remix: Remix and describe.

In eusebe/remix: Remix your data

Description

A quick and easy function for describing datasets.

Usage

  remix(formula = cbind(...) ~ ., data = NULL, funs =
  c(mean, sd, quantile, n, na), ..., cum = FALSE, margin =
  0:2, addmargins = FALSE, useNA = c("no", "ifany",
  "always"), propNA = TRUE, revert = FALSE, method =
  c("pearson", "kendall", "spearman"), times = NULL,
  followup = FALSE, test = FALSE, test.summarize =
  test.summarize.auto, test.survival =
  test.survival.logrank, test.tabular = test.tabular.auto,
  show.test = display.test, plim = 4, show.method = TRUE,
  label = FALSE)

Arguments

formula	a formula (see Details).
data	a data.frame.
funs	functions for describing numeric variable. Can be c(fun1, fun2, fun3) or c("fun1", "fun2", "fun3") or a list.
...	further arguments (all passed to funs), for example na.rm = TRUE
cum	should cumulated frequencies be reported?
margin	index, or vector of indices to generate proportion in frequency tables (0: cell, 1: row, 2: col).
addmargins	whether to add margins
useNA	whether to include NA as a level (factor)
propNA	whether to include NA in proportion calculation
revert	whether to regroup factors or numeric variables when crossing factor with numeric variables
method	a character string indicating which correlation coefficient is to be used. One of "pearson", "kendall", or "spearman", can be abbreviated.
times	vector of times (see ?summary.survival un package survival)
followup	whether to display follow-up time
test	whether to perform tests
test.summarize	a function of two arguments (continuous variable and grouping variable) used to compare continuous variable, that return a list of two components : p.value and method (the test name). See test.summarize.auto, test.summarize.kruskal, test.summarize.oneway.equalvar, or test.summarize.unequalvar for example of such functions. Users can provide their own function.
test.survival	a function of one argument (a formula) used to compare survival estimations, that returns the same components as created by test.summarize. See test.survival.logrank. Users can provide their own function.
test.tabular	a function of three arguments (two categorical variables and a logical na) used to test association between two factors, that returns the same components as created by test.summarize. See test.tabular.auto and test.tabular.fisher. Users can provide their own function.
show.test	a function used to display the test result. See display.test.
plim	number of digits for the p value
show.method	should display the test name?
label	whether to display labels of variables (using label in package Hmisc)

Value

A remix object, basically a list with descriptive tables. It uses ascii package for printing output, and can be use with ascii function.

Note

The formula has the following format: x_1 + x_2 + ... ~ y_1 + y_2 + ...

There are a couple of special variables: ... represents all other variables not used in the formula and . represents no variable, so you can do formula = var1 ~ ..

If var1 is numeric, var1 ~ . produce a summary table using funs. If var1 is a factor, var1 ~ . produce a frequency table. If var1 is of class Surv, var1 ~ . produce a table with the estimates of survival at times. If var1 is numeric and var2 is numeric, var1 ~ var2 gives correlation. if var1 is numeric and var2 is a factor, var1 ~ var2 produce a summary table using funs according to the levels of var2. If var1 is a factor and var2 is a factor, var1 ~ var2 produce a contingency table. If var1 is of class Surv and var2 is a factor, var1 ~ var2 produce a table with the estimates of survival for each level of var2.

You can group several variables of the same type (numeric or factor) together with cbind(var1, var2, var3), they will be grouped in the same table. cbind(...) works (ie regroups all variables of the same type).

Author(s)

David Hajage, inspired by the design and the code of summary.formula (Hmisc package, FE Harrell) and cast (reshape package, H Wickham).

See Also

cast (reshape) and summary.formula (Hmisc).

Examples

parwidth <- getOption("width")
options(width = 100)

library(remix)
remix(data = iris)
remix(cbind(...) ~ ., iris[, sapply(iris, is.numeric)], funs = c(median, mad, min, max))
remix(cbind(Sepal.Length, I(Sepal.Width^2)) ~ Species, iris, funs = quantile, probs = c(1/3, 2/3))
remix(Sepal.Length + Sepal.Width ~ Petal.Length + Petal.Width, iris)
remix(cbind(Sepal.Length, Sepal.Width) ~ cbind(Petal.Length, Petal.Width), iris)
remix(... ~ ., esoph, cum = TRUE)
remix(alcgp ~ tobgp, esoph, cum = TRUE)
remix(Surv(time, status) ~ x, data = aml, times = seq(0, 120, 12))

options(width = parwidth)

eusebe/remix documentation built on May 16, 2019, 9:35 a.m.