Compute Descriptive Summary Statistics of Groups in a cgOneFactorData object
Create a table of quantiles and other summary statistics of the data in a
One of three valid values:
Additional arguments. Currently only one is valid:
The returned table contains quantiles, means, sample sizes, and
estimates of variability for each group. If censored data are present,
the estimated quantiles accomodate that with the Kaplan-Meier
method, following Gentleman and Crowley (1991) .
The number of censored / incomplete and number of complete observations
are also included when censored data is present in any of the groups.
logscale option is specified (either explicitly, or implicitly
cgOneFactorData object), then the geometric mean and
geometric standard error for each group are also included. See the Value section
below for details.
Creates an object of class
cgOneFactorDescriptiveTable, with the
The table of descriptive summary statistics for each group. See below for the data frame structure of the table.
A list of settings carried from the
dataobject. These are used for the
print.cgOneFactorDescriptiveTablemethod, invoked for example when
The data frame structure of the descriptive table in a
slot consists of
row.names that specify the group, and these columns:
The sample size of the group.
The minimum value of the group.
The 25th percentile of the group, estimated with the
The median value of the group.
The 75th percentile of the group, estimated with the
The maximum value of the group.
The arithmetic mean value of the group.
The standard deviation value of the group.
The standard error value of the group.
logscale=TRUE, then two additional columns are added:
The geometric mean value of the group.
The estimated standard error associated withthe geometric mean. This is calculated with the Delta Method, and will particularly lose accuracy in its useful approximation once the standard error in the log scale exceeds 0.50. A warning message is issued when this occurs.
If censored data are present in the
then two more columns are added:
The number of censored / incomplete observations.
The number of complete observations.
ncomplete quantities will add up
n above and be placed
adjacent to it.
The presence of censored observations will convert columns such as the
Max to character values, with the appropriate ">"
and "<" symbols for right-censoring and left-censoring, respectively.
For censored data, Kaplan-Meier estimates are used for the quantiles, as
proposed by Gentleman and Crowley (1991). The survreg::
conventions are followed for interpolation of these quantiles.
With enough censored data
observations in a group, certain quantiles may not be estimable. If
any censored observations are present, the mean, geometric mean,
and associated standard errors will not be
calculated. The <NA> character representation is used.
Contact email@example.com for bug reports, questions, concerns, and comments.
Bill Pikounis [aut, cre, cph], John Oleynick [aut], Eva Ye [ctb]
Gentleman, R.C. and Crowley, J. (1991). "Graphical Methods for Censored Data", Journal of the American Statistical Association, Volume 86, 678-683.
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data(canine) canine.data <- prepareCGOneFactorData(canine, format="groupcolumns", analysisname="Canine", endptname="Prostate Volume", endptunits=expression(plain(cm)^3), digits=1, logscale=TRUE, refgrp="CC") descriptiveTable(canine.data) ## Remove the geometric mean and standard error columns descriptiveTable(canine.data, logscale=FALSE) ## Censored Data data(gmcsfcens) gmcsfcens.data <- prepareCGOneFactorData(gmcsfcens, format="groupcolumns", analysisname="cytokine", endptname="GM-CSF (pg/ml)", logscale=TRUE) descriptiveTable(gmcsfcens.data)