library(tidyverse)── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.4.0 ✔ purrr 1.0.1
✔ tibble 3.2.1 ✔ dplyr 1.1.2
✔ tidyr 1.3.0 ✔ stringr 1.5.0
✔ readr 2.1.3 ✔ forcats 0.5.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()library(survival)
library(tableone)
library(gtsummary)if (Sys.info()["sysname"] == "Darwin") {
model_data <- read_rds("/Volumes/lss_jsimmeri/als/model_data.rds")
} else {
model_data <- read_rds("/Shared/lss_jsimmeri/als/model_data.rds")
}model_data <- model_data |>
mutate(
age = first_year - dobyr,
female = sex == 1,
stratum = as.numeric(as.factor(glue::glue("{first_year}-{last_year}-{dobyr}-{sex}")))
) |>
mutate(any_sx = motor | bulbar,
n_groups = motor + bulbar,
n_bulbar = speech + swallowing,
n_motor = strength + gait + involuntary_movement + pain + other + falls,
n_total = speech + swallowing + strength + gait + involuntary_movement + pain + other + falls)First, the data summary by ALS status:
all_vars <- c(
"age", "female",
"first_year", "last_year",
"rate_outpatient_visits", "intensity_outpatient_visits_dx",
"rate_inpatient_stays", "intensity_inpatient_stays_los",
"elix_CHF", "elix_Valvular", "elix_PHTN", "elix_PVD", "elix_HTN",
"elix_HTNcx", "elix_Paralysis", "elix_NeuroOther", "elix_Pulmonary", "elix_DM",
"elix_DMcx", "elix_Hypothyroid", "elix_Renal", "elix_Liver", "elix_PUD",
"elix_HIV", "elix_Lymphoma", "elix_Mets", "elix_Tumor", "elix_Rheumatic",
"elix_Coagulopathy", "elix_Obesity", "elix_WeightLoss", "elix_FluidsLytes", "elix_BloodLoss",
"elix_Anemia", "elix_Alcohol", "elix_Drugs", "elix_Psychoses", "elix_Depression",
"lives_in_msa",
"any_sx", "motor", "bulbar",
"n_groups", "n_bulbar", "n_motor", "n_total",
"speech", "swallowing",
"strength", "gait", "involuntary_movement", "pain", "other", "falls")
factor_vars <- c("n_groups", "n_bulbar", "n_motor", "n_total")
nonnormal_vars <- c("age", "first_year", "last_year", "rate_outpatient_visits",
"intensity_outpatient_visits_dx", "rate_inpatient_stays",
"intensity_inpatient_stays_los")
CreateTableOne(
data = model_data,
vars = all_vars,
factorVars = factor_vars,
strata = c("als")
) |>
print(nonnormal = nonnormal_vars, smd = TRUE) Stratified by als
FALSE
n 96126
age (median [IQR]) 56.00 [47.00, 65.00]
female = TRUE (%) 54325 (56.5)
first_year (median [IQR]) 2007.00 [2003.00, 2010.00]
last_year (median [IQR]) 2012.00 [2008.00, 2015.00]
rate_outpatient_visits (median [IQR]) 7.10 [2.89, 14.56]
intensity_outpatient_visits_dx (median [IQR]) 1.51 [1.21, 2.03]
