title: "Package moonBook" author: "Keon-Woong Moon" date: "2017-11-11" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{package moonBook} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc}
Function "mytable"" produce table for descriptive analysis easily. It is most useful to make table to describe baseline characteristics common in medical research papers.
require(moonBook)
data(acs)
mytable(Dx~.,data=acs)
Descriptive Statistics by '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 0.000
- 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 0.000
height 163.3 ± 8.2 165.1 ± 8.2 161.7 ± 9.7 0.000
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 0.000
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 0.000
- 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%)
-----------------------------------------------------------------
The first argument of function mytable
is an object of class formula
. Left side of ~ must contain the name of one grouping variable or two grouping variables in an additive way(e.g. sex+group~), and the right side of ~ must have variables in an additive way. .
is allowed on the right side of formula which means all variables in the data.frame specified by the 2nd argument data
. The sample data 'acs' containing demographic data and laboratory data of 857 patients with acute coronary syndrome(ACS). For more information about the data acs, type ?acs in your R console.
str(acs)
'data.frame': 857 obs. of 17 variables:
$ age : int 62 78 76 89 56 73 58 62 59 71 ...
$ sex : chr "Male" "Female" "Female" "Female" ...
$ cardiogenicShock: chr "No" "No" "Yes" "No" ...
$ entry : chr "Femoral" "Femoral" "Femoral" "Femoral" ...
$ Dx : chr "STEMI" "STEMI" "STEMI" "STEMI" ...
$ EF : num 18 18.4 20 21.8 21.8 22 24.7 26.6 28.5 31.1 ...
$ height : num 168 148 NA 165 162 153 167 160 152 168 ...
$ weight : num 72 48 NA 50 64 59 78 50 67 60 ...
$ BMI : num 25.5 21.9 NA 18.4 24.4 ...
$ obesity : chr "Yes" "No" "No" "No" ...
$ TC : num 215 NA NA 121 195 184 161 136 239 169 ...
$ LDLC : int 154 NA NA 73 151 112 91 88 161 88 ...
$ HDLC : int 35 NA NA 20 36 38 34 33 34 54 ...
$ TG : int 155 166 NA 89 63 137 196 30 118 141 ...
$ DM : chr "Yes" "No" "No" "No" ...
$ HBP : chr "No" "Yes" "Yes" "No" ...
$ smoking : chr "Smoker" "Never" "Never" "Never" ...
You can choose the grouping variable(s) and row-variable(s) with the formula
.
mytable(sex~age+Dx,data=acs)
Descriptive Statistics by 'sex'
__________________________________________________
Female Male p
(N=287) (N=570)
--------------------------------------------------
age 68.7 ± 10.7 60.6 ± 11.2 0.000
Dx 0.012
- NSTEMI 50 (17.4%) 103 (18.1%)
- STEMI 84 (29.3%) 220 (38.6%)
- Unstable Angina 153 (53.3%) 247 (43.3%)
--------------------------------------------------
You can choose row-variable(s) with .
and +
and -
and variable name in an additive way.
mytable(am~.-hp-disp-cyl-carb-gear,data=mtcars)
Descriptive Statistics by 'am'
____________________________________
0 1 p
(N=19) (N=13)
------------------------------------
mpg 17.1 ± 3.8 24.4 ± 6.2 0.000
drat 3.3 ± 0.4 4.0 ± 0.4 0.000
wt 3.8 ± 0.8 2.4 ± 0.6 0.000
qsec 18.2 ± 1.8 17.4 ± 1.8 0.206
vs 0.556
- 0 12 (63.2%) 6 (46.2%)
- 1 7 (36.8%) 7 (53.8%)
------------------------------------
By default continuous variables are analyzed as normal-distributed and are described with mean and standard deviation. To change default options, you can use the method
argument. Possible values of method
argument are:
When continuous variables are analyzed as non-normal, they are described with median and interquartile range.
mytable(sex~height+weight+BMI,data=acs,method=3)
Descriptive Statistics by 'sex'
_____________________________________________________
Female Male p
(N=287) (N=570)
-----------------------------------------------------
height 155.0 [150.0;158.0] 168.0 [164.0;172.0] 0.000
weight 58.0 [50.0;63.0] 68.0 [62.0;75.0] 0.000
BMI 24.0 [22.1;26.2] 24.2 [22.2;26.2] 0.471
-----------------------------------------------------
Because the method
argument is selected as 3, a Shapiro-Wilk test normality test is used to decide if the variable is normal or non-normal distributed. Note that height
and BMI
was described as mean $\pm$ sd, whereas the weight was described as median and interquartile range.
