Draw a hazard ratio plot

Description

Draw a hazard ratio plot

Usage

HRplot(
  out,
  type = 1,
  xlab = "",
  ylab = "",
  show.OR = TRUE,
  show.CI = FALSE,
  sig.level = 1,
  cex = 1.2,
  lwd = 2,
  pch = 18,
  col = NULL,
  ...
)

Arguments

Value

This function return NULL invisibly and draw graphs

Examples

require(survival)
attach(colon)
colon$TS=Surv(time,status==1)
out=mycph(TS~.,data=colon)
out
HRplot(out)
## Not run: 
HRplot(out,type=1,pch=2,col=c("blue","red"))
HRplot(out,type=2,show.CI=TRUE,pch=2,cex=2,main="Hazard ratios of all individual variables")

## End(Not run)

Plot for odds ratios for a S3 object of glm

Description

Plot for odds ratios for a S3 object of glm

Usage

ORplot(
  x,
  type = 1,
  xlab = "",
  ylab = "",
  show.OR = TRUE,
  show.CI = FALSE,
  sig.level = 1,
  cex = 1.2,
  lwd = 2,
  pch = 18,
  col = NULL,
  ...
)

Arguments

Value

This function return NULL invisibly and draw graphs

Examples

require(survival)
data(colon)
out1=glm(status~sex+age+rx+obstruct+node4,data=colon)
out2=glm(status~rx+node4,data=colon)
ORplot(out1,type=2,show.CI=TRUE,xlab="This is xlab",main="Main Title")
ORplot(out2,type=1,main="Main Title")
ORplot(out1,type=2,show.CI=TRUE,main="Main Title")
ORplot(out1,type=3,show.CI=TRUE,main="Main Title",sig.level=0.05)
ORplot(out1,type=3,show.CI=TRUE,main="Main Title",sig.level=0.05,
       pch=1,cex=2,lwd=4,col=c("red","blue"))

A sub function for ORplot and HRplot

Description

Plot for odds ratios for a S3 object of glm

Usage

ORplot.sub(
  result,
  type = 1,
  xlab = "",
  ylab = "",
  show.OR = TRUE,
  show.CI = FALSE,
  sig.level = 1,
  cex = 1.2,
  lwd = 2,
  pch = 18,
  col = NULL,
  ...
)

Arguments

Value

This function return NULL invisibly and draw graphs

Demographic data of 857 patients with ACS

Description

A dataset containing demographic data and laboratory data of 857 patients with acute coronary syndrome(ACS).

Format

A data frame with 857 rows and 17 variables:

age

patient age in years

sex

"Male" or "Female"

cardiogenicShock

"No" or "Yes"

entry

vascular access route, either "Femoral" or "Radial"

Dx

Final diagnosis, One of the followings : STEMI, NSTEMI or Unstable Angina

EF

ejection fraction, percentage by echocardiography

height

height in centimeter

weight

weight in kilogram

BMI

body mass index in kg/m2

obesity

obesity, "No" or "Yes"

TC

total cholesterol level in mg/dL

LDLC

low density lipoprotein cholesterol level in mg/dL

HDLC

high density lipoprotein cholesterol level in mg/dL

TG

triglyceride level in mg/dL

DM

history of diabetes mellitus,"No" or "Yes"

HBP

history of hypertension,"No" or "Yes"

smoking

history of smoking, One of the followings : "Never","Ex-smoker","Smoker"

Change numbers into formatted numbers

Description

Change numbers into formatted numbers

Usage

addComma(x)

## S3 method for class 'mytable'
addComma(x)

## S3 method for class 'mytable.df'
addComma(x)

## S3 method for class 'cbind.mytable'
addComma(x)

## S3 method for class 'data.frame'
addComma(x)

## S3 method for class 'character'
addComma(x)

Arguments

Methods (by class)

• mytable: S3 method for class mytable

• mytable.df: S3 method for class mytable.df

• cbind.mytable: S3 method for class cbind.mytable

• data.frame: S3 method for class data.frame

• character: S3 method for class character

Examples

## Not run: 
require(stringr)
require(magrittr)
require(ggplot2)
mytable(cut~.,data=diamonds) %>% addComma
x=mytable(Dx~sex,data=acs)
addComma(x)

## End(Not run)

Add value labels to the data.frame

Description

Add value labels to the data.frame

Usage

addLabelDf(data, mapping = NULL)

Arguments

Perform chisq.test or fisher test

Description

Perform chisq.test or fisher test

Usage

cat.test(x, mode = 1, ...)

Arguments

cbind function for class "mytable"

Description

cbind function for class "mytable"

Usage

## S3 method for class 'mytable'
cbind(..., caption, y = NULL)

Arguments

Internal mytable functions

Description

Internal mytable functions These are not to be called by the user

Usage

centerprint(x, ..., width = 10)

Arguments

Change column names with labels

Description

Change column names with labels

Usage

changeColnameLabel(data)

Arguments

Convert number to formatted number

Description

Convert number to formatted number

Usage

comma(x, ...)

