Enrollment.Rmd
This package vignette demonstrates how to use the ADNIMERGE package to generate simple enrollment and longitudinal summaries and plots with R and knitr.
Report generated from Enrollment.Rmd
options(digits = 3)
library(knitr)
library(ADNIMERGE)
library(ggplot2)
library(Hmisc)
library(gridExtra)
library(RColorBrewer)
library(tidyverse)
library(kableExtra)
source("https://adni.bitbucket.io/myfunctions.R")
theme_set(theme_bw())
c("#2b8cbe", "#74a9cf", "#fdcc8a", "#fc8d59", "#e34a33")
dxpal <- function(...) scale_colour_manual(..., values = dxpal)
scale_colour_discrete <- function(...) scale_fill_manual(..., values = dxpal) scale_fill_discrete <-
CN (N=534) | SMC (N=349) | EMCI (N=410) | LMCI (N=677) | AD (N=401) | Total (N=2371) | p value | |
---|---|---|---|---|---|---|---|
Age | < 0.0011 | ||||||
N-Miss | 1 | 0 | 1 | 2 | 0 | 4 | |
Mean (SD) | 73.321 (6.368) | 70.497 (6.785) | 71.278 (7.427) | 73.744 (7.464) | 74.701 (7.925) | 72.906 (7.348) | |
Range | 55.100 - 89.600 | 50.400 - 90.300 | 55.000 - 89.100 | 55.000 - 91.400 | 55.100 - 90.900 | 50.400 - 91.400 | |
Age | |||||||
N-Miss | 1 | 0 | 1 | 2 | 0 | 4 | |
(39,49] | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | |
(49,59] | 11 (2.1%) | 17 (4.9%) | 19 (4.6%) | 20 (3.0%) | 17 (4.2%) | 84 (3.5%) | |
(59,69] | 106 (19.9%) | 150 (43.0%) | 144 (35.2%) | 146 (21.6%) | 67 (16.7%) | 613 (25.9%) | |
(69,79] | 321 (60.2%) | 145 (41.5%) | 180 (44.0%) | 336 (49.8%) | 188 (46.9%) | 1170 (49.4%) | |
(79,89] | 94 (17.6%) | 33 (9.5%) | 65 (15.9%) | 169 (25.0%) | 122 (30.4%) | 483 (20.4%) | |
(89,99] | 1 (0.2%) | 4 (1.1%) | 1 (0.2%) | 4 (0.6%) | 7 (1.7%) | 17 (0.7%) | |
(99,109] | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | |
Sex | < 0.0012 | ||||||
Female | 282 (52.8%) | 218 (62.5%) | 186 (45.4%) | 262 (38.7%) | 175 (43.6%) | 1123 (47.4%) | |
Male | 252 (47.2%) | 131 (37.5%) | 224 (54.6%) | 415 (61.3%) | 226 (56.4%) | 1248 (52.6%) | |
Education | < 0.0011 | ||||||
Mean (SD) | 16.412 (2.613) | 16.693 (2.337) | 16.020 (2.642) | 15.966 (2.835) | 15.212 (2.905) | 16.055 (2.733) | |
Range | 6.000 - 20.000 | 8.000 - 20.000 | 10.000 - 20.000 | 4.000 - 20.000 | 4.000 - 20.000 | 4.000 - 20.000 | |
Marital | < 0.0012 | ||||||
N-Miss | 0 | 0 | 1 | 0 | 0 | 1 | |
Divorced | 56 (10.5%) | 48 (13.8%) | 45 (11.0%) | 59 (8.7%) | 14 (3.5%) | 222 (9.4%) | |
Married | 367 (68.7%) | 243 (69.6%) | 315 (77.0%) | 524 (77.4%) | 338 (84.3%) | 1787 (75.4%) | |
Never married | 32 (6.0%) | 20 (5.7%) | 17 (4.2%) | 13 (1.9%) | 11 (2.7%) | 93 (3.9%) | |
Unknown | 1 (0.2%) | 2 (0.6%) | 4 (1.0%) | 2 (0.3%) | 0 (0.0%) | 9 (0.4%) | |
Widowed | 78 (14.6%) | 36 (10.3%) | 28 (6.8%) | 79 (11.7%) | 38 (9.5%) | 259 (10.9%) | |
Ethnicity | 0.1432 | ||||||
Unknown | 2 (0.4%) | 2 (0.6%) | 2 (0.5%) | 3 (0.4%) | 3 (0.7%) | 12 (0.5%) | |
Not Hisp/Latino | 506 (94.8%) | 320 (91.7%) | 386 (94.1%) | 651 (96.2%) | 384 (95.8%) | 2247 (94.8%) | |
Hisp/Latino | 26 (4.9%) | 27 (7.7%) | 22 (5.4%) | 23 (3.4%) | 14 (3.5%) | 112 (4.7%) | |
Race | < 0.0012 | ||||||
