ADNI Enrollment
ATRI Biostatistics
Enrollment.RmdADNI enrollment summaries using the ADNIMERGE R package
Description
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
Load required R packages and functions
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())
dxpal <- c("#2b8cbe", "#74a9cf", "#fdcc8a", "#fc8d59", "#e34a33")
scale_colour_discrete <- function(...) scale_colour_manual(..., values = dxpal)
scale_fill_discrete <- function(...) scale_fill_manual(..., values = dxpal)Demographic Summaries by Diagnosis
Baseline
| CN (N=534) | SMC (N=341) | EMCI (N=409) | LMCI (N=671) | AD (N=401) | Total (N=2356) | p value | |
|---|---|---|---|---|---|---|---|
| Age | < 0.0011 | ||||||
| N-Miss | 1 | 0 | 1 | 2 | 0 | 4 | |
| Mean (SD) | 73.321 (6.368) | 70.673 (6.779) | 71.298 (7.425) | 73.774 (7.468) | 74.701 (7.925) | 72.950 (7.339) | |
| 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%) | 16 (4.7%) | 19 (4.7%) | 20 (3.0%) | 17 (4.2%) | 83 (3.5%) | |
| (59,69] | 106 (19.9%) | 144 (42.2%) | 143 (35.0%) | 144 (21.5%) | 67 (16.7%) | 604 (25.7%) | |
| (69,79] | 321 (60.2%) | 143 (41.9%) | 180 (44.1%) | 332 (49.6%) | 188 (46.9%) | 1164 (49.5%) | |
| (79,89] | 94 (17.6%) | 34 (10.0%) | 65 (15.9%) | 169 (25.3%) | 122 (30.4%) | 484 (20.6%) | |
| (89,99] | 1 (0.2%) | 4 (1.2%) | 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%) | 212 (62.2%) | 185 (45.2%) | 260 (38.7%) | 175 (43.6%) | 1114 (47.3%) | |
| Male | 252 (47.2%) | 129 (37.8%) | 224 (54.8%) | 411 (61.3%) | 226 (56.4%) | 1242 (52.7%) | |
| Education | < 0.0011 | ||||||
| Mean (SD) | 16.412 (2.613) | 16.692 (2.353) | 16.029 (2.637) | 15.963 (2.830) | 15.212 (2.905) | 16.054 (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%) | 46 (13.5%) | 45 (11.0%) | 59 (8.8%) | 14 (3.5%) | 220 (9.3%) | |
| Married | 367 (68.7%) | 240 (70.4%) | 314 (77.0%) | 519 (77.3%) | 338 (84.3%) | 1778 (75.5%) | |
| Never married | 32 (6.0%) | 19 (5.6%) | 17 (4.2%) | 13 (1.9%) | 11 (2.7%) | 92 (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%) | 34 (10.0%) | 28 (6.9%) | 78 (11.6%) | 38 (9.5%) | 256 (10.9%) | |
| Ethnicity | 0.1172 | ||||||
| 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%) | 313 (91.8%) | 385 (94.1%) | 647 (96.4%) | 384 (95.8%) | 2235 (94.9%) | |
| Hisp/Latino | 26 (4.9%) | 26 (7.6%) | 22 (5.4%) | 21 (3.1%) | 14 (3.5%) | 109 (4.6%) | |
| 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%) | 15 (4.4%) | 6 (1.5%) | 12 (1.8%) | 10 (2.5%) | 56 (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%) | 45 (13.2%) | 16 (3.9%) | 38 (5.7%) | 22 (5.5%) | 168 (7.1%) | |
| White | 469 (87.8%) | 268 (78.6%) | 373 (91.2%) | 613 (91.4%) | 365 (91.0%) | 2088 (88.6%) | |
| More than one | 2 (0.4%) | 10 (2.9%) | 7 (1.7%) | 3 (0.4%) | 4 (1.0%) | 26 (1.1%) | |
| Unknown | 1 (0.2%) | 3 (0.9%) | 4 (1.0%) | 3 (0.4%) | 0 (0.0%) | 11 (0.5%) | |
| Amyloid Status | < 0.0012 | ||||||
| N-Miss | 126 | 31 | 13 | 218 | 94 | 482 | |
| Negative | 120 (29.4%) | 144 (46.5%) | 71 (17.9%) | 67 (14.8%) | 17 (5.5%) | 419 (22.4%) | |
| Positive | 288 (70.6%) | 166 (53.5%) | 325 (82.1%) | 386 (85.2%) | 290 (94.5%) | 1455 (77.6%) | |
| CDR-SB | < 0.0011 | ||||||
| Mean (SD) | 0.031 (0.124) | 0.051 (0.157) | 1.322 (0.866) | 1.634 (0.944) | 4.448 (1.688) | 1.466 (1.777) | |
| 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) | 8.994 (4.421) | 8.621 (4.293) | 12.846 (5.396) | 18.487 (6.646) | 29.882 (7.994) | 15.833 (9.509) | |
| Range | 0.000 - 26.330 | 1.330 - 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) | 29.097 (1.131) | 28.230 (1.644) | 27.197 (1.887) | 23.155 (2.193) | 27.384 (2.650) | |
| 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 |
- Linear Model ANOVA
- Pearson’s Chi-squared test
Baseline summary statistics
ADAS 13
| Min. | X1st.Qu. | Median | Mean | X3rd.Qu. | Max. | N | |
|---|---|---|---|---|---|---|---|
| CN | 0.00 | 5.67 | 9.0 | 8.99 | 12.0 | 26.3 | 534 |
| SMC | 1.33 | 5.33 | 8.0 | 8.62 | 11.3 | 26.3 | 337 |
| EMCI | 2.00 | 9.00 | 12.0 | 12.85 | 16.0 | 29.0 | 406 |
| LMCI | 0.67 | 13.67 | 18.3 | 18.49 | 23.1 | 39.7 | 668 |
| AD | 12.67 | 24.00 | 29.3 | 29.88 | 34.7 | 54.7 | 393 |
MMSE
| 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 | 340 |
| EMCI | 21 | 27 | 29 | 28.2 | 29 | 30 | 409 |
| LMCI | 19 | 26 | 27 | 27.2 | 29 | 30 | 671 |
| AD | 16 | 21 | 23 | 23.2 | 25 | 30 | 401 |
CDR-SB
| 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 | 0.0513 | 0 | 1.0 | 341 |
| EMCI | 0 | 0.5 | 1.0 | 1.3215 | 2 | 6.0 | 409 |
| LMCI | 0 | 1.0 | 1.5 | 1.6341 | 2 | 5.5 | 671 |
| AD | 1 | 3.5 | 4.5 | 4.4476 | 5 | 10.0 | 401 |
Pt ECog - Mem
| 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 | 1.81 | 2.12 | 3.62 | 340 |
| EMCI | 1 | 1.75 | 2.25 | 2.28 | 2.75 | 4.00 | 406 |
| LMCI | 1 | 1.81 | 2.25 | 2.35 | 2.88 | 4.00 | 275 |
| AD | 1 | 1.88 | 2.38 | 2.42 | 3.00 | 4.00 | 212 |