Arguments

Compress an object of class mytable or cbind.mytable

Description

Compress an object of class mytable or cbind.mytable

Usage

compress(x, no = 2, add.label = TRUE)

## S3 method for class 'mytable'
compress(x, no = 2, add.label = TRUE)

## S3 method for class 'cbind.mytable'
compress(x, no = 2, add.label = TRUE)

## S3 method for class 'data.frame'
compress(x, no = 2, add.label = TRUE)

Arguments

Methods (by class)

• mytable: S3 method for class mytable

• cbind.mytable: S3 method for class cbind.mytable

• data.frame: S3 method for class data.frame

Examples

require(stringr)
require(magrittr)
mytable(acs) %>% compress
mytable(Dx~.,data=acs) %>% compress
## Not run: 
require(ztable)
mytable(Dx~.,data=acs) %>% compress %>% ztable
mytable(Dx+sex~.,data=acs) %>% compress

## End(Not run)

Delete rows of class mytable object

Description

Delete rows of class mytable object

Usage

deleteRows(x, rows)

Arguments

Make Kernel density plot

Description

Make Kernel density plot

Usage

densityplot(formula, data, main = "", xlab = "", ylab = "", ...)

Arguments

Value

This function return NULL invisibly and draw graphs.

Examples

  require(moonBook)
  data(acs)
  densityplot(age~Dx,data=acs)

Extract hazard ratio from a data.frame

Description

Extract hazard ratio from a data.frame

Usage

extractHR(x, digits = 2)

Arguments

Value

a data.frame consist of hazard ratio and 95 the p values.

Examples

require(survival)
data(cancer)
fit=coxph(Surv(time,status)~age+sex+obstruct+perfor,data=colon)
extractHR(fit)

Extract kind of an object of class mytable

Description

Extract kind of an object of class mytable

Usage

extractKind(df)

Arguments

Extract the odds ratios from a S3 object of glm

Description

Extract the odds ratios from a S3 object of glm

Usage

extractOR(x, digits = 2, method = "default")

Arguments

Value

A data.frame consist of odds ratios and 95 p values

Examples

data(cancer,package="survival")
x=glm(status~rx+sex+age+obstruct+nodes,data=colon,family="binomial")
extractOR(x)

Add column labels to the data.frame

Description

Add column labels to the data.frame

Usage

getLabel(data, colname, use.column.label = TRUE)

Arguments

extract variable name from mapping, aes

Description

extract variable name from mapping, aes

Usage

getMapping(mapping, varname)

Arguments

Value

variable name in character

Examples

require(ggplot2)
mapping=aes(colour=sex)
getMapping(mapping,"colour")
getMapping(mapping,"x")

Internal mytable functions

Description

Internal mytable functions These are not to be called by the user

Usage

my.chisq.test(x, y, mydata, catMethod = 2)

Arguments

Internal mytable functions

Description

Internal mytable functions These are not to be called by the user

Usage

my.t.test(y, x)

Arguments

Perform coxph of individual expecting variables

Description

Perform coxph of individual expecting variables

Usage

mycph(formula, data, digits = 2)

Arguments

Value

a data.frame consist of hazard ratio and 95% confidence intervals and the p values.

Examples

require(survival)
data(cancer)
attach(colon)
colon$TS=Surv(time,status==1)
out=mycph(TS~.,data=colon)
out
HRplot(out,type=2,show.CI=TRUE,main="Hazard ratios of all individual variables")

Export to csv file for class "mytable" or "cbind.mytable"

Description

Export to csv file for class "mytable" or "cbind.mytable"

Usage

mycsv(x, row.names = FALSE, ...)

Arguments

Examples

## Not run: 
require(moonBook)
res=mytable(sex~age+DM,data=acs)
mycsv(res,file="test.csv")
mycsv(summary(res),file="testsummary.csv")

## End(Not run)

Export to csv file for class "cbind.mytable"

Description

Export to csv file for class "cbind.mytable"

Usage

## S3 method for class 'cbind.mytable'
mycsv(x, row.names = FALSE, ...)

Arguments

Examples

## Not run: 
require(moonBook)
res1=mytable(sex+Dx~age+DM,data=acs)
mycsv(res1,file="test1.csv")
mycsv(summary(res1),file="testsummary1.csv")

## End(Not run)

Export to csv file for class "mytable"

Description

Export to csv file for class "mytable"

Usage

## S3 method for class 'mytable'
mycsv(x, row.names = FALSE, ...)

Arguments

Examples

## Not run: 
require(moonBook)
res=mytable(sex~age+DM,data=acs)
mycsv(res,file="test.csv")
mycsv(summary(res),file="testsummary.csv")
mycsv=function(x,row.names=FALSE) UseMethod("mycsv")

