ADNI 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

Demographic Summaries by Diagnosis

Baseline

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
  1. Linear Model ANOVA
  2. Pearson’s Chi-squared test

Baseline box plots

Baseline summary statistics

ADAS 13

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

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 30 348
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

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 0.0516 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

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 1.80 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

Pt ECog - Total

Min. X1st.Qu. Median Mean X3rd.Qu. Max. N
CN 1 1.08 1.18 1.26 1.34 2.49 308
SMC 1 1.21 1.37 1.47 1.67 3.00 348
EMCI 1 1.38 1.69 1.83 2.18 3.82 408
LMCI 1 1.45 1.67 1.84 2.13 3.85 282
AD 1 1.43 1.79 1.92 2.28 3.61 212

SP ECog - Total

Min. X1st.Qu. Median Mean X3rd.Qu. Max. N
CN 1.00 1.00 1.05 1.14 1.20 2.87 304
SMC 1.00 1.03 1.11 1.21 1.31 2.90 343
EMCI 1.00 1.23 1.48 1.65 1.97 3.90 400
LMCI 1.00 1.38 1.75 1.91 2.32 3.79 280
AD 1.12 2.34 2.82 2.75 3.26 3.95 215