rate_inpatient_stays (median [IQR]) 0.00 [0.00, 0.12]
intensity_inpatient_stays_los (median [IQR]) 0.00 [0.00, 1.50]
elix_CHF = TRUE (%) 8899 ( 9.3)
elix_Valvular = TRUE (%) 12631 (13.1)
elix_PHTN = TRUE (%) 3107 ( 3.2)
elix_PVD = TRUE (%) 12089 (12.6)
elix_HTN = TRUE (%) 48410 (50.4)
elix_HTNcx = TRUE (%) 11065 (11.5)
elix_Paralysis = TRUE (%) 2065 ( 2.1)
elix_NeuroOther = TRUE (%) 9944 (10.3)
elix_Pulmonary = TRUE (%) 21899 (22.8)
elix_DM = TRUE (%) 20001 (20.8)
elix_DMcx = TRUE (%) 8413 ( 8.8)
elix_Hypothyroid = TRUE (%) 13543 (14.1)
elix_Renal = TRUE (%) 6213 ( 6.5)
elix_Liver = TRUE (%) 4626 ( 4.8)
elix_PUD = TRUE (%) 491 ( 0.5)
elix_HIV = TRUE (%) 188 ( 0.2)
elix_Lymphoma = TRUE (%) 1326 ( 1.4)
elix_Mets = TRUE (%) 3508 ( 3.6)
elix_Tumor = TRUE (%) 12044 (12.5)
elix_Rheumatic = TRUE (%) 5852 ( 6.1)
elix_Coagulopathy = TRUE (%) 3999 ( 4.2)
elix_Obesity = TRUE (%) 11063 (11.5)
elix_WeightLoss = TRUE (%) 5374 ( 5.6)
elix_FluidsLytes = TRUE (%) 13387 (13.9)
elix_BloodLoss = TRUE (%) 2005 ( 2.1)
elix_Anemia = TRUE (%) 16207 (16.9)
elix_Alcohol = TRUE (%) 2022 ( 2.1)
elix_Drugs = TRUE (%) 1292 ( 1.3)
elix_Psychoses = TRUE (%) 7433 ( 7.7)
elix_Depression = TRUE (%) 11856 (12.3)
lives_in_msa = TRUE (%) 81245 (84.5)
any_sx = TRUE (%) 48713 (50.7)
motor = TRUE (%) 47089 (49.0)
bulbar = TRUE (%) 7679 ( 8.0)
n_groups (%)
0 47413 (49.3)
1 42658 (44.4)
2 6055 ( 6.3)
n_bulbar (%)
0 88447 (92.0)
1 7273 ( 7.6)
2 406 ( 0.4)
n_motor (%)
0 49037 (51.0)
1 29389 (30.6)
2 9280 ( 9.7)
3 4885 ( 5.1)
4 2391 ( 2.5)
5 944 ( 1.0)
6 200 ( 0.2)
n_total (%)
0 47413 (49.3)
1 28523 (29.7)
2 10312 (10.7)
3 5302 ( 5.5)
4 2596 ( 2.7)
5 1296 ( 1.3)
6 541 ( 0.6)
7 134 ( 0.1)
8 9 ( 0.0)
speech = TRUE (%) 6620 ( 6.9)
swallowing = TRUE (%) 1465 ( 1.5)
strength = TRUE (%) 5028 ( 5.2)
gait = TRUE (%) 8373 ( 8.7)
involuntary_movement = TRUE (%) 6078 ( 6.3)
pain = TRUE (%) 41847 (43.5)
other = TRUE (%) 14195 (14.8)
falls = TRUE (%) 2567 ( 2.7)
Stratified by als
TRUE
n 19226
age (median [IQR]) 56.00 [47.00, 65.00]
female = TRUE (%) 10865 (56.5)
first_year (median [IQR]) 2007.00 [2003.00, 2010.00]
last_year (median [IQR]) 2012.00 [2008.00, 2015.00]
rate_outpatient_visits (median [IQR]) 13.66 [7.26, 24.11]
intensity_outpatient_visits_dx (median [IQR]) 1.61 [1.29, 2.13]
rate_inpatient_stays (median [IQR]) 0.00 [0.00, 0.25]
intensity_inpatient_stays_los (median [IQR]) 0.00 [0.00, 2.50]
elix_CHF = TRUE (%) 1771 ( 9.2)
elix_Valvular = TRUE (%) 3090 (16.1)
elix_PHTN = TRUE (%) 755 ( 3.9)
