get.summary2: sumamrizes and does association test for 2 or more variables

In arorarshi/utilar: Personalized utility functions used for my analysis

Description

Sumamrize and provide p-value after association test of 2 or more variables. Percentages are reported for discrete variables. Users can choose the type of test they want. For continuous variable median and range are reported if the test specifid is non parametric, mean and standard deviation are reported for a parametric test. For discrete categories we perform Fisher's Exact Test, for continous following options are available - parametric - Students' T-Test or one way ANNOVA, for non-paramteric Wilcoxon Rank sum test or Kruskal Wallis test.

Usage

get.summary2(fac,var,type,test.type="np",skip.test=FALSE, var.n=NULL)

Arguments

fac	vector, a dicrete vector of interest for which association is to be tested against other categorical or continuous variables
var	vector, can be discrete or continuous
type	type=1 - meaning both fac and var are categorical, and Fisher's Exact test will be performed type=2 - var is continous and you can choose from available parameteric (Students' T-Test or one way ANNOVA) and non parametric tests. (Wilcoxon Rank sum test or Kruskal Wallis test.)
test.type	possible values - "np" or "p", Default is "np" (non parametric). Use "p" for parametric tests
skip.test	logical, Default is "TRUE". A association test is always performed. However, if there are too many categories in fac, it might slow down computation required for Fishers Exact test, one can decide to skip test by skip.test=FALSE to prevent limbo.
var.n	character, If a variable name is provided, it will add this to output.

Details

Summary statistics are rounded to nearest 2 decimal points. Note that length of fac and var should be the same. For Wilcoxon Rank sum test ties are handled through wilcox.test function in coin package. workspace parameter in Fisher's Exact test is set to workspace=2e8. All p-values < 0.0001 are replaced with a character string P<0.0001 or otherwise rounded to three decimal points.

Value

fmat	returns a character matrix summarixing fac and var. See examples

Author(s)

Arshi Arora

See Also

get.summary

Examples

#two categorical variables
set.seed(100)
fac<-sample(1:2, 50, replace=TRUE)
var<-sample(1:3, 50, replace=TRUE)
get.summary2(fac,var, type=1,var.n="Example, Type=1" )

#Performing Fisher's Exact test

#|                |1(n=23;46%) |2(n=27;54%) |RowTotal |pval   |
#|:---------------|:-----------|:-----------|:--------|:------|
#|Example, Type=1 |            |            |         |0.5971 |
#|1               |9(39%)      |8(30%)      |17(34%)  |       |
#|2               |7(30%)      |12(44%)     |19(38%)  |       |
#|3               |7(30%)      |7(26%)      |14(28%)  |       |

#continuous with two categories of fac
var<-rnorm(50)
get.summary2(fac, var,  type=2, test.type="p", var.n="2-Way, test.type=p")

#Performing T-Test


#|                   |1           |2           |RowTotal |pval  |
#|:------------------|:-----------|:-----------|:--------|:-----|
#|2-Way, test.type=p |-0.11(1.42) |-0.05(0.99) |         |0.855 |
#|NA                 |0           |0           |         |      |


get.summary2(fac, var,  type=2, test.type="np", var.n="2-Way, test.type=np")
#Performing Wilcoxon Rank Sum test
#                    1                  2                   RowTotal pval
#2-Way, test.type=np "-0.1[-2.27-2.58]" "-0.07[-1.93-1.73]" ""       "0.676"
#NA                  "2.58"             "1.73"              ""       ""


fac<-sample(1:3, 50, replace=TRUE)
get.summary2(fac, var,  type=2, test.type="p",var.n="Example, test.type=p")
#Performing one way ANOVA
#|                     |1           |2          |3         |RowTotal |pval  |
#|:--------------------|:-----------|:----------|:---------|:--------|:-----|
#|Example, test.type=p |-0.46(1.31) |-0.16(0.9) |0.38(1.3) |         |0.132 |
#|NA                   |0           |0          |0         |         |      |

get.summary2(fac, var,  type=2, test.type="np",var.n="Example, test.type=np")

#Performing Kruskal-Wallis test
#|                      |1                 |2                 |3                |RowTotal |pval  |
#|:---------------------|:-----------------|:-----------------|:----------------|:--------|:-----|
#|Example, test.type=np |-0.53[-2.27-2.58] |-0.07[-1.93-1.82] |0.42[-1.74-2.45] |         |0.131 |
#|NA                    |2.58              |1.82              |2.45             |         |      |

arorarshi/utilar documentation built on Feb. 13, 2021, 10:22 a.m.