Am Indian/Alaskan | 2 (0.4%) | 0 (0.0%) | 2 (0.5%) | 1 (0.1%) | 0 (0.0%) | 5 (0.2%) | |
Asian | 13 (2.4%) | 16 (4.6%) | 7 (1.7%) | 12 (1.8%) | 10 (2.5%) | 58 (2.4%) | |
Hawaiian/Other PI | 0 (0.0%) | 0 (0.0%) | 1 (0.2%) | 1 (0.1%) | 0 (0.0%) | 2 (0.1%) | |
Black | 47 (8.8%) | 51 (14.6%) | 16 (3.9%) | 38 (5.6%) | 22 (5.5%) | 174 (7.3%) | |
White | 469 (87.8%) | 268 (76.8%) | 373 (91.0%) | 617 (91.1%) | 365 (91.0%) | 2092 (88.2%) | |
More than one | 2 (0.4%) | 11 (3.2%) | 7 (1.7%) | 4 (0.6%) | 4 (1.0%) | 28 (1.2%) | |
Unknown | 1 (0.2%) | 3 (0.9%) | 4 (1.0%) | 4 (0.6%) | 0 (0.0%) | 12 (0.5%) | |
Amyloid Status | < 0.0012 | ||||||
N-Miss | 126 | 38 | 14 | 224 | 94 | 496 | |
Negative | 120 (29.4%) | 145 (46.6%) | 71 (17.9%) | 67 (14.8%) | 17 (5.5%) | 420 (22.4%) | |
Positive | 288 (70.6%) | 166 (53.4%) | 325 (82.1%) | 386 (85.2%) | 290 (94.5%) | 1455 (77.6%) | |
CDR-SB | < 0.0011 | ||||||
Mean (SD) | 0.031 (0.124) | 0.052 (0.157) | 1.318 (0.867) | 1.636 (0.949) | 4.448 (1.688) | 1.462 (1.775) | |
Range | 0.000 - 1.000 | 0.000 - 1.000 | 0.000 - 6.000 | 0.000 - 5.500 | 1.000 - 10.000 | 0.000 - 10.000 | |
ADAS 13 | < 0.0011 | ||||||
N-Miss | 0 | 4 | 3 | 3 | 8 | 18 | |
Mean (SD) | 8.966 (4.358) | 8.590 (4.301) | 12.862 (5.398) | 18.517 (6.646) | 29.882 (7.994) | 15.814 (9.503) | |
Range | 0.000 - 24.670 | 0.670 - 26.330 | 2.000 - 29.000 | 0.670 - 39.670 | 12.670 - 54.670 | 0.000 - 54.670 | |
MMSE | < 0.0011 | ||||||
N-Miss | 0 | 1 | 0 | 0 | 0 | 1 | |
Mean (SD) | 29.058 (1.144) | 29.083 (1.162) | 28.222 (1.649) | 27.196 (1.886) | 23.155 (2.193) | 27.386 (2.647) | |
Range | 24.000 - 30.000 | 24.000 - 30.000 | 21.000 - 30.000 | 19.000 - 30.000 | 16.000 - 30.000 | 16.000 - 30.000 |
Min. | X1st.Qu. | Median | Mean | X3rd.Qu. | Max. | N | |
---|---|---|---|---|---|---|---|
CN | 0.00 | 5.67 | 9.0 | 8.97 | 12.0 | 24.7 | 534 |
SMC | 0.67 | 5.33 | 8.0 | 8.59 | 11.3 | 26.3 | 345 |
EMCI | 2.00 | 9.00 | 12.0 | 12.86 | 16.0 | 29.0 | 407 |
LMCI | 0.67 | 13.67 | 18.3 | 18.52 | 23.3 | 39.7 | 674 |
AD | 12.67 | 24.00 | 29.3 | 29.88 | 34.7 | 54.7 | 393 |
Min. | X1st.Qu. | Median | Mean | X3rd.Qu. | Max. | N | |
---|---|---|---|---|---|---|---|
CN | 24 | 29 | 29 | 29.1 | 30 | 30 | 534 |
SMC | 24 | 29 | 29 | 29.1 | 30 | 30 | 348 |
EMCI | 21 | 27 | 29 | 28.2 | 29 | 30 | 410 |
LMCI | 19 | 26 | 27 | 27.2 | 29 | 30 | 677 |
AD | 16 | 21 | 23 | 23.2 | 25 | 30 | 401 |
Min. | X1st.Qu. | Median | Mean | X3rd.Qu. | Max. | N | |
---|---|---|---|---|---|---|---|
CN | 0 | 0.0 | 0.0 | 0.0309 | 0 | 1.0 | 534 |
SMC | 0 | 0.0 | 0.0 | 0.0516 | 0 | 1.0 | 349 |
EMCI | 0 | 0.5 | 1.0 | 1.3183 | 2 | 6.0 | 410 |
LMCI | 0 | 1.0 | 1.5 | 1.6359 | 2 | 5.5 | 677 |
AD | 1 | 3.5 | 4.5 | 4.4476 | 5 | 10.0 | 401 |
Min. | X1st.Qu. | Median | Mean | X3rd.Qu. | Max. | N | |
---|---|---|---|---|---|---|---|
CN | 1 | 1.12 | 1.38 | 1.44 | 1.62 | 2.88 | 308 |
SMC | 1 | 1.38 | 1.75 | 1.80 | 2.12 | 3.62 | 348 |
EMCI | 1 | 1.75 | 2.25 | 2.28 | 2.81 | 4.00 | 407 |
LMCI | 1 | 1.88 | 2.29 | 2.36 | 2.88 | 4.00 | 281 |
AD | 1 | 1.88 | 2.38 | 2.42 | 3.00 | 4.00 | 212 |