In many cases, categorical variables are usually coded as numeric. For example, many people usually code 0 and 1 instead of "No" and "Yes". Similarly, factor variables with three or four levels are coded 0/1/2 or 0/1/2/3. In many cases, if we analyze these variables as continuous variables, we are not able to get the right result. In mytable
, variables with less than five unique
values are treated as a categorical variables.
mytable(am~.,data=mtcars)
Descriptive Statistics by 'am'
_______________________________________
0 1 p
(N=19) (N=13)
---------------------------------------
mpg 17.1 ± 3.8 24.4 ± 6.2 0.000
cyl 0.013
- 4 3 (15.8%) 8 (61.5%)
- 6 4 (21.1%) 3 (23.1%)
- 8 12 (63.2%) 2 (15.4%)
disp 290.4 ± 110.2 143.5 ± 87.2 0.000
hp 160.3 ± 53.9 126.8 ± 84.1 0.180
drat 3.3 ± 0.4 4.0 ± 0.4 0.000
wt 3.8 ± 0.8 2.4 ± 0.6 0.000
qsec 18.2 ± 1.8 17.4 ± 1.8 0.206
vs 0.556
- 0 12 (63.2%) 6 (46.2%)
- 1 7 (36.8%) 7 (53.8%)
gear 0.000
- 3 15 (78.9%) 0 ( 0.0%)
- 4 4 (21.1%) 8 (61.5%)
- 5 0 ( 0.0%) 5 (38.5%)
carb 2.7 ± 1.1 2.9 ± 2.2 0.781
---------------------------------------
In mtcars
data, all variables are expressed as numeric. But as you can see, cyl
, vs
and gear
is treated as categorical variables. The carb
variables has six unique
values and treated as continuous variables. If you wanted the carb
variable to be treated as categorical variable, you can changed the max.ylev
argument.
mytable(am~carb,data=mtcars,max.ylev=6)
Descriptive Statistics by 'am'
__________________________________
0 1 p
(N=19) (N=13)
----------------------------------
carb 0.284
- 1 3 (15.8%) 4 (30.8%)
- 2 6 (31.6%) 4 (30.8%)
- 3 3 (15.8%) 0 ( 0.0%)
- 4 7 (36.8%) 3 (23.1%)
- 6 0 ( 0.0%) 1 ( 7.7%)
- 8 0 ( 0.0%) 1 ( 7.7%)
----------------------------------
If you wanted to make two separate tables and combine into one table, mytable
is the function of choice. For example, if you wanted to build separate table for female and male patients stratified by presence or absence of DM and combine it,
mytable(sex+DM~.,data=acs)
Descriptive Statistics stratified by 'sex' and 'DM'
_____________________________________________________________________________________
Male Female
-------------------------------- -------------------------------
No Yes p No Yes p
(N=380) (N=190) (N=173) (N=114)
-------------------------------------------------------------------------------------
age 60.9 ± 11.5 60.1 ± 10.6 0.472 69.3 ± 11.4 67.8 ± 9.7 0.257
cardiogenicShock 0.685 0.296
- No 355 (93.4%) 175 (92.1%) 168 (97.1%) 107 (93.9%)
- Yes 25 ( 6.6%) 15 ( 7.9%) 5 ( 2.9%) 7 ( 6.1%)
entry 0.552 0.665
- Femoral 125 (32.9%) 68 (35.8%) 74 (42.8%) 45 (39.5%)
- Radial 255 (67.1%) 122 (64.2%) 99 (57.2%) 69 (60.5%)
Dx 0.219 0.240
- NSTEMI 71 (18.7%) 32 (16.8%) 25 (14.5%) 25 (21.9%)