elix_PVD = TRUE (%) 3035 (15.8)
elix_HTN = TRUE (%) 10604 (55.2)
elix_HTNcx = TRUE (%) 2338 (12.2)
elix_Paralysis = TRUE (%) 2219 (11.5)
elix_NeuroOther = TRUE (%) 7838 (40.8)
elix_Pulmonary = TRUE (%) 5312 (27.6)
elix_DM = TRUE (%) 3958 (20.6)
elix_DMcx = TRUE (%) 1639 ( 8.5)
elix_Hypothyroid = TRUE (%) 3550 (18.5)
elix_Renal = TRUE (%) 1052 ( 5.5)
elix_Liver = TRUE (%) 1079 ( 5.6)
elix_PUD = TRUE (%) 127 ( 0.7)
elix_HIV = TRUE (%) 51 ( 0.3)
elix_Lymphoma = TRUE (%) 371 ( 1.9)
elix_Mets = TRUE (%) 386 ( 2.0)
elix_Tumor = TRUE (%) 2322 (12.1)
elix_Rheumatic = TRUE (%) 2130 (11.1)
elix_Coagulopathy = TRUE (%) 1011 ( 5.3)
elix_Obesity = TRUE (%) 2218 (11.5)
elix_WeightLoss = TRUE (%) 2344 (12.2)
elix_FluidsLytes = TRUE (%) 3348 (17.4)
elix_BloodLoss = TRUE (%) 397 ( 2.1)
elix_Anemia = TRUE (%) 4267 (22.2)
elix_Alcohol = TRUE (%) 491 ( 2.6)
elix_Drugs = TRUE (%) 397 ( 2.1)
elix_Psychoses = TRUE (%) 2327 (12.1)
elix_Depression = TRUE (%) 3617 (18.8)
lives_in_msa = TRUE (%) 16726 (87.0)
any_sx = TRUE (%) 16097 (83.7)
motor = TRUE (%) 15208 (79.1)
bulbar = TRUE (%) 5561 (28.9)
n_groups (%)
0 3129 (16.3)
1 11425 (59.4)
2 4672 (24.3)
n_bulbar (%)
0 13665 (71.1)
1 5194 (27.0)
2 367 ( 1.9)
n_motor (%)
0 4018 (20.9)
1 4527 (23.5)
2 3343 (17.4)
3 3572 (18.6)
4 2531 (13.2)
5 1053 ( 5.5)
6 182 ( 0.9)
n_total (%)
0 3129 (16.3)
1 4254 (22.1)
2 3481 (18.1)
3 3451 (17.9)
4 2663 (13.9)
5 1523 ( 7.9)
6 578 ( 3.0)
7 142 ( 0.7)
8 5 ( 0.0)
speech = TRUE (%) 5356 (27.9)
swallowing = TRUE (%) 572 ( 3.0)
strength = TRUE (%) 6749 (35.1)
gait = TRUE (%) 5761 (30.0)
involuntary_movement = TRUE (%) 4561 (23.7)
pain = TRUE (%) 11147 (58.0)
other = TRUE (%) 9050 (47.1)
falls = TRUE (%) 1142 ( 5.9)
Stratified by als
p test SMD
n
age (median [IQR]) 0.993 nonnorm <0.001
female = TRUE (%) 1.000 <0.001
first_year (median [IQR]) 0.999 nonnorm <0.001
last_year (median [IQR]) 0.997 nonnorm <0.001
rate_outpatient_visits (median [IQR]) <0.001 nonnorm 0.465
intensity_outpatient_visits_dx (median [IQR]) <0.001 nonnorm 0.196
rate_inpatient_stays (median [IQR]) <0.001 nonnorm 0.168
intensity_inpatient_stays_los (median [IQR]) <0.001 nonnorm 0.127
elix_CHF = TRUE (%) 0.851 0.002
elix_Valvular = TRUE (%) <0.001 0.083
elix_PHTN = TRUE (%) <0.001 0.037
elix_PVD = TRUE (%) <0.001 0.092
elix_HTN = TRUE (%) <0.001 0.096
elix_HTNcx = TRUE (%) 0.011 0.020
elix_Paralysis = TRUE (%) <0.001 0.379
elix_NeuroOther = TRUE (%) <0.001 0.744
elix_Pulmonary = TRUE (%) <0.001 0.112
elix_DM = TRUE (%) 0.498 0.005
