base.functions {kyotil}

Some Base Functions

Description

cbinduneven binds together a list of matrixes/dataframes of different lengths, rows are matched by names binary returns binary representation of an integer. binary2 returns binary representatin of an integer with leading 0, the length of string is n. mysystem can call any exe file that is in the PATH f2c convert temperature from f to c/

Usage

mytable (..., exclude = if (useNA == "no") c(NA, NaN), useNA = "ifany", 
  dnn = list.names(...), deparse.level = 1) 

cbinduneven(li)

binary(i)

multi.outer (f, ... ) 

myreshapelong(dat, cols.to.be.stacked, label.cols.to.be.stacked, new.col.name)

binary2(i, n)

f2c(f)

ftoi(f)

keepWarnings(expr)

meanmed(x, na.rm = FALSE)


myaggregate(x, by, FUN, new.col.name = "aggregate.value", ...)

myreshapewide(formula, dat, idvar, keep.extra.col=FALSE)

mysapply(X, FUN, ..., simplify = TRUE, USE.NAMES = TRUE, ret.mat = TRUE)

myscale(x)

mysystem(cmd, ...)

mytapply(X, INDEX, FUN = NULL, ..., simplify = TRUE)

read.sv(file, header = TRUE, ...)

read.tsv(file, header = TRUE, sep = "\t", ...)

table.prop(x,y=NULL,digit=1,style=2,whole.table.add.to.1=FALSE,useNA="ifany",
    add.perc=FALSE, add.total.column = FALSE)

table.cases  (case,group,include.all=TRUE,desc="cases")
table.cases.3(case,group1,group2)

unix()

mycor (x, use = "everything", method = c("pearson", "kendall", "spearman"), 
    alternative = c("two.sided", "less", "greater"), exact = NULL, 
    conf.level = 0.95, continuity = FALSE, 
    digits.coef=2, digits.pval=3,
    ...) 

Arguments

exclude

exclude

dnn

dnn

deparse.level

deparse.level

add.total.column

tbdi

use

tbdi

method

tbdi

alternative

tbdi

exact

tbdi

conf.level

tbdi

continuity

tbdi

digits.coef

tbdi

digits.pval

tbdi

cols.to.be.stacked

tbdi

label.cols.to.be.stacked

tbdi

li

a list

i

tbdi

n

tbdn

f

In multi.out, f is a function.

case

vector of 0/1

group

vector of multi-group indicators

formula

a formula object.

expr

tbdexpr

x

tbdx

na.rm

tbdna.rm

desc

tbdby

by

tbdby

whole.table.add.to.1

Boolean

new.col.name

tbdnew.col.name

...

tbd...

dat

tbddat

idvar

tbdidvar

X

tbdX

simplify

tbdsimplify

USE.NAMES

tbdUSE.NAMES

ret.mat

tbdret.mat

cmd

tbdcmd

INDEX

tbdINDEX

file

tbdfile

header

tbdheader

sep

tbdsep

y

tbdy

digit

tbddigit

style

tbdstyle

FUN

tbdFUN

keep.extra.col

tbdFUN

useNA

tbdFUN

add.perc

tbdFUN

include.all

tbdFUN

group1

tbdFUN

group2

tbdFUN

Examples

binary(5) ###  101
binary2(5, 4)

a=data.frame("x"=1:2)
b=data.frame("y"=3:5);#rownames(b)[3]=""
cbinduneven(list(a,b))

## Not run: 
# the formula in myreshapewide can only have one variable in the right hand side
    myreshapewide(fi~week, dat, c("ptid","stim"))

    myreshapelong(dat.201.neut, cols.to.be.stacked=c("MN.3","SF162","SVA.MLV"), 
        label.cols.to.be.stacked="antigen", new.col.name="y")

    myaggregate(subset(dat.poc, select=c(HIV, trt)), list(dat.poc$f), function(x) 
      with(x, c(fisher.test(HIV, trt)$estimate, fisher.test(HIV, trt)$p.value)))



## End(Not run)