R package rrtable

Reproducible Research with a Table of R codes

Keon-Woong Moon

2018-04-15

require(moonBook)
require(ztable)
require(rrtable)
require(ggplot2)

Introduction

If you are a data scientist or researcher, you will certainly be interested in reproducible research. R package rrtable makes it possible to make reports with HTML, LaTex, MS word or MS Powerpoint formats from a table of R codes.

Package Installation

You can install R package rrtable with the following command.

if(!require(devtools)){ install.packages("devtools") }
devtools::install_github("cardiomoon/rrtable") 

Package Loading

You can load the rrtable package with the following R command.

require(rrtable) 

Sample Data

Sample data sampleData3 is included in rrtable package. You can see the sampleData3 by folllowing R command.

str(sampleData3) 
'data.frame':   15 obs. of  5 variables:
 $ type  : chr  "title" "subtitle" "author" "text" ...
 $ title : chr  "" "" "" "Introduction" ...
 $ text  : chr  "R package `rrtable`" "Reproducible Research with a Table of R codes" "Keon-Woong Moon" "If you are a data scientist or researcher, you will certainly be interested in reproducible research. R package"| __truncated__ ...
 $ code  : chr  "" "" "" "" ...
 $ option: chr  "" "" "" "" ...

Paragraph

You can make a paragraph with this data

df2flextable2( sampleData3 ,vanilla= FALSE )

type

title

text

code

option

title

R package rrtable

subtitle

Reproducible Research with a Table of R codes

author

Keon-Woong Moon

text

Introduction

If you are a data scientist or researcher, you will certainly be interested in reproducible research. R package rrtable makes it possible to make reports with HTML, LaTex, MS word or MS Powerpoint formats from a table of R codes.

header2

Package Installation

You can install R package rrtable with the following command.

if(!require(devtools)){ install.packages(“devtools”) } devtools::install_github(“cardiomoon/rrtable”)

echo=TRUE, eval=FALSE

header2

Package Loading

You can load the rrtable package with the following R command.

require(rrtable)

echo=TRUE

header2

Sample Data

Sample data sampleData3 is included in rrtable package. You can see the sampleData3 by folllowing R command.

str(sampleData3)

echo=TRUE, eval=TRUE

Data

Paragraph

You can make a paragraph with this data

sampleData3

landscape=TRUE

mytable

mytable object

You can add mytable object with the following R code.

mytable(Dx~.,data=acs)

plot

Plot

You can insert a plot into your document.

plot(Sepal.Width~Sepal.Length,data=iris)

ggplot

ggplot

You can insert a ggplot into a document

ggplot(iris,aes(x=Sepal.Length,y=Sepal.Width,color=Species))+ geom_point()

Rcode

R code

You can insert the result of R code. For example, you can insert the result of regression analysis.

fit=lm(mpg~wt*hp,data=mtcars) summary(fit)

2ggplots

Two ggplots

You can insert two parallel ggplots with the following code.

ggplot(iris,aes(Sepal.Length,Sepal.Width))+geom_point() ggplot(iris,aes(Sepal.Length,Sepal.Width,colour=Species))+ geom_point()+guides(colour=FALSE)

2plots

Two plots

You can insert two parallel plots with the following code.

hist(rnorm(1000)) plot(1:10)

header2

HTML Report

You can get report with HTML format(this file) by following R command.

data2HTML(sampleData3)

echo=TRUE, eval=FALSE

mytable object

You can add mytable object with the following R code.

mytable2flextable( mytable(Dx~.,data=acs) ,vanilla= FALSE )

Dx

NSTEMI

STEMI

Unstable.Angina

p

(N=153)

(N=304)

(N=400)

age

64.3 ± 12.3

62.1 ± 12.1

63.8 ± 11.0

0.073

sex

0.012

- Female

50 (32.7%)

84 (27.6%)

153 (38.2%)

- Male

103 (67.3%)

220 (72.4%)

247 (61.8%)

cardiogenicShock

< 0.001

- No

149 (97.4%)

256 (84.2%)

400 (100.0%)

- Yes

4 ( 2.6%)

48 (15.8%)