elix_DMcx = TRUE (%) 0.315 0.008
elix_Hypothyroid = TRUE (%) <0.001 0.119
elix_Renal = TRUE (%) <0.001 0.042
elix_Liver = TRUE (%) <0.001 0.036
elix_PUD = TRUE (%) 0.011 0.020
elix_HIV = TRUE (%) 0.064 0.015
elix_Lymphoma = TRUE (%) <0.001 0.043
elix_Mets = TRUE (%) <0.001 0.099
elix_Tumor = TRUE (%) 0.085 0.014
elix_Rheumatic = TRUE (%) <0.001 0.179
elix_Coagulopathy = TRUE (%) <0.001 0.052
elix_Obesity = TRUE (%) 0.923 0.001
elix_WeightLoss = TRUE (%) <0.001 0.234
elix_FluidsLytes = TRUE (%) <0.001 0.096
elix_BloodLoss = TRUE (%) 0.875 0.001
elix_Anemia = TRUE (%) <0.001 0.135
elix_Alcohol = TRUE (%) <0.001 0.030
elix_Drugs = TRUE (%) <0.001 0.056
elix_Psychoses = TRUE (%) <0.001 0.147
elix_Depression = TRUE (%) <0.001 0.179
lives_in_msa = TRUE (%) <0.001 0.071
any_sx = TRUE (%) <0.001 0.752
motor = TRUE (%) <0.001 0.661
bulbar = TRUE (%) <0.001 0.560
n_groups (%) <0.001 0.831
0
1
2
n_bulbar (%) <0.001 0.561
0
1
2
n_motor (%) <0.001 0.910
0
1
2
3
4
5
6
n_total (%) <0.001 1.008
0
1
2
3
4
5
6
7
8
speech = TRUE (%) <0.001 0.576
swallowing = TRUE (%) <0.001 0.098
strength = TRUE (%) <0.001 0.802
gait = TRUE (%) <0.001 0.559
involuntary_movement = TRUE (%) <0.001 0.502
pain = TRUE (%) <0.001 0.292
other = TRUE (%) <0.001 0.746
falls = TRUE (%) <0.001 0.162And then by ALS and whether they live in an MSA:
CreateTableOne(
data = model_data,
vars = all_vars,
factorVars = factor_vars,
strata = c("als", "lives_in_msa")
) |>
print(nonnormal = nonnormal_vars, smd = TRUE) Stratified by als:lives_in_msa
FALSE:FALSE
n 14881
age (median [IQR]) 57.00 [48.00, 65.00]
female = TRUE (%) 8636 (58.0)
first_year (median [IQR]) 2007.00 [2002.00, 2010.00]
last_year (median [IQR]) 2011.00 [2008.00, 2014.00]
rate_outpatient_visits (median [IQR]) 6.86 [2.83, 13.91]
intensity_outpatient_visits_dx (median [IQR]) 1.51 [1.22, 2.04]
rate_inpatient_stays (median [IQR]) 0.00 [0.00, 0.14]
intensity_inpatient_stays_los (median [IQR]) 0.00 [0.00, 1.50]
elix_CHF = TRUE (%) 1310 ( 8.8)
elix_Valvular = TRUE (%) 1660 (11.2)
elix_PHTN = TRUE (%) 439 ( 3.0)
elix_PVD = TRUE (%) 1724 (11.6)
elix_HTN = TRUE (%) 7787 (52.3)
elix_HTNcx = TRUE (%) 1433 ( 9.6)
elix_Paralysis = TRUE (%) 305 ( 2.0)
elix_NeuroOther = TRUE (%) 1432 ( 9.6)
elix_Pulmonary = TRUE (%) 3524 (23.7)
elix_DM = TRUE (%) 3025 (20.3)
elix_DMcx = TRUE (%) 1125 ( 7.6)
elix_Hypothyroid = TRUE (%) 1987 (13.4)
elix_Renal = TRUE (%) 822 ( 5.5)
elix_Liver = TRUE (%) 621 ( 4.2)
elix_PUD = TRUE (%) 65 ( 0.4)
elix_HIV = TRUE (%) 8 ( 0.1)