## End(Not run)

Export to html file for class "mytable" or "cbind.mytable" of "data.frame"

Description

Export to html file for class "mytable" or "cbind.mytable" of "data.frame"

Usage

myhtml(x, caption = NULL, rownames = TRUE)

## Default S3 method:
myhtml(x, caption = NULL, rownames = TRUE)

## S3 method for class 'mytable'
myhtml(x, caption = NULL, rownames = TRUE)

## S3 method for class 'cbind.mytable'
myhtml(x, caption = NULL, rownames = TRUE)

Arguments

Methods (by class)

• default:

• mytable:

• cbind.mytable:

Examples

require(moonBook)
res=mytable(sex~age+Dx,data=acs)
myhtml(res)
res1=mytable(sex+Dx~.,data=acs)
myhtml(res1)
x=head(iris)
myhtml(x)
myhtml(x,caption="Table 1. myhtml Test")
myhtml(x,caption="Table 1. myhtml Test",rownames=FALSE)

Print my html style

Description

Print my html style

Usage

myhtmlHead()

Exporting "cbind.mytable","mytable" to LaTeX format

Description

Exporting "cbind.mytable","mytable" to LaTeX format

Usage

mylatex(
  myobj,
  size = 5,
  caption = NULL,
  caption.placement = "top",
  caption.position = "c"
)

## Default S3 method:
mylatex(
  myobj,
  size = 5,
  caption = NULL,
  caption.placement = "top",
  caption.position = "c"
)

## S3 method for class 'mytable'
mylatex(
  myobj,
  size = 5,
  caption = NULL,
  caption.placement = "top",
  caption.position = "c"
)

## S3 method for class 'cbind.mytable'
mylatex(
  myobj,
  size = 5,
  caption = NULL,
  caption.placement = "top",
  caption.position = "c"
)

Arguments

Methods (by class)

• default: Exporting "cbind.mytable","mytable" to LaTeX format

• mytable: Exporting "cbind.mytable","mytable" to LaTeX format

• cbind.mytable: Exporting "cbind.mytable","mytable" to LaTeX format

Examples

require(moonBook)
out=mytable(sex~.,data=acs)
mylatex(out)
out1=mytable(sex+Dx~.,data=acs)
mylatex(out1,size=6)

Produce table for descriptive statistics

Description

Produce table for descriptive statistics by groups for several variables easily. Depending on the nature of these variables, different descriptive statistical methods were used(t-test, ANOVA,Kruskal-Wallis, chisq, Fisher,...)

Usage

mytable(x, ...)

## S3 method for class 'formula'
mytable(x, ...)

## S3 method for class 'data.frame'
mytable(x, ...)

Arguments

Methods (by class)

• formula: S3 method for formula

• data.frame: S3 method for data.frame

Examples

mytable(acs)
mytable(~age+sex,data=acs)
mytable(Dx~age+sex+height+weight+TC+TG+HDLC,data=acs,method=3,digits=2)
mytable(am+cyl~.,data=mtcars)
out=mytable(sex~.,data=acs)
out
summary(out)
## Not run: 
require(ztable)
ztable(out)

## End(Not run)
mytable(acs)

Produce combined table for descriptive statistics

Description

Produce table for descriptive statistics by two grouping variables for several variables easily. Depending on the nature of these variables, different descriptive statistical methods were used(t-test, ANOVA,Kruskal-Wallis, chisq, Fisher,...)

Usage

mytable2(
  formula,
  data,
  use.labels = TRUE,
  use.column.label = TRUE,
  max.ylev = 5,
  maxCatLevel = 20,
  digits = 2,
  method = 1,
  catMethod = 2,
  show.all = FALSE,
  exact = FALSE,
  show.total = FALSE,
  origData = NULL
)

Arguments

Value

An object of class "cbind.mytable"

Convert mytable object to data.frame

Description

Add N number into data.frame

Usage

mytable2df(x)

Arguments

Value

a data.frame with N number

Prepare mytable object to data.frame ready to html

Description

Add N number into data.frame

Usage

mytable2html(x)

Arguments

Value

a data.frame with N number

make mytable from data.frame

Description

make mytable from data.frame

Usage

mytable_df(
  x,
  use.labels = TRUE,
  use.column.label = TRUE,
  max.ylev = 5,
  maxCatLevel = 20,
  digits = 1,
  method = 1,
  show.all = FALSE
)

Arguments

Value

An object of class "mytable.df". 'print' returns a table for descriptive statistics.

Produce table for descriptive statistics

Description

Produce table for descriptive statistics by groups for several variables easily. Depending on the nature of these variables, different descriptive statistical methods were used(t-test, ANOVA,Kruskal-Wallis, chisq, Fisher,...)

