covsum_nested {BiostatsUHNplus} | R Documentation |
Nested version of reportRmd covsum()
Description
Nested version of reportRmd covsum()
Usage
covsum_nested(
data,
covs,
maincov = NULL,
id = NULL,
digits = 1,
numobs = NULL,
markup = TRUE,
sanitize = TRUE,
nicenames = TRUE,
IQR = FALSE,
all.stats = FALSE,
pvalue = TRUE,
effSize = TRUE,
show.tests = TRUE,
nCores = NULL,
nested.test = NULL,
nsim = NULL,
excludeLevels = NULL,
dropLevels = TRUE,
full = TRUE,
digits.cat = 0,
testcont = c("rank-sum test", "ANOVA"),
testcat = c("Chi-squared", "Fisher"),
include_missing = FALSE,
percentage = c("column", "row")
)
Arguments
data |
dataframe containing data |
covs |
character vector with the names of columns to include in table |
maincov |
covariate to stratify table by |
id |
covariates to nest summary by |
digits |
number of digits for summarizing mean data, does not affect p-values |
numobs |
named list overriding the number of people you expect to have the covariate |
markup |
boolean indicating if you want latex markup |
sanitize |
boolean indicating if you want to sanitize all strings to not break LaTeX |
nicenames |
boolean indicating if you want to replace . and _ in strings with a space |
IQR |
boolean indicating if you want to display the inter quantile range (Q1,Q3) as opposed to (min,max) in the summary for continuous variables |
all.stats |
boolean indicating if all summary statistics (Q1,Q3 + min,max on a separate line) should be displayed. Overrides IQR. |
pvalue |
boolean indicating if you want p-values included in the table |
effSize |
boolean indicating if you want effect sizes included in the table. Can only be obtained if pvalue is also requested. |
show.tests |
boolean indicating if the type of statistical used should be shown in a column beside the p-values. Ignored if pvalue=FALSE. |
nCores |
if > 1, specifies number of cores to use for parallel processing for calculating the nested p-value (default: 1). |
nested.test |
specifies test used for calculating nested p-value from afex::mixed function. Either parametric bootstrap method or likelihood ratio test method (default: "LRT"). Parametric bootstrap takes longer. |
nsim |
specifies number of simulations to use for calculating nested p-value with parametric bootstrap method used for nested.test (default: 1000). |
excludeLevels |
a named list of covariate levels to exclude from statistical tests in the form list(varname =c('level1','level2')). These levels will be excluded from association tests, but not the table. This can be useful for levels where there is a logical skip (i.e. not missing, but not presented). Ignored if pvalue=FALSE. |
dropLevels |
logical, indicating if empty factor levels be dropped from the output, default is TRUE. |
full |
boolean indicating if you want the full sample included in the table, ignored if maincov is NULL |
digits.cat |
number of digits for the proportions when summarizing categorical data (default: 0) |
testcont |
test of choice for continuous variables,one of rank-sum (default) or ANOVA |
testcat |
test of choice for categorical variables,one of Chi-squared (default) or Fisher |
include_missing |
Option to include NA values of maincov. NAs will not be included in statistical tests |
percentage |
choice of how percentages are presented, one of column (default) or row |
See Also
fisher.test
,chisq.test
,
wilcox.test
,kruskal.test
,
anova
and mixed