| title | subtitle | author | date | output | ||||
|---|---|---|---|---|---|---|---|---|
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)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.
You can install R package rrtable with the following command.
if(!require(devtools)){ install.packages("devtools") }
devtools::install_github("cardiomoon/rrtable") You can load the rrtable package with the following R command.
require(rrtable) Sample data sampleData3 is included in rrtable package. You can see the sampleData3 by following 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 "" "" "" "" ...
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 | 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 | |
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(mpgwt*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 |
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%) | |
You can insert a plot into your document.
hist(rnorm(1000))
You can insert a ggplot into a document
ggplot(iris,aes(x=Sepal.Length,y=Sepal.Width,color=Species))+ geom_point() 
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
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) 
You can insert two parallel plots with the following code.
hist(rnorm(1000))
plot(1:10) 
You can get report with HTML format(this file) by following R command.
data2HTML(sampleData3) 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
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
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