elix_Lymphoma = TRUE (%) 163 ( 1.1)
elix_Mets = TRUE (%) 534 ( 3.6)
elix_Tumor = TRUE (%) 1775 (11.9)
elix_Rheumatic = TRUE (%) 891 ( 6.0)
elix_Coagulopathy = TRUE (%) 557 ( 3.7)
elix_Obesity = TRUE (%) 1613 (10.8)
elix_WeightLoss = TRUE (%) 818 ( 5.5)
elix_FluidsLytes = TRUE (%) 1977 (13.3)
elix_BloodLoss = TRUE (%) 276 ( 1.9)
elix_Anemia = TRUE (%) 2094 (14.1)
elix_Alcohol = TRUE (%) 280 ( 1.9)
elix_Drugs = TRUE (%) 173 ( 1.2)
elix_Psychoses = TRUE (%) 954 ( 6.4)
elix_Depression = TRUE (%) 1763 (11.8)
lives_in_msa = TRUE (%) 0 ( 0.0)
any_sx = TRUE (%) 7381 (49.6)
motor = TRUE (%) 7123 (47.9)
bulbar = TRUE (%) 1098 ( 7.4)
n_groups (%)
0 7500 (50.4)
1 6541 (44.0)
2 840 ( 5.6)
n_bulbar (%)
0 13783 (92.6)
1 1045 ( 7.0)
2 53 ( 0.4)
n_motor (%)
0 7758 (52.1)
1 4545 (30.5)
2 1450 ( 9.7)
3 713 ( 4.8)
4 286 ( 1.9)
5 102 ( 0.7)
6 27 ( 0.2)
n_total (%)
0 7500 (50.4)
1 4453 (29.9)
2 1585 (10.7)
3 771 ( 5.2)
4 355 ( 2.4)
5 129 ( 0.9)
6 66 ( 0.4)
7 22 ( 0.1)
8 0 ( 0.0)
speech = TRUE (%) 948 ( 6.4)
swallowing = TRUE (%) 203 ( 1.4)
strength = TRUE (%) 666 ( 4.5)
gait = TRUE (%) 1079 ( 7.3)
involuntary_movement = TRUE (%) 923 ( 6.2)
pain = TRUE (%) 6309 (42.4)
other = TRUE (%) 2038 (13.7)
falls = TRUE (%) 385 ( 2.6)
Stratified by als:lives_in_msa
TRUE:FALSE
n 2500
age (median [IQR]) 57.00 [49.00, 65.00]
female = TRUE (%) 1438 (57.5)
first_year (median [IQR]) 2006.00 [2002.00, 2010.00]
last_year (median [IQR]) 2011.00 [2008.00, 2014.00]
rate_outpatient_visits (median [IQR]) 12.84 [6.75, 22.02]
intensity_outpatient_visits_dx (median [IQR]) 1.66 [1.32, 2.19]
rate_inpatient_stays (median [IQR]) 0.00 [0.00, 0.23]
intensity_inpatient_stays_los (median [IQR]) 0.00 [0.00, 2.00]
elix_CHF = TRUE (%) 235 ( 9.4)
elix_Valvular = TRUE (%) 329 (13.2)
elix_PHTN = TRUE (%) 101 ( 4.0)
elix_PVD = TRUE (%) 362 (14.5)
elix_HTN = TRUE (%) 1466 (58.6)
elix_HTNcx = TRUE (%) 230 ( 9.2)
elix_Paralysis = TRUE (%) 266 (10.6)
elix_NeuroOther = TRUE (%) 1015 (40.6)
elix_Pulmonary = TRUE (%) 726 (29.0)
elix_DM = TRUE (%) 472 (18.9)
elix_DMcx = TRUE (%) 163 ( 6.5)
elix_Hypothyroid = TRUE (%) 412 (16.5)
elix_Renal = TRUE (%) 119 ( 4.8)
elix_Liver = TRUE (%) 119 ( 4.8)
elix_PUD = TRUE (%) 16 ( 0.6)
elix_HIV = TRUE (%) 0 ( 0.0)
elix_Lymphoma = TRUE (%) 41 ( 1.6)
elix_Mets = TRUE (%) 37 ( 1.5)
elix_Tumor = TRUE (%) 259 (10.4)
elix_Rheumatic = TRUE (%) 279 (11.2)
elix_Coagulopathy = TRUE (%) 115 ( 4.6)
elix_Obesity = TRUE (%) 282 (11.3)
elix_WeightLoss = TRUE (%) 322 (12.9)
