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=533) SMC (N=335) EMCI (N=408) LMCI (N=669) AD (N=401) Total (N=2346) p value
Age < 0.0011
   N-Miss 1 0 1 2 0 4
   Mean (SD) 73.352 (6.334) 70.730 (6.743) 71.281 (7.425) 73.778 (7.477) 74.701 (7.925) 72.969 (7.330)
   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] 10 (1.9%) 15 (4.5%) 19 (4.7%) 20 (3.0%) 17 (4.2%) 81 (3.5%)
   (59,69] 106 (19.9%) 140 (41.8%) 143 (35.1%) 144 (21.6%) 67 (16.7%) 600 (25.6%)
   (69,79] 321 (60.3%) 143 (42.7%) 179 (44.0%) 330 (49.5%) 188 (46.9%) 1161 (49.6%)
   (79,89] 94 (17.7%) 33 (9.9%) 65 (16.0%) 169 (25.3%) 122 (30.4%) 483 (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 (52.9%) 208 (62.1%) 184 (45.1%) 259 (38.7%) 175 (43.6%) 1108 (47.2%)
   Male 251 (47.1%) 127 (37.9%) 224 (54.9%) 410 (61.3%) 226 (56.4%) 1238 (52.8%)
Education < 0.0011
   Mean (SD) 16.417 (2.613) 16.707 (2.361) 16.034 (2.639) 15.967 (2.829) 15.212 (2.905) 16.058 (2.736)
   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%) 45 (13.4%) 45 (11.1%) 58 (8.7%) 14 (3.5%) 218 (9.3%)
   Married 367 (68.9%) 236 (70.4%) 313 (76.9%) 518 (77.4%) 338 (84.3%) 1772 (75.6%)
   Never married 31 (5.8%) 19 (5.7%) 17 (4.2%) 13 (1.9%) 11 (2.7%) 91 (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%) 33 (9.9%) 28 (6.9%) 78 (11.7%) 38 (9.5%) 255 (10.9%)
Ethnicity 0.2982
   Unknown 2 (0.4%) 2 (0.6%) 2 (0.5%) 3 (0.4%) 3 (0.7%) 12 (0.5%)
   Not Hisp/Latino 505 (94.7%) 310 (92.5%) 385 (94.4%) 645 (96.4%) 384 (95.8%) 2229 (95.0%)
   Hisp/Latino 26 (4.9%) 23 (6.9%) 21 (5.1%) 21 (3.1%) 14 (3.5%) 105 (4.5%)
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 12 (2.3%) 15 (4.5%) 6 (1.5%) 12 (1.8%) 10 (2.5%) 55 (2.3%)
   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%) 42 (12.5%) 16 (3.9%) 37 (5.5%) 22 (5.5%) 164 (7.0%)
   White 469 (88.0%) 265 (79.1%) 372 (91.2%) 612 (91.5%) 365 (91.0%) 2083 (88.8%)
   More than one 2 (0.4%) 10 (3.0%) 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 27 13 216 94 476
   Negative 119 (29.2%) 142 (46.1%) 70 (17.7%) 67 (14.8%) 17 (5.5%) 415 (22.2%)
   Positive 288 (70.8%) 166 (53.9%) 325 (82.3%) 386 (85.2%) 290 (94.5%) 1455 (77.8%)
CDR-SB < 0.0011
   Mean (SD) 0.031 (0.124) 0.051 (0.156) 1.322 (0.867) 1.632 (0.940) 4.448 (1.688) 1.470 (1.778)
   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) 8.996 (4.425) 8.634 (4.304) 12.821 (5.378) 18.500 (6.648) 29.882 (7.994) 15.855 (9.516)
   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 (1.145) 29.096 (1.138) 28.240 (1.632) 27.193 (1.888) 23.155 (2.193) 27.380 (2.652)
   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 9.00 12.0 26.3 533
SMC 1.33 5.33 8.0 8.63 11.5 26.3 331
EMCI 2.00 9.00 12.0 12.82 16.0 29.0 405
LMCI 0.67 13.67 18.3 18.50 23.2 39.7 666
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 29.0 29 29.1 30 30 533
SMC 24 29.0 29 29.1 30 30 334
EMCI 21 27.8 29 28.2 29 30 408
LMCI 19 26.0 27 27.2 29 30 669
AD 16 21.0 23 23.2 25 30 401

CDR-SB

Min. X1st.Qu. Median Mean X3rd.Qu. Max. N
CN 0 0.0 0.0 0.0310 0 1.0 533
SMC 0 0.0 0.0 0.0507 0 1.0 335
EMCI 0 0.5 1.0 1.3223 2 6.0 408
LMCI 0 1.0 1.5 1.6323 2 5.5 669
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 2.88 307
SMC 1 1.38 1.75 1.81 2.12 3.62 334
EMCI 1 1.75 2.25 2.28 2.75 4.00 405
LMCI 1 1.88 2.25 2.35 2.88 4.00 273
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 2.49 307
SMC 1 1.21 1.37 1.48 1.67 3.00 334
EMCI 1 1.38 1.69 1.82 2.16 3.82 406
LMCI 1 1.45 1.67 1.83 2.11 3.85 274
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 2.87 302
SMC 1.00 1.03 1.11 1.21 1.31 2.90 328
EMCI 1.00 1.23 1.49 1.65 1.97 3.90 398
LMCI 1.00 1.38 1.76 1.91 2.33 3.72 272
AD 1.12 2.34 2.82 2.75 3.26 3.95 215