package to create descriptive tables
compareGroups is an R package available on CRAN which performs
descriptive tables displaying means, standard deviation, quantiles or
frequencies of several variables. Also, p-value to test equality between
groups is computed using the appropiate test.
With a very simple code, nice, compact and ready-to-publish descriptives
table are displayed on R console. They can also be exported to different
formats, such as Word, Excel, PDF or inserted in a R-Sweave or
R-markdown document.
You will find an extensive manual describing all compareGropus
capabilities with real examples in the
vignette.
Also, compareGroups package has been published in Journal of Statistical Software [Subirana et al, 2014] (https://www.jstatsoft.org/v57/i12/).
compareGroups is developed and maintained by Isaac Subirana,
Hector Sanz, Joan Vila and collaborators at the cardiovascular
epidemiology research unit (URLEC), located at Barcelona Biomedical
Research Park (PRBB) .
As the driving force behind the REGICOR study, URLEC has extensive experience in statistical epidemiology, and is a national reference centre for research into cardiovascular diseases and their risk factors.
Install the package from CRAN
install.packages("compareGroups")
or the lattest version from Github
library(devtools)
devtools::install_github("isubirana/compareGroups")
library(compareGroups)
data(regicor)
tab <- descrTable(year ~ . -id , regicor, hide.no = "no",
method=c(triglyc=2, tocv=2, todeath=2), sd.type = 3)
export2md(tab, header.background = "black", header.color = "white",
caption = "Summary by intervention group")
| 1995 | 2000 | 2005 | p.overall | |
|---|---|---|---|---|
| N=431 | N=786 | N=1077 | ||
| Age | 54.1±11.7 | 54.3±11.2 | 55.3±10.6 | 0.078 |
| Sex: | 0.506 | |||
| Male | 206 (47.8%) | 390 (49.6%) | 505 (46.9%) | |
| Female | 225 (52.2%) | 396 (50.4%) | 572 (53.1%) | |
| Smoking status: | <0.001 | |||
| Never smoker | 234 (56.4%) | 414 (54.6%) | 553 (52.2%) | |
| Current or former < 1y | 109 (26.3%) | 267 (35.2%) | 217 (20.5%) | |
| Former >= 1y | 72 (17.3%) | 77 (10.2%) | 290 (27.4%) | |
| Systolic blood pressure | 133±19.2 | 133±21.3 | 129±19.8 | <0.001 |
| Diastolic blood pressure | 77.0±10.5 | 80.8±10.3 | 79.9±10.6 | <0.001 |
| History of hypertension | 111 (25.8%) | 233 (29.6%) | 379 (35.5%) | <0.001 |
| Hypertension treatment | 71 (16.5%) | 127 (16.2%) | 230 (22.2%) | 0.002 |
| Total cholesterol | 225±43.1 | 224±44.4 | 213±45.9 | <0.001 |
| HDL cholesterol | 51.9±14.5 | 52.3±15.6 | 53.2±14.2 | 0.208 |
| Triglycerides | 94.0 \[71.0;136\] | 98.0 \[72.0;133\] | 98.0 \[72.0;139\] | 0.762 |
| LDL cholesterol | 152±38.4 | 149±38.6 | 136±39.7 | <0.001 |
| History of hyperchol. | 97 (22.5%) | 256 (33.2%) | 356 (33.2%) | <0.001 |
| Cholesterol treatment | 28 (6.50%) | 68 (8.80%) | 132 (12.8%) | <0.001 |
| Height (cm) | 163±9.21 | 162±9.39 | 163±9.05 | 0.003 |
| Weight (Kg) | 72.3±12.6 | 73.8±14.0 | 73.6±13.9 | 0.150 |
| Body mass index | 27.0±4.15 | 28.1±4.62 | 27.6±4.63 | <0.001 |
| Physical activity (Kcal/week) | 491±419 | 422±377 | 351±378 | <0.001 |