elix_FluidsLytes = TRUE (%) 414 (16.6)
elix_BloodLoss = TRUE (%) 44 ( 1.8)
elix_Anemia = TRUE (%) 473 (18.9)
elix_Alcohol = TRUE (%) 39 ( 1.6)
elix_Drugs = TRUE (%) 35 ( 1.4)
elix_Psychoses = TRUE (%) 214 ( 8.6)
elix_Depression = TRUE (%) 437 (17.5)
lives_in_msa = TRUE (%) 0 ( 0.0)
any_sx = TRUE (%) 2131 (85.2)
motor = TRUE (%) 2023 (80.9)
bulbar = TRUE (%) 764 (30.6)
n_groups (%)
0 369 (14.8)
1 1475 (59.0)
2 656 (26.2)
n_bulbar (%)
0 1736 (69.4)
1 729 (29.2)
2 35 ( 1.4)
n_motor (%)
0 477 (19.1)
1 572 (22.9)
2 452 (18.1)
3 522 (20.9)
4 332 (13.3)
5 121 ( 4.8)
6 24 ( 1.0)
n_total (%)
0 369 (14.8)
1 509 (20.4)
2 486 (19.4)
3 486 (19.4)
4 381 (15.2)
5 177 ( 7.1)
6 74 ( 3.0)
7 18 ( 0.7)
8 0 ( 0.0)
speech = TRUE (%) 743 (29.7)
swallowing = TRUE (%) 56 ( 2.2)
strength = TRUE (%) 942 (37.7)
gait = TRUE (%) 725 (29.0)
involuntary_movement = TRUE (%) 601 (24.0)
pain = TRUE (%) 1462 (58.5)
other = TRUE (%) 1244 (49.8)
falls = TRUE (%) 145 ( 5.8)
Stratified by als:lives_in_msa
FALSE:TRUE
n 81245
age (median [IQR]) 56.00 [47.00, 65.00]
female = TRUE (%) 45689 ( 56.2)
first_year (median [IQR]) 2007.00 [2003.00, 2010.00]
last_year (median [IQR]) 2012.00 [2008.00, 2015.00]
rate_outpatient_visits (median [IQR]) 7.16 [2.90, 14.69]
intensity_outpatient_visits_dx (median [IQR]) 1.51 [1.21, 2.03]
rate_inpatient_stays (median [IQR]) 0.00 [0.00, 0.12]
intensity_inpatient_stays_los (median [IQR]) 0.00 [0.00, 1.50]
elix_CHF = TRUE (%) 7589 ( 9.3)
elix_Valvular = TRUE (%) 10971 ( 13.5)
elix_PHTN = TRUE (%) 2668 ( 3.3)
elix_PVD = TRUE (%) 10365 ( 12.8)
elix_HTN = TRUE (%) 40623 ( 50.0)
elix_HTNcx = TRUE (%) 9632 ( 11.9)
elix_Paralysis = TRUE (%) 1760 ( 2.2)
elix_NeuroOther = TRUE (%) 8512 ( 10.5)
elix_Pulmonary = TRUE (%) 18375 ( 22.6)
elix_DM = TRUE (%) 16976 ( 20.9)
elix_DMcx = TRUE (%) 7288 ( 9.0)
elix_Hypothyroid = TRUE (%) 11556 ( 14.2)
elix_Renal = TRUE (%) 5391 ( 6.6)
elix_Liver = TRUE (%) 4005 ( 4.9)
elix_PUD = TRUE (%) 426 ( 0.5)
elix_HIV = TRUE (%) 180 ( 0.2)
elix_Lymphoma = TRUE (%) 1163 ( 1.4)
elix_Mets = TRUE (%) 2974 ( 3.7)
elix_Tumor = TRUE (%) 10269 ( 12.6)
elix_Rheumatic = TRUE (%) 4961 ( 6.1)
elix_Coagulopathy = TRUE (%) 3442 ( 4.2)
elix_Obesity = TRUE (%) 9450 ( 11.6)
elix_WeightLoss = TRUE (%) 4556 ( 5.6)
elix_FluidsLytes = TRUE (%) 11410 ( 14.0)
elix_BloodLoss = TRUE (%) 1729 ( 2.1)
elix_Anemia = TRUE (%) 14113 ( 17.4)
elix_Alcohol = TRUE (%) 1742 ( 2.1)
elix_Drugs = TRUE (%) 1119 ( 1.4)
elix_Psychoses = TRUE (%) 6479 ( 8.0)
elix_Depression = TRUE (%) 10093 ( 12.4)