0 ( 0.0%)

entry

0.001

- Femoral

58 (37.9%)

133 (43.8%)

121 (30.2%)

- Radial

95 (62.1%)

171 (56.2%)

279 (69.8%)

EF

55.0 ± 9.3

52.4 ± 9.5

59.2 ± 8.7

< 0.001

height

163.3 ± 8.2

165.1 ± 8.2

161.7 ± 9.7

< 0.001

weight

64.3 ± 10.2

65.7 ± 11.6

64.5 ± 11.6

0.361

BMI

24.1 ± 3.2

24.0 ± 3.3

24.6 ± 3.4

0.064

obesity

0.186

- No

106 (69.3%)

209 (68.8%)

252 (63.0%)

- Yes

47 (30.7%)

95 (31.2%)

148 (37.0%)

TC

193.7 ± 53.6

183.2 ± 43.4

183.5 ± 48.3

0.057

LDLC

126.1 ± 44.7

116.7 ± 39.5

112.9 ± 40.4

0.004

HDLC

38.9 ± 11.9

38.5 ± 11.0

37.8 ± 10.9

0.501

TG

130.1 ± 88.5

106.5 ± 72.0

137.4 ± 101.6

< 0.001

DM

0.209

- No

96 (62.7%)

208 (68.4%)

249 (62.2%)

- Yes

57 (37.3%)

96 (31.6%)

151 (37.8%)

HBP

0.002

- No

62 (40.5%)

150 (49.3%)

144 (36.0%)

- Yes

91 (59.5%)

154 (50.7%)

256 (64.0%)

smoking

< 0.001

- Ex-smoker

42 (27.5%)

66 (21.7%)

96 (24.0%)

- Never

50 (32.7%)

97 (31.9%)

185 (46.2%)

- Smoker

61 (39.9%)

141 (46.4%)

119 (29.8%)

Plot

You can insert a plot into your document.

hist(rnorm(1000))

ggplot

You can insert a ggplot into a document

ggplot(iris,aes(x=Sepal.Length,y=Sepal.Width,color=Species))+ geom_point() 

R code

You can insert the result of R code. For example, you can insert the result of regression analysis.

fit=lm(mpg~wt*hp,data=mtcars)
summary(fit) 

Call:
lm(formula = mpg ~ wt * hp, data = mtcars)

Residuals:
    Min      1Q  Median      3Q     Max 
-3.0632 -1.6491 -0.7362  1.4211  4.5513 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept) 49.80842    3.60516  13.816 5.01e-14 ***
wt          -8.21662    1.26971  -6.471 5.20e-07 ***
hp          -0.12010    0.02470  -4.863 4.04e-05 ***
wt:hp        0.02785    0.00742   3.753 0.000811 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 2.153 on 28 degrees of freedom
Multiple R-squared:  0.8848,    Adjusted R-squared:  0.8724 
F-statistic: 71.66 on 3 and 28 DF,  p-value: 2.981e-13

Two ggplots

You can insert two parallel ggplots with the following code.

ggplot(iris,aes(Sepal.Length,Sepal.Width))+geom_point()
ggplot(iris,aes(Sepal.Length,Sepal.Width,colour=Species))+ geom_point()+guides(colour=FALSE) 

Two plots

You can insert two parallel plots with the following code.

hist(rnorm(1000))
plot(1:10) 

HTML Report

You can get report with HTML format(this file) by following R command.

data2HTML(sampleData3) 

MS word document

You can get a report with MS word format.

data2docx(sampleData3) 

You can download sample data: sampleData3.docx - view with office web viewer

data2docx(sampleData2) 

You can download sample data: sampleData2.docx - view with office web viewer

MS powerpoint document

You can get a report with MS word format.

data2pptx(sampleData3) 

You can download sample data: sampleData3.pptx - view with office web viewer

data2pptx(sampleData2) 

You can download sample data: sampleData2.pptx - view with office web viewer

pdf document

You can get a report with pdf format.

data2pdf(sampleData3) 

You can download sample data: sampleData3.pdf

data2pdf(sampleData2) 

You can download sample data: sampleData2.pdf