| Physical component | 49.3±8.08 | 49.0±9.63 | 50.1±8.91 | 0.032 |
| Mental component | 49.2±11.3 | 48.9±11.0 | 46.9±10.8 | <0.001 |
| Cardiovascular event | 10 (2.51%) | 35 (4.72%) | 47 (4.59%) | 0.161 |
| Days to cardiovascular event or end of follow-up | 1728 \[746;2767\] | 1617 \[723;2596\] | 1775 \[835;2723\] | 0.096 |
| Overall death | 18 (4.65%) | 81 (11.0%) | 74 (7.23%) | <0.001 |
| Days to overall death or end of follow-up | 1557 \[812;2689\] | 1609 \[734;2549\] | 1734 \[817;2713\] | 0.249 |
tabstrat <- strataTable(update(tab, . ~ . -sex), "sex")
export2md(tabstrat, header.background = "black", header.color = "white", size=9)
|
|
Male |
Female |
||||||
|---|---|---|---|---|---|---|---|---|
| 1995 | 2000 | 2005 | p.overall | 1995 | 2000 | 2005 | p.overall | |
| N=206 | N=390 | N=505 | N=225 | N=396 | N=572 | |||
| Age | 54.1±11.8 | 54.3±11.2 | 55.4±10.7 | 0.212 | 54.1±11.7 | 54.4±11.2 | 55.2±10.6 | 0.351 |
| Smoking status: | <0.001 | <0.001 | ||||||
| Never smoker | 52 (26.5%) | 112 (29.7%) | 137 (27.5%) | 182 (83.1%) | 302 (79.3%) | 416 (74.0%) | ||
| Current or former < 1y | 77 (39.3%) | 199 (52.8%) | 134 (26.9%) | 32 (14.6%) | 68 (17.8%) | 83 (14.8%) | ||
| Former >= 1y | 67 (34.2%) | 66 (17.5%) | 227 (45.6%) | 5 (2.28%) | 11 (2.89%) | 63 (11.2%) | ||
| Systolic blood pressure | 134±18.4 | 137±19.3 | 132±18.7 | 0.002 | 132±19.8 | 129±22.6 | 127±20.5 | 0.008 |
| Diastolic blood pressure | 79.0±9.27 | 83.0±9.54 | 81.7±10.8 | <0.001 | 75.2±11.3 | 78.6±10.6 | 78.3±10.0 | <0.001 |
| History of hypertension | 50 (24.3%) | 110 (28.2%) | 181 (36.2%) | 0.002 | 61 (27.1%) | 123 (31.1%) | 198 (34.8%) | 0.097 |
| Hypertension treatment | 31 (15.0%) | 48 (12.3%) | 110 (22.8%) | <0.001 | 40 (17.8%) | 79 (19.9%) | 120 (21.7%) | 0.446 |
| Total cholesterol | 224±43.9 | 224±43.9 | 210±40.3 | <0.001 | 226±42.4 | 224±44.9 | 216±50.3 | 0.004 |
| HDL cholesterol | 46.5±13.1 | 47.3±12.6 | 48.1±12.4 | 0.290 | 56.9±13.9 | 57.4±16.7 | 57.8±14.2 | 0.783 |
| Triglycerides | 110 \[79.0;149\] | 113 \[84.0;145\] | 108 \[79.0;149\] | 0.825 | 86.0 \[66.0;113\] | 87.0 \[66.0;118\] | 90.0 \[66.0;128\] | 0.496 |
| LDL cholesterol | 153±39.6 | 152±39.1 | 137±36.0 | <0.001 | 150±37.3 | 146±38.0 | 136±42.6 | <0.001 |
| History of hyperchol. | 48 (23.3%) | 138 (35.8%) | 167 (33.2%) | 0.007 | 49 (21.8%) | 118 (30.6%) | 189 (33.3%) | 0.006 |
| Cholesterol treatment | 17 (8.25%) | 38 (9.84%) | 59 (12.2%) | 0.256 | 11 (4.89%) | 30 (7.75%) | 73 (13.2%) | <0.001 |
| Height (cm) | 170±7.34 | 168±7.17 | 170±7.43 | 0.021 | 158±6.31 | 156±6.50 | 158±6.24 | <0.001 |
| Weight (Kg) | 77.6±11.7 | 80.1±12.3 | 80.2±11.6 | 0.023 | 67.3±11.3 | 67.6±12.6 | 67.7±13.0 | 0.919 |
| Body mass index | 26.9±3.64 | 28.2±3.89 | 27.9±3.58 | <0.001 | 27.2±4.57 | 28.0±5.25 | 27.3±5.39 | 0.084 |
| Physical activity (Kcal/week) | 422±418 | 356±362 | 439±467 | 0.014 | 553±412 | 486±382 | 273±253 | <0.001 |
| Physical component | 50.1±6.71 | 50.9±8.58 | 51.5±8.07 | 0.110 | 48.6±9.16 | 47.1±10.2 | 48.9±9.45 | 0.027 |
| Mental component | 52.1±9.67 | 50.9±10.2 | 49.2±9.67 | 0.001 | 46.5±12.2 | 46.9±11.3 | 44.7±11.2 | 0.017 |
