View source: R/tableby.control.R
tableby.control | R Documentation |
tableby
functionControl test and summary settings for the tableby
function.
tableby.control( test = TRUE, total = TRUE, total.pos = c("after", "before"), test.pname = NULL, numeric.simplify = FALSE, cat.simplify = FALSE, cat.droplevels = FALSE, ordered.simplify = FALSE, date.simplify = FALSE, numeric.test = "anova", cat.test = "chisq", ordered.test = "trend", surv.test = "logrank", date.test = "kwt", selectall.test = "notest", test.always = FALSE, numeric.stats = c("Nmiss", "meansd", "range"), cat.stats = c("Nmiss", "countpct"), ordered.stats = c("Nmiss", "countpct"), surv.stats = c("Nmiss", "Nevents", "medSurv"), date.stats = c("Nmiss", "median", "range"), selectall.stats = c("Nmiss", "countpct"), stats.labels = list(), digits = 3L, digits.count = 0L, digits.pct = 1L, digits.p = 3L, format.p = TRUE, digits.n = 0L, conf.level = 0.95, wilcox.correct = FALSE, wilcox.exact = NULL, chisq.correct = FALSE, simulate.p.value = FALSE, B = 2000, times = 1:5, ... )
test |
logical, telling |
total |
logical, telling |
total.pos |
One of |
test.pname |
character string denoting the p-value column name in |
numeric.simplify, date.simplify |
logical, tell |
cat.simplify, ordered.simplify |
logical, tell |
cat.droplevels |
Should levels be dropped for categorical variables? If set to true, p-values will not be displayed
unless |
numeric.test |
name of test for numeric RHS variables in |
cat.test |
name of test for categorical variables: chisq, fe (Fisher's Exact) |
ordered.test |
name of test for ordered variables: trend |
surv.test |
name of test for survival variables: logrank |
date.test |
name of test for date variables: kwt |
selectall.test |
name of test for date variables: notest |
test.always |
Should the test be performed even if one or more by-group has 0 observations? Relevant for kwt and anova. |
numeric.stats, cat.stats, ordered.stats, surv.stats, date.stats, selectall.stats |
summary statistics to include for the respective class of RHS variables within the levels of the group LHS variable. |
stats.labels |
A named list of labels for all the statistics function names, where the function name is the named element in the list
and the value that goes with it is a string containing the formal name that will be printed in all printed renderings of the output,
e.g., |
digits |
Number of decimal places for numeric values. |
digits.count |
Number of decimal places for count values. |
digits.pct |
Number of decimal places for percents. |
digits.p |
Number of decimal places for p-values. |
format.p |
Logical, denoting whether to format p-values, or character, a |
digits.n |
Number of decimal places for N's in the header. Set it to NA to suppress the N's. |
conf.level |
Numeric, denoting what confidence level to use for confidence intervals.
(See, e.g., |
wilcox.correct, wilcox.exact |
See |
chisq.correct |
logical, correction factor for chisq.test |
simulate.p.value |
logical, simulate p-value for categorical tests (fe and chisq) |
B |
number of simulations to perform for simulation-based p-value |
times |
A vector of times to use for survival summaries. |
... |
additional arguments. |
All tests can be turned off by setting test
to FALSE.
Otherwise, test are set to default settings in this list, or set explicitly in the formula of tableby
.
If format.p
is FALSE
, digits.p
denotes the number of significant digits shown. The
p-values will be in exponential notation if necessary. If format.p
is TRUE
,
digits.p
will determine the number of digits after the decimal point to show. If the p-value
is less than the resulting number of places, it will be formatted to show so. If format.p
is a character string,
it will be treated as a glue
specification: the p-value is exposed as "p", and "digits.p" as "digits.p".
Options for statistics are described more thoroughly in the vignette and are listed in tableby.stats
A list with settings to be used within the tableby
function.
Jason Sinnwell, Beth Atkinson, Ethan Heinzen, Terry Therneau, adapted from SAS Macros written by Paul Novotny and Ryan Lennon
anova
, chisq.test
, tableby
, summary.tableby
,
tableby.stats
.
set.seed(100) ## make 3+ categories for Response mdat <- data.frame(Response=c(0,0,0,0,0,1,1,1,1,1), Sex=sample(c("Male", "Female"), 10,replace=TRUE), Age=round(rnorm(10,mean=40, sd=5)), HtIn=round(rnorm(10,mean=65,sd=5))) ## allow default summaries in RHS variables, and pass control args to ## main function, to be picked up with ... when calling tableby.control outResp <- tableby(Response ~ Sex + Age + HtIn, data=mdat, total=FALSE, test=TRUE) outCtl <- tableby(Response ~ Sex + Age + HtIn, data=mdat, control=tableby.control(total=TRUE, cat.simplify=TRUE, cat.stats=c("Nmiss","countpct"),digits=1)) summary(outResp, text=TRUE) summary(outCtl, text=TRUE)
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