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=530) | SMC (N=333) | EMCI (N=405) | LMCI (N=665) | AD (N=401) | Total (N=2334) | p value | |
|---|---|---|---|---|---|---|---|
| Age | < 0.0011 | ||||||
| N-Miss | 1 | 0 | 1 | 2 | 0 | 4 | |
| Mean (SD) | 73.414 (6.290) | 70.756 (6.747) | 71.333 (7.414) | 73.741 (7.478) | 74.701 (7.925) | 72.988 (7.318) | |
| 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] | 9 (1.7%) | 15 (4.5%) | 18 (4.5%) | 20 (3.0%) | 17 (4.2%) | 79 (3.4%) | |
| (59,69] | 104 (19.7%) | 139 (41.7%) | 142 (35.1%) | 144 (21.7%) | 67 (16.7%) | 596 (25.6%) | |
| (69,79] | 321 (60.7%) | 142 (42.6%) | 178 (44.1%) | 327 (49.3%) | 188 (46.9%) | 1156 (49.6%) | |
| (79,89] | 94 (17.8%) | 33 (9.9%) | 65 (16.1%) | 168 (25.3%) | 122 (30.4%) | 482 (20.7%) | |
| (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 | 280 (52.8%) | 206 (61.9%) | 181 (44.7%) | 257 (38.6%) | 175 (43.6%) | 1099 (47.1%) | |
| Male | 250 (47.2%) | 127 (38.1%) | 224 (55.3%) | 408 (61.4%) | 226 (56.4%) | 1235 (52.9%) | |
| Education | < 0.0011 | ||||||
| Mean (SD) | 16.419 (2.621) | 16.700 (2.361) | 16.054 (2.637) | 15.964 (2.835) | 15.212 (2.905) | 16.059 (2.739) | |
| 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 (10.6%) | 45 (13.5%) | 44 (10.9%) | 57 (8.6%) | 14 (3.5%) | 216 (9.3%) | |
| Married | 367 (69.2%) | 235 (70.6%) | 312 (77.2%) | 516 (77.6%) | 338 (84.3%) | 1768 (75.8%) | |
| Never married | 29 (5.5%) | 19 (5.7%) | 17 (4.2%) | 13 (2.0%) | 11 (2.7%) | 89 (3.8%) | |
| Unknown | 1 (0.2%) | 2 (0.6%) | 4 (1.0%) | 2 (0.3%) | 0 (0.0%) | 9 (0.4%) | |
| Widowed | 77 (14.5%) | 32 (9.6%) | 27 (6.7%) | 77 (11.6%) | 38 (9.5%) | 251 (10.8%) | |
| Ethnicity | 0.3762 | ||||||
| Unknown | 2 (0.4%) | 2 (0.6%) | 2 (0.5%) | 3 (0.5%) | 3 (0.7%) | 12 (0.5%) | |
| Not Hisp/Latino | 502 (94.7%) | 309 (92.8%) | 382 (94.3%) | 641 (96.4%) | 384 (95.8%) | 2218 (95.0%) | |
| Hisp/Latino | 26 (4.9%) | 22 (6.6%) | 21 (5.2%) | 21 (3.2%) | 14 (3.5%) | 104 (4.5%) | |
| Race | < 0.0012 | ||||||
| Am Indian/Alaskan | 2 (0.4%) | 0 (0.0%) | 2 (0.5%) | 1 (0.2%) | 0 (0.0%) | 5 (0.2%) | |
| Asian | 11 (2.1%) | 15 (4.5%) | 6 (1.5%) | 12 (1.8%) | 10 (2.5%) | 54 (2.3%) | |
| Hawaiian/Other PI | 0 (0.0%) | 0 (0.0%) | 1 (0.2%) | 1 (0.2%) | 0 (0.0%) | 2 (0.1%) | |
| Black | 45 (8.5%) | 41 (12.3%) | 15 (3.7%) | 35 (5.3%) | 22 (5.5%) | 158 (6.8%) | |
| White | 469 (88.5%) | 264 (79.3%) | 370 (91.4%) | 610 (91.7%) | 365 (91.0%) | 2078 (89.0%) | |
| More than one | 2 (0.4%) | 10 (3.0%) | 7 (1.7%) | 3 (0.5%) | 4 (1.0%) | 26 (1.1%) | |
| Unknown | 1 (0.2%) | 3 (0.9%) | 4 (1.0%) | 3 (0.5%) | 0 (0.0%) | 11 (0.5%) | |
| Amyloid Status | < 0.0012 | ||||||
| N-Miss | 123 | 26 | 11 | 213 | 94 | 467 | |
| Negative | 119 (29.2%) | 141 (45.9%) | 69 (17.5%) | 67 (14.8%) | 17 (5.5%) | 413 (22.1%) | |
| Positive | 288 (70.8%) | 166 (54.1%) | 325 (82.5%) | 385 (85.2%) | 290 (94.5%) | 1454 (77.9%) | |
| CDR-SB | < 0.0011 | ||||||
| Mean (SD) | 0.031 (0.125) | 0.051 (0.157) | 1.326 (0.866) | 1.638 (0.940) | 4.448 (1.688) | 1.475 (1.781) | |
| 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) | 9.021 (4.421) | 8.641 (4.311) | 12.831 (5.396) | 18.513 (6.630) | 29.882 (7.994) | 15.881 (9.519) | |
| 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) | 29.055 (1.147) | 29.102 (1.135) | 28.244 (1.628) | 27.200 (1.887) | 23.155 (2.193) | 27.378 (2.655) | |
| 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 | 9.02 | 12.0 | 26.3 | 530 |
| SMC | 1.33 | 5.33 | 8.0 | 8.64 | 11.7 | 26.3 | 329 |
| EMCI | 2.00 | 9.00 | 12.0 | 12.83 | 16.0 | 29.0 | 402 |
| LMCI | 0.67 | 13.67 | 18.5 | 18.51 | 23.2 | 39.7 | 662 |
| 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 | 530 |
| SMC | 24 | 29 | 29 | 29.1 | 30 | 30 | 332 |
| EMCI | 21 | 28 | 29 | 28.2 | 29 | 30 | 405 |
| LMCI | 19 | 26 | 27 | 27.2 | 29 | 30 | 665 |
| 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 | 0.0311 | 0 | 1.0 | 530 |
| SMC | 0 | 0.0 | 0.0 | 0.0511 | 0 | 1.0 | 333 |
| EMCI | 0 | 0.5 | 1.0 | 1.3259 | 2 | 6.0 | 405 |
| LMCI | 0 | 1.0 | 1.5 | 1.6376 | 2 | 5.5 | 665 |
| 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 | 1.45 | 1.62 | 2.88 | 304 |
| SMC | 1 | 1.38 | 1.75 | 1.81 | 2.12 | 3.62 | 332 |
| EMCI | 1 | 1.75 | 2.25 | 2.28 | 2.75 | 4.00 | 402 |
| LMCI | 1 | 1.88 | 2.25 | 2.35 | 2.88 | 4.00 | 269 |
| AD | 1 | 1.88 | 2.38 | 2.42 | 3.00 | 4.00 | 212 |