| Cardiovascular event | 6 (3.06%) | 21 (5.74%) | 19 (3.96%) | 0.272 | 4 (1.98%) | 14 (3.73%) | 28 (5.15%) | 0.139 |
| Days to cardiovascular event or end of follow-up | 1619 \[719;2715\] | 1613 \[667;2509\] | 1822 \[897;2794\] | 0.043 | 1828 \[853;2779\] | 1617 \[772;2679\] | 1750 \[746;2692\] | 0.427 |
| Overall death | 12 (6.45%) | 46 (12.5%) | 29 (6.08%) | 0.002 | 6 (2.99%) | 35 (9.43%) | 45 (8.24%) | 0.018 |
| Days to overall death or end of follow-up | 1557 \[836;2680\] | 1606 \[751;2490\] | 1688 \[785;2516\] | 0.947 | 1587 \[786;2717\] | 1620 \[730;2583\] | 1809 \[867;2804\] | 0.141 |
plot(tab["sex"]) |
plot(tab["age"]) |
 |
 |
data(SNPs)
tabor <- descrTable(casco ~ .-id, SNPs, show.ratio=TRUE, show.p.overall=FALSE)
export2md(tabor[1:4])
| 0 | 1 | OR | p.ratio | |
|---|---|---|---|---|
| N=47 | N=110 | |||
| sex: | ||||
| Male | 21 (44.7%) | 54 (49.1%) | Ref. | Ref. |
| Female | 26 (55.3%) | 56 (50.9%) | 0.84 \[0.42;1.67\] | 0.619 |
| blood.pre | 13.1 (0.88) | 12.9 (1.03) | 0.78 \[0.55;1.11\] | 0.174 |
| protein | 39938 (19770) | 44371 (24897) | 1.00 \[1.00;1.00\] | 0.280 |
| snp10001: | ||||
| CC | 2 (4.26%) | 10 (9.09%) | Ref. | Ref. |
| CT | 21 (44.7%) | 32 (29.1%) | 0.33 \[0.04;1.43\] | 0.147 |
| TT | 24 (51.1%) | 68 (61.8%) | 0.60 \[0.08;2.55\] | 0.521 |
library(survival)
regicor$tcv <- Surv(regicor$tocv, regicor$cv=="Yes")
tabhr <- descrTable(tcv ~ .-id-cv-tocv, regicor,
method=c(triglyc=2, tocv=2, todeath=2),
hide.no="no", ref.no="no",
show.ratio=TRUE, show.p.overall=FALSE)
export2md(tabhr[1:10], header.label=c("p.ratio"="p-value"),
caption="Descriptives by cardiovascular event")
| No event | Event | HR | p-value | |
|---|---|---|---|---|
| N=2071 | N=92 | |||
| Recruitment year: | ||||
| 1995 | 388 (18.7%) | 10 (10.9%) | Ref. | Ref. |
| 2000 | 706 (34.1%) | 35 (38.0%) | 1.95 \[0.96;3.93\] | 0.063 |
| 2005 | 977 (47.2%) | 47 (51.1%) | 1.82 \[0.92;3.59\] | 0.087 |
| Age | 54.6 (11.1) | 57.5 (11.0) | 1.02 \[1.00;1.04\] | 0.021 |
| Sex: | ||||
| Male | 996 (48.1%) | 46 (50.0%) | Ref. | Ref. |
| Female | 1075 (51.9%) | 46 (50.0%) | 0.92 \[0.61;1.39\] | 0.696 |
| Smoking status: | ||||
| Never smoker | 1099 (54.3%) | 37 (40.2%) | Ref. | Ref. |
| Current or former < 1y | 506 (25.0%) | 47 (51.1%) | 2.67 \[1.74;4.11\] | <0.001 |
| Former >= 1y | 419 (20.7%) | 8 (8.70%) | 0.55 \[0.26;1.18\] | 0.123 |
| Systolic blood pressure | 131 (20.3) | 138 (21.5) | 1.02 \[1.01;1.02\] | 0.001 |
| Diastolic blood pressure | 79.5 (10.4) | 82.9 (12.3) | 1.03 \[1.01;1.05\] | 0.002 |
| History of hypertension | 647 (31.3%) | 38 (41.3%) | 1.52 \[1.01;2.31\] | 0.047 |
| Hypertension treatment | 382 (18.7%) | 22 (23.9%) | 1.37 \[0.85;2.22\] | 0.195 |
| Total cholesterol | 218 (44.5) | 224 (50.4) | 1.00 \[1.00;1.01\] | 0.207 |
| HDL cholesterol | 52.8 (14.8) | 50.4 (13.3) | 0.99 \[0.97;1.00\] | 0.114 |
For those not familiar to R syntax, a Web User Interface (WUI) has
been implemented using Shiny tools, which
can be used off line by typing cGroupsWUI() after having
compareGroups package installed and loaded, or remotely just accessing
the application hosted in a shinyapp.io
server.
