pmtables: pmtables: Tables for Pharmacometrics.

In metrumresearchgroup/pmtables: Tables for Pharmacometrics

pmtables: Tables for Pharmacometrics.

Description

Summarize data sets and create publication-quality tables for inclusion in 'tex' documents.

Creating general tables

• To create a table with a single function call, use stable() for single page tables and stable_long() for longtable

• Alternatively, use st_new() to create a s-table object and pipe to other st-functions; see the documentation links in stable() to discover these functions; finally, create an stable object with st_make()

Table data grooming and sanitization

• The functions tab_prime() and triage_data() are called to get the data frame ready to be in tabular format (see make_tabular()

• The function tab_escape() is used to escape ⁠%⁠ and ⁠_⁠ in the table (sanitization); use options(pmtables.escape = ...) to change the set of escape characters or set that option to NULL to prevent any sanitization

• Any unit of data that has a character escaped with double backslash (⁠\\⁠) or that contains a math expression with two $ will not be sanitized

• The function tab_escape() also performs the following substitutions:

  • change ~ to ⁠$\\sim$⁠

  • change > to ⁠$>$⁠

  • change < to ⁠$<$⁠

Summarizing and creating tables

• Use pt_cont_wide() to create continuous data summary in wide format

• Use pt_cont_long() to create continuous data summary in long format

• Use pt_cat_wide() to create discrete data summaries in wide format

• Use pt_cat_long() to create discrete data summaries in long format

• Use pt_data_inventory() to create a table summarizing observations and individuals in a data set

• All of the above functions return an object with class pmtable, which is a list; you can access the summarized data by looking at the data slot; otherwise, pass the pmtable object to stable() or as_stable() in order to create the table. See class-pmtable for details around this object

• You can configure the digits in these summaries with new_digits()

Helper functions for working with data frames

• Make text bold with tex_bold() or italics with tex_it()

• Clear repeated values in a column with clear_grouped_values() and tab_clear_reps()

• Use tab_edit() to do find / replace on your data frame

• Use df_grep_rows() and df_grepl_rows() to find rows that match a given pattern

• Use sig() or digit1() to control the number of digits that are displayed; both these functions return character

Functions to align columns

• When you want latex to figure out column widths: cols_left(), cols_right(), cols_center(), cols_align()

• When you want to fix the width of a specific column in the table: col_ragged(), col_fixed()

Functions to modify or configure a table

• Alter column names: tab_cols()

• Partition a table into panels: as.panel() and rowpanel()

• Create groups of columns with column spanners: colgroup() and colsplit()

• Configure row spacing, column spacing, or font size: tab_size()

• Configure the appearance of table notes: noteconf()

• Identify rows that are "summary" rows: sumrow(); these rows can get automatically styled with a label (optionally in bold font) and a horizontal line above

Preview tables

• Use st2viewer() to send s-table output to texPreview::tex_preview()

• Use st2article() or st2report() to render several tables in a stand-alone tex document rendered directly by pdflatex (no involvement of Rmarkdown or pandoc); this requires pdflatex to be installed and in your PATH.

• Use st2doc() to render a pdf file with one or more tables using pandoc; in general, use st2article() instead

• Pipe tables to st_asis() to render a table in line while knitting an Rmd document

• Use st_wrap() to wrap s-table output in a table environment and optionally send the output to stdout(); this is helpful when rendering tables in Rmarkdown documents. There is an st_wrap() method for longtables that won't add the table environment.

• Use as_lscape() to mark stable() or stable_long() output for display in landscape environment

Save s-tables

• Use stable_save() to write an stable or stable_long object to file

• Note that there is a dir argument to that function that lets you route the table to a specific directory; dir defaults to the pmtables.dir option, so setting options(pmtables.dir = "../deliv/table") will route the table to that directory without requiring additional input

Latex / markdown information

The following latex packages are required in your Rmd or latex document:

• threeparttable

• array

• booktabs

• pdflscape

• longtable (only when long tables are in the document)

• float (mainly if you want to use H placement in your Rmd output)

In Rmd, include these as extra_dependencies. Or try using st_use_knit_deps() to include these packages via knitr::knit_meta_add(); this is only when you are including a table in a knit Rmd document.

You may also want to include this package:

• mathdesign with option utopia

The tables are generated with defaults that look sensible when the table is rendered with single spacing. If you are working in a 1.5 spaced environment, the table may look roomy. In that case, load the setspace package and switch to singlespacing prior to sourcing the table.

If you render tables in an Rmarkdown document with processing by pandoc, pandoc may make mistakes when parsing the latex code. To keep pandoc from making parsing errors, use latex code fence. This formatting can be added to your table with the st_latex() command. You can see what the fence looks like by running st_latex("abc"). Asserting that the code is latex can also be accomplished with pt_wrap() and using the context = "rmd" option. See st2article() for instructions on how to view a complete working latex example.

Glossaries

• Use read_glossary() to read abbreviations and definitions from a file in .tex or .yaml format.

• Use as_glossary() to create a glossary object in R.

• Use select_glossary() to select specific labels from a glossary object.

• Use glossary_notes() to create table notes from a glossary object.

• Use st_notes_glo() to create glossary notes from a glossary object and attach to a table in a pipeline.

Data sets

• analysis1 - a NMTRAN-style data set; the basis for most other example data sets

• pmt_pk - this is analysis1, but with only PK observation records

• pmt_obs - this is analysis1, but with only observations

• pmt_first - this is analysis1 but with only the first record from each individual

• pmt_summarized - an example data set that has been summarized

Author(s)

Maintainer: Kyle Baron [e-mail]

Other contributors:

• Anna-Christina Nevison [e-mail] [contributor]

• Katherine Kay [e-mail] [contributor]

• Devin Pastoor [e-mail] [contributor]

• Kyle Barrett [e-mail] [contributor]

See Also

Useful links:

• https://metrumresearchgroup.github.io/pmtables

• https://github.com/metrumresearchgroup/pmtables

• Report bugs at https://github.com/metrumresearchgroup/pmtables/issues

metrumresearchgroup/pmtables documentation built on Dec. 22, 2024, 1:34 a.m.