ADNI Enrollment

ATRI Biostatistics

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=351) EMCI (N=411) LMCI (N=678) AD (N=401) Total (N=2375) p value
Age < 0.0011
   N-Miss 1 0 1 2 0 4
   Mean (SD) 73.323 (6.366) 70.546 (6.798) 71.272 (7.419) 73.726 (7.472) 74.701 (7.925) 72.905 (7.347)
   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 (4.8%) 19 (4.6%) 20 (3.0%) 17 (4.2%) 84 (3.5%)
   (59,69] 106 (19.9%) 150 (42.7%) 145 (35.4%) 147 (21.7%) 67 (16.7%) 615 (25.9%)
   (69,79] 321 (60.2%) 146 (41.6%) 180 (43.9%) 336 (49.7%) 188 (46.9%) 1171 (49.4%)
   (79,89] 94 (17.6%) 34 (9.7%) 65 (15.9%) 169 (25.0%) 122 (30.4%) 484 (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%) 220 (62.7%) 187 (45.5%) 261 (38.5%) 175 (43.6%) 1125 (47.4%)
   Male 252 (47.2%) 131 (37.3%) 224 (54.5%) 417 (61.5%) 226 (56.4%) 1250 (52.6%)
Education < 0.0011
   Mean (SD) 16.412 (2.613) 16.681 (2.336) 16.024 (2.640) 15.968 (2.833) 15.212 (2.905) 16.055 (2.731)
   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 57 (10.7%) 48 (13.7%) 45 (11.0%) 59 (8.7%) 14 (3.5%) 223 (9.4%)
   Married 366 (68.5%) 244 (69.5%) 315 (76.8%) 525 (77.4%) 338 (84.3%) 1788 (75.3%)
   Never married 32 (6.0%) 20 (5.7%) 18 (4.4%) 13 (1.9%) 11 (2.7%) 94 (4.0%)
   Unknown 1 (0.2%) 2 (0.6%) 4 (1.0%) 2 (0.3%) 0 (0.0%) 9 (0.4%)
   Widowed 78 (14.6%) 37 (10.5%) 28 (6.8%) 79 (11.7%) 38 (9.5%) 260 (11.0%)
Ethnicity 0.0992
   Unknown 2 (0.4%) 2 (0.6%) 2 (0.5%) 3 (0.4%) 3 (0.7%) 12 (0.5%)
   Not Hisp/Latino 507 (94.9%) 321 (91.5%) 387 (94.2%) 652 (96.2%) 384 (95.8%) 2251 (94.8%)
   Hisp/Latino 25 (4.7%) 28 (8.0%) 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 (14.5%) 17 (4.1%) 38 (5.6%) 22 (5.5%) 175 (7.4%)
   White 469 (87.8%) 269 (76.6%) 373 (90.8%) 618 (91.2%) 365 (91.0%) 2094 (88.2%)
   More than one 2 (0.4%) 12 (3.4%) 7 (1.7%) 4 (0.6%) 4 (1.0%) 29 (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 125 40 15 225 94 499
   Negative 121 (29.6%) 145 (46.6%) 71 (17.9%) 67 (14.8%) 17 (5.5%) 421 (22.4%)
   Positive 288 (70.4%) 166 (53.4%) 325 (82.1%) 386 (85.2%) 290 (94.5%) 1455 (77.6%)
CDR-SB < 0.0011
   Mean (SD) 0.030 (0.123) 0.051 (0.157) 1.316 (0.867) 1.634 (0.949) 4.448 (1.688) 1.460 (1.774)
   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) 8.961 (4.363) 8.628 (4.345) 12.847 (5.399) 18.517 (6.638) 29.872 (7.987) 15.808 (9.496)
   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) 29.066 (1.130) 29.083 (1.161) 28.226 (1.650) 27.201 (1.888) 23.155 (2.193) 27.392 (2.646)
   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 8.96 12.0 24.7 534
SMC 0.67 5.33 8.0 8.63 11.5 26.3 347
EMCI 2.00 9.00 12.0 12.85 16.0 29.0 408
LMCI 0.67 13.67 18.3 18.52 23.3 39.7 675
AD 12.67 24.00 29.3 29.87 34.3 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 30 350
EMCI 21 27 29 28.2 29 30 411
LMCI 19 26 27 27.2 29 30 678
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 0.0300 0 1.0 534
SMC 0 0.0 0.0 0.0513 0 1.0 351
EMCI 0 0.5 1.0 1.3163 2 6.0 411
LMCI 0 1.0 1.5 1.6342 2 5.5 678
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 3.62 350
EMCI 1 1.75 2.25 2.28 2.78 4.00 408
LMCI 1 1.81 2.25 2.35 2.88 4.00 283
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 3.00 350
EMCI 1 1.38 1.69 1.83 2.18 3.82 409
LMCI 1 1.44 1.67 1.83 2.11 3.85 284
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 1.02 1.11 1.21 1.31 2.90 344
EMCI 1.00 1.23 1.47 1.65 1.97 3.90 401
LMCI 1.00 1.37 1.74 1.90 2.31 3.79 283
AD 1.12 2.34 2.82 2.75 3.26 3.95 215