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=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
  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 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

Pt ECog - Total

Min. X1st.Qu. Median Mean X3rd.Qu. Max. N
CN 1 1.08 1.18 1.26 1.34 2.49 304
SMC 1 1.21 1.37 1.48 1.67 3.00 332
EMCI 1 1.38 1.69 1.82 2.16 3.82 403
LMCI 1 1.45 1.67 1.83 2.11 3.85 270
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 2.87 299
SMC 1.00 1.03 1.11 1.21 1.31 2.90 327
EMCI 1.00 1.23 1.49 1.65 1.97 3.90 395
LMCI 1.00 1.39 1.77 1.92 2.36 3.72 268
AD 1.12 2.34 2.82 2.75 3.26 3.95 215