tangram.clmm2: Table creation methods

Description

The tangram method is the principal method to create tables. It uses R3 method dispatch. If one specifies rows and columns, one gets an empty table of the given size. A formula or character will invoke the parser and process the specified data into a table like Hmisc::summaryM. Given an rms object it will summarize that model in a table. A data.frame is converted directly into a table as well for later rendering. Can create tables from summary.rms(), anova.rms(), and other rms object info to create a single pretty table of model results. The rms and Hmisc packages are required.

Usage

# S3 method for clmm2
tangram(
  x,
  id = NULL,
  style = "hmisc",
  caption = NULL,
  footnote = NULL,
  digits = NULL,
  ...
)
# S3 method for summary.clmm2
tangram(
  x,
  id = NULL,
  style = "hmisc",
  caption = NULL,
  footnote = NULL,
  digits = NULL,
  pformat = "%1.3f",
  include_p = FALSE,
  ...
)
tangram(x, ...)
# S3 method for numeric
tangram(
  x,
  cols,
  id = NULL,
  caption = NULL,
  style = "hmisc",
  footnote = NULL,
  fixed_thead = NULL,
  ...
)
# S3 method for anova.lme
tangram(
  x,
  id = NULL,
  style = "hmisc",
  caption = NULL,
  footnote = NULL,
  digits = NULL,
  fixed_thead = NULL,
  ...
)
# S3 method for data.frame
tangram(
  x,
  id = NULL,
  colheader = NA,
  caption = NULL,
  style = "hmisc",
  footnote = NULL,
  after = NA,
  quant = seq(0, 1, 0.25),
  msd = TRUE,
  as.character = NULL,
  fixed_thead = NULL,
  exclude = NULL,
  ...
)
# S3 method for formula
tangram(
  x,
  data = NULL,
  id = NULL,
  transforms = NULL,
  caption = NULL,
  style = "hmisc",
  footnote = NULL,
  after = NA,
  digits = NA,
  fixed_thead = NULL,
  exclude = NULL,
  ...
)
# S3 method for character
tangram(x, ...)
# S3 method for table
tangram(
  x,
  id = NULL,
  percents = FALSE,
  digits = 1,
  test = FALSE,
  footnote = NULL,
  ...
)
# S3 method for ftable
tangram(x, id = NULL, ...)
# S3 method for matrix
tangram(x, digits = NULL, ...)
# S3 method for tbl_df
tangram(x, ...)
# S3 method for lm
tangram(x, ...)
# S3 method for summary.lm
tangram(x, id = NULL, format = NULL, pformat = NULL, tformat = NULL, ...)
# S3 method for rms
tangram(
  x,
  data = NULL,
  short.labels = NULL,
  footnote = NULL,
  rnd.digits = 2,
  rnd.stats = rnd.digits,
  ...
)

Value

A tangram object (a table).

Arguments

x: object; depends on S3 type, could be rows, formula, string of a formula, data.frame or numerical rows, an rms.model
id: character; A unique charcter id used to identify this table over multiple runs. No spaces.
style: character; Desired rendering style, currently supports "hmisc", "nejm", and "lancet". Defaults to "hmisc"
caption: character; A string with the desired caption
footnote: character; A vector of character strings as footnotes
digits: numeric; default number of digits to use for display of numerics
...: addition models or data supplied to table construction routines
pformat: function or character; A function to format p values
include_p: logical; Include p-value when printing statistic
cols: numeric; An integer of the number of cols to create
fixed_thead: logical; On conversion to HTML5 should headers be treated as fixed?
colheader: character; Use as column headers in final table
after: function or list of functions; one or more functions to further process an abstract table
quant: numeric; A vector of quantiles to use for summaries
msd: logical; Include mean and standard deviation in numeric summary
as.character: logical; if true data.frames all variables are passed through as.character and no numerical summary is provided.
exclude: vector or list; When x is a data.frame this exclusion criteria is applied to the data. If this is a list then each list pair is the (column name, criteria). It is preferred to use a list to be specific.
data: data.frame; data to use for rendering tangram object
transforms: list of lists of functions; that contain the transformation to apply for summarization
percents: logical; Display percents when rendering a table object. Defaults to FALSE
test: logical or function; Perform default test or a statistical function that will return a test result when passed a row and column
format: numeric or character; Format to apply to statistic
tformat: numeric or character; format to apply to t-value
short.labels: numeric; Named vector of variable labels to replace in interaction rows. Must be in format c("variable name" = "shortened label").
rnd.digits: numeric; Digits to round reference, comparison, result and CI values to. Defaults to 2.
rnd.stats: numeric; Digits to round model LR, R2, etc to. Defaults to rnd.digits.

Details

Note that additional arguments are passed to any subsequent transform. This means that a lot of possible arguments are not documented here but in the transform applied. Examine their documentations for additional possible arguments if needed.

Examples

Run this code

tangram(1, 1)
tangram(data.frame(x=1:3, y=c('a','b','c')), id="mytbl1")
tangram(drug ~ bili + albumin + protime + sex + age + spiders, pbc, id="mytbl2")
tangram("drug~bili+albumin+stage::Categorical+protime+sex+age+spiders", pbc,"mytbl3")