- STEMI 154 (40.5%) 66 (34.7%) 54 (31.2%) 30 (26.3%)
- Unstable Angina 155 (40.8%) 92 (48.4%) 94 (54.3%) 59 (51.8%)
EF 56.5 ± 8.3 53.9 ± 11.0 0.007 56.0 ± 10.1 56.6 ± 10.0 0.655
height 168.1 ± 5.8 167.5 ± 6.7 0.386 153.9 ± 6.5 153.6 ± 5.8 0.707
weight 68.1 ± 10.4 69.8 ± 10.2 0.070 56.5 ± 8.7 58.4 ± 10.0 0.106
BMI 24.0 ± 3.1 24.9 ± 3.5 0.005 23.8 ± 3.2 24.8 ± 4.0 0.046
obesity 0.027 0.359
- No 261 (68.7%) 112 (58.9%) 121 (69.9%) 73 (64.0%)
- Yes 119 (31.3%) 78 (41.1%) 52 (30.1%) 41 (36.0%)
TC 184.1 ± 46.7 181.8 ± 44.5 0.572 186.0 ± 43.1 193.3 ± 60.8 0.274
LDLC 117.9 ± 41.8 112.1 ± 39.4 0.115 116.3 ± 35.2 119.8 ± 48.6 0.519
HDLC 38.4 ± 11.4 36.8 ± 9.6 0.083 39.2 ± 10.9 38.8 ± 12.2 0.821
TG 115.2 ± 72.2 153.4 ± 130.7 0.000 114.2 ± 82.4 128.4 ± 65.5 0.112
HBP 0.000 0.356
- No 205 (53.9%) 68 (35.8%) 54 (31.2%) 29 (25.4%)
- Yes 175 (46.1%) 122 (64.2%) 119 (68.8%) 85 (74.6%)
smoking 0.386 0.093
- Ex-smoker 101 (26.6%) 54 (28.4%) 34 (19.7%) 15 (13.2%)
- Never 77 (20.3%) 46 (24.2%) 118 (68.2%) 91 (79.8%)
- Smoker 202 (53.2%) 90 (47.4%) 21 (12.1%) 8 ( 7.0%)
-------------------------------------------------------------------------------------
If you want more beautiful table in your R markdown file, you can use myhtml function.
out=mytable(Dx~.,data=acs)
myhtml(out)
table, th, td { border: 1px solid #bcbcbc; }
Descriptive Statistics by 'Dx' DxNSTEMI(N=153)STEMI(N=304)Unstable Angina(N=400)p age 64.3 ± 12.362.1 ± 12.163.8 ± 11.00.073 sex 0.012 Female 50 (32.7%)84 (27.6%)153 (38.2%) Male 103 (67.3%)220 (72.4%)247 (61.8%) cardiogenicShock0.000 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 ± 9.352.4 ± 9.559.2 ± 8.70.000 height 163.3 ± 8.2165.1 ± 8.2161.7 ± 9.70.000 weight 64.3 ± 10.265.7 ± 11.664.5 ± 11.60.361 BMI 24.1 ± 3.224.0 ± 3.324.6 ± 3.40.064 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 ± 53.6183.2 ± 43.4183.5 ± 48.30.057 LDLC 126.1 ± 44.7116.7 ± 39.5112.9 ± 40.40.004 HDLC 38.9 ± 11.938.5 ± 11.037.8 ± 10.90.501 TG 130.1 ± 88.5106.5 ± 72.0137.4 ± 101.60.000 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 0.000 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%)out1=mytable(sex+DM~.,data=acs)
myhtml(out1)
table, th, td { border: 1px solid #bcbcbc; }
Descriptive Statistics stratified by sex and DM sexMaleFemale DMNo(N=380)Yes(N=190)pNo(N=173)Yes(N=114)p age 60.9 ± 11.560.1 ± 10.60.47269.3 ± 11.467.8 ± 9.70.257 cardiogenicShock 0.6850.296 No 355 (93.4%)175 (92.1%)168 (97.1%)107 (93.9%) Yes 25 ( 6.6%)15 ( 7.9%)5 ( 2.9%)7 ( 6.1%) entry 0.5520.665 Femoral 125 (32.9%)68 (35.8%)74 (42.8%)45 (39.5%) Radial 255 (67.1%)122 (64.2%)99 (57.2%)69 (60.5%) Dx 0.2190.240 NSTEMI 71 (18.7%)32 (16.8%)25 (14.5%)25 (21.9%) STEMI 154 (40.5%)66 (34.7%)54 (31.2%)30 (26.3%) Unstable Angina155 (40.8%)92 (48.4%)94 (54.3%)59 (51.8%) EF 56.5 ± 8.353.9 ± 11.00.00756.0 ± 10.156.6 ± 10.00.655 height 168.1 ± 5.8167.5 ± 6.70.386153.9 ± 6.5153.6 ± 5.80.707 weight 68.1 ± 10.469.8 ± 10.20.07056.5 ± 8.758.4 ± 10.00.106 BMI 24.0 ± 3.124.9 ± 3.50.00523.8 ± 3.224.8 ± 4.00.046 obesity 0.0270.359 No 261 (68.7%)112 (58.9%)121 (69.9%)73 (64.0%) Yes 119 (31.3%)78 (41.1%)52 (30.1%)41 (36.0%) TC 184.1 ± 46.7181.8 ± 44.50.572186.0 ± 43.1193.3 ± 60.80.274 LDLC 117.9 ± 41.8112.1 ± 39.40.115116.3 ± 35.2119.8 ± 48.60.519 HDLC 38.4 ± 11.436.8 ± 9.60.08339.2 ± 10.938.8 ± 12.20.821 TG 115.2 ± 72.2153.4 ± 130.70.000114.2 ± 82.4128.4 ± 65.50.112 HBP 0.0000.356 No 205 (53.9%)68 (35.8%)54 (31.2%)29 (25.4%) Yes 175 (46.1%)122 (64.2%)119 (68.8%)85 (74.6%) smoking 0.3860.093 Ex-smoker 101 (26.6%)54 (28.4%)34 (19.7%)15 (13.2%) Never 77 (20.3%)46 (24.2%)118 (68.2%)91 (79.8%) Smoker 202 (53.2%)90 (47.4%)21 (12.1%)8 ( 7.0%)If you want more beautiful table, you can use mylatex function.
mylatex(mytable(sex+DM~age+Dx,data=acs))
You can adjust font size of latex table by using parameter size from 1 to 10.
out=mytable(sex~age+Dx,data=acs)
for(i in c(3,5))
mylatex(out,size=i,caption=paste("Table ",i,". Fontsize=",i,sep=""))
If you want to export your table into csv file format, you can use mycsv function.
mycsv(out,file="test.csv")
mycsv(out1,fil="test1.csv")
Following figure is a screen-shot in which test.csv and test1.csv files are opened with Numbers.
library(moonBook)
densityplot(age~sex,data=acs)
densityplot(age~Dx,data=acs)
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="Odds Ratio")
ORplot(out2,type=1)
ORplot(out1,type=1,show.CI=TRUE,col=c("blue","red"))
ORplot(out1,type=4,show.CI=TRUE,sig.level=0.05)
ORplot(out1,type=1,show.CI=TRUE,main="Odds Ratio",sig.level=0.05,
pch=1,cex=2,lwd=4,col=c("red","blue"))
attach(colon)
The following objects are masked from colon (pos = 4):
adhere, age, differ, etype, extent, id, node4, nodes,
obstruct, perfor, rx, sex, status, study, surg, time
colon$TS=Surv(time,status==1)
out=mycph(TS~.,data=colon)
mycph : perform coxph of individual expecting variables
Call: TS ~ ., data= colon
study was excluded : NaN
status was excluded : infinite
out
HR lcl ucl p
id 1.00 1.00 1.00 0.317
rxLev 0.98 0.84 1.14 0.786
rxLev+5FU 0.64 0.55 0.76 0.000
sex 0.97 0.85 1.10 0.610
age 1.00 0.99 1.00 0.382
obstruct 1.27 1.09 1.49 0.003
perfor 1.30 0.92 1.85 0.142
adhere 1.37 1.16 1.62 0.000
nodes 1.09 1.08 1.10 0.000
differ 1.36 1.19 1.55 0.000
extent 1.78 1.53 2.07 0.000
surg 1.28 1.11 1.47 0.001
node4 2.47 2.17 2.83 0.000
time 0.75 0.74 0.76 0.000
etype 0.81 0.71 0.92 0.001
HRplot(out,type=2,show.CI=TRUE,cex=2,sig=0.05,
main="Hazard ratios of all individual variables")
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