%, but where the second argument is a regular expression to match.
• New function gt2refalt() creates a two-letter genotype from a GT field from a VCF file.
• Installs an RStudio add-in to insert %in%.
• Added aliases for low-level manipulation in a dplyr pipeline:
  • brackets()
  • dollar()
  • is_in()
  • and()
  • or()
  • equals()
  • is_gt()
  • is_geq()
  • is_lt()
  • is_leq()
  • not()
  • set_colnames()
  • set_rownames()
  • set_names()
  • set_attributes()
  • set_attr()

• New function mat2df() creates a pairwise distance data frame from a square matrix.

• keep_top_n() thanks to Jeroen Janssens.
• deseqresult2tbl() now lets you name the column extracted from the DESeq result’s rownames anything you want.
• Added the Datasaurus Dozen.
• Small updates to enable documentation with pkgdown.
• Inconsequential update to %nin%.

• Cs() (from Hmisc): Convenience function to create a quoted character vector from unquoted strings.

• Minor bugfixes

• convert_to_NA() converts string values to true NA values (adapted from sfirke/janitor)
• clean_names() cleans up the names in a data frame. Resulting names are unique and consist only of the _ character, lowercase letters, and numbers (taken from sfirke/janitor).
• remove_empty_rows() and remove_empty_cols() removes any rows or columns composed entirely of NA values (taken from sfirke/janitor).

• Tpairs() displays better pairwise scatterplot matrices than pairs().
• Thist() plots a histogram with either a normal distribution or density plot overlay.
• corner() displays the first few rows and columns of a data frame or matrix.
• beep() plays a short beep to alert when something’s done (from the beepr package).

• Minor bugfixes.

• jsd() compute the Jensen-Shannon divergence from a matrix of probabilities.
• Mode() returns the mode of a vector.
• gg_na() produces a plot showing the missing values in a data frame.
• are_all_equal() assess whether all the components of a numeric vector are (approximately) equal.

• gghues() generates color palette emulating ggplot2’s default hues.

• fisherp() uses Fisher’s method to combine p-values.

• dokuwiki() will convert a data.frame to a dokuwiki-formatted table, and will copy said table to the system clipboard if you’re on Mac OS X.

• strSort() alphabetically sorts characters in a string.

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