Usage

mytable_sub(
  x,
  data,
  use.labels = TRUE,
  use.column.label = TRUE,
  max.ylev = 5,
  maxCatLevel = 20,
  digits = 1,
  method = 1,
  catMethod = 2,
  show.all = FALSE,
  exact = FALSE,
  show.total = FALSE,
  missing = FALSE
)

Arguments

Value

An object of class "mytable". 'print' returns a table for descriptive statistics. 'summary' returns a table with all statistical values.

Internal mytable functions

Description

Internal mytable functions These are not to be called by the user

Usage

mytable_sub2(
  y,
  x,
  data,
  max.ylev = 5,
  maxCatLevel = 20,
  method = 1,
  catMethod = 2,
  show.total = FALSE,
  origData
)

Arguments

Internal mytable functions

Description

Internal mytable functions These are not to be called by the user

Usage

num_summary(x)

Arguments

Internal mytable functions

Description

Internal mytable functions These are not to be called by the user

Usage

obj2linecount(myobj)

Arguments

Internal mytable functions

Description

Internal mytable functions These are not to be called by the user

Usage

p2sig(value)

Arguments

Print function for class "cbind.mytable"

Description

Print function for class "cbind.mytable"

Usage

## S3 method for class 'cbind.mytable'
print(x, ...)

Arguments

Print function for class "mytable"

Description

Print function for class "mytable"

Usage

## S3 method for class 'mytable'
print(x, ...)

Arguments

Print an object of mytable.df

Description

Print an object of mytable.df

Usage

## S3 method for class 'mytable.df'
print(x, ...)

Arguments

Internal mytable functions

Description

Internal mytable functions These are not to be called by the user

Usage

printmytable2(obj, digits = 1)

Arguments

Subfunction used in mylatex

Description

Subfunction used in mylatex

Usage

r(string)

Arguments

Demographic data of 115 patients performing IVUS(intravascular ultrasound) examination of a radial artery.

Description

A dataset containing demographic data and laboratory data of 115 patients performing IVUS(intravascular ultrasound) examination of a radial artery after tansradial coronary angiography.

Format

A data frame with 115 rows and 15 variables:

male

if Male, 1; if Female 0

age

patient age in years

height

height in centimeter

weight

weight in kilogram

HBP

history of hypertension, 1 for yes or 0 for no

DM

history of diabetes mellitus, 1 for yes or 0 for no

smoking

history of smoking, One of the followings : "non-smoker","ex-smoker","smoker"

TC

total cholesterol level in mg/dL

TG

triglyceride level in mg/dL

HDL

high density lipoprotein cholesterol level in mg/dL

LDL

low density lipoprotein cholesterol level in mg/dL

hsCRP

high-sensitive C reactive protein

NTAV

normalized total atheroma volume measured by IVUS in cubic mm

PAV

percent atheroma volume in percentage

sex

Factor with two levels; "Male" or "Female"

rank a numeric vector and returns a new ordinal vector

Description

rank a numeric vector and returns a new ordinal vector

Usage

rank2group(y, k = 4)

Arguments

Value

a ordinal vector(numeric) with the same length of y

Examples

require(ggplot2)
data(diamonds)
diamonds$PriceGroup=rank2group(diamonds$price,4)
table(diamonds$PriceGroup)
aggregate(price~PriceGroup,data=diamonds,range)

diamonds$PriceGroup3=rank2group(diamonds$price,3)
table(diamonds$PriceGroup3)
aggregate(price~PriceGroup3,data=diamonds,range)
diamonds$PriceGroup5=rank2group(diamonds$price,5)
table(diamonds$PriceGroup5)
aggregate(price~PriceGroup5,data=diamonds,range)

Internal mytable functions

Description

Internal mytable functions These are not to be called by the user

Usage

reprint(x, times)

Arguments

Internal mytable functions

Description

Internal mytable functions These are not to be called by the user

Usage

space(num)

Arguments

Summarizing function for class "cbind.mytable"

Description

Summarizing function for class "cbind.mytable"

Usage

## S3 method for class 'cbind.mytable'
summary(object, ...)

Arguments

Examples

out=mytable(am+cyl~.,data=mtcars)
summary(out)

Summarizing function for class "mytable"

Description

Summarizing function for class "mytable"

Usage

## S3 method for class 'mytable'
summary(object, ...)

Arguments

Examples

out=mytable(am~.,data=mtcars)
summary(out)

Find valid string among character vector from approximate string

Description

Find valid string among character vector from approximate string

Usage

validColname(pattern, x)

Arguments

Value

returns NA in case of no matched string found or a character string in string vector x

Examples

a="dx"
b=c("Age","Sex","Dx")
validColname(a,b)