lives_in_msa = TRUE (%) 81245 (100.0)
any_sx = TRUE (%) 41332 ( 50.9)
motor = TRUE (%) 39966 ( 49.2)
bulbar = TRUE (%) 6581 ( 8.1)
n_groups (%)
0 39913 ( 49.1)
1 36117 ( 44.5)
2 5215 ( 6.4)
n_bulbar (%)
0 74664 ( 91.9)
1 6228 ( 7.7)
2 353 ( 0.4)
n_motor (%)
0 41279 ( 50.8)
1 24844 ( 30.6)
2 7830 ( 9.6)
3 4172 ( 5.1)
4 2105 ( 2.6)
5 842 ( 1.0)
6 173 ( 0.2)
n_total (%)
0 39913 ( 49.1)
1 24070 ( 29.6)
2 8727 ( 10.7)
3 4531 ( 5.6)
4 2241 ( 2.8)
5 1167 ( 1.4)
6 475 ( 0.6)
7 112 ( 0.1)
8 9 ( 0.0)
speech = TRUE (%) 5672 ( 7.0)
swallowing = TRUE (%) 1262 ( 1.6)
strength = TRUE (%) 4362 ( 5.4)
gait = TRUE (%) 7294 ( 9.0)
involuntary_movement = TRUE (%) 5155 ( 6.3)
pain = TRUE (%) 35538 ( 43.7)
other = TRUE (%) 12157 ( 15.0)
falls = TRUE (%) 2182 ( 2.7)
Stratified by als:lives_in_msa
TRUE:TRUE
n 16726
age (median [IQR]) 56.00 [47.00, 65.00]
female = TRUE (%) 9427 ( 56.4)
first_year (median [IQR]) 2007.00 [2003.00, 2010.00]
last_year (median [IQR]) 2012.00 [2008.00, 2015.00]
rate_outpatient_visits (median [IQR]) 13.80 [7.35, 24.43]
intensity_outpatient_visits_dx (median [IQR]) 1.60 [1.28, 2.12]
rate_inpatient_stays (median [IQR]) 0.00 [0.00, 0.25]
intensity_inpatient_stays_los (median [IQR]) 0.00 [0.00, 2.50]
elix_CHF = TRUE (%) 1536 ( 9.2)
elix_Valvular = TRUE (%) 2761 ( 16.5)
elix_PHTN = TRUE (%) 654 ( 3.9)
elix_PVD = TRUE (%) 2673 ( 16.0)
elix_HTN = TRUE (%) 9138 ( 54.6)
elix_HTNcx = TRUE (%) 2108 ( 12.6)
elix_Paralysis = TRUE (%) 1953 ( 11.7)
elix_NeuroOther = TRUE (%) 6823 ( 40.8)
elix_Pulmonary = TRUE (%) 4586 ( 27.4)
elix_DM = TRUE (%) 3486 ( 20.8)
elix_DMcx = TRUE (%) 1476 ( 8.8)
elix_Hypothyroid = TRUE (%) 3138 ( 18.8)
elix_Renal = TRUE (%) 933 ( 5.6)
elix_Liver = TRUE (%) 960 ( 5.7)
elix_PUD = TRUE (%) 111 ( 0.7)
elix_HIV = TRUE (%) 51 ( 0.3)
elix_Lymphoma = TRUE (%) 330 ( 2.0)
elix_Mets = TRUE (%) 349 ( 2.1)
elix_Tumor = TRUE (%) 2063 ( 12.3)
elix_Rheumatic = TRUE (%) 1851 ( 11.1)
elix_Coagulopathy = TRUE (%) 896 ( 5.4)
elix_Obesity = TRUE (%) 1936 ( 11.6)
elix_WeightLoss = TRUE (%) 2022 ( 12.1)
elix_FluidsLytes = TRUE (%) 2934 ( 17.5)
elix_BloodLoss = TRUE (%) 353 ( 2.1)
elix_Anemia = TRUE (%) 3794 ( 22.7)
elix_Alcohol = TRUE (%) 452 ( 2.7)
elix_Drugs = TRUE (%) 362 ( 2.2)
elix_Psychoses = TRUE (%) 2113 ( 12.6)
elix_Depression = TRUE (%) 3180 ( 19.0)
lives_in_msa = TRUE (%) 16726 (100.0)
any_sx = TRUE (%) 13966 ( 83.5)
motor = TRUE (%) 13185 ( 78.8)
bulbar = TRUE (%) 4797 ( 28.7)
n_groups (%)
0 2760 ( 16.5)
1 9950 ( 59.5)
2 4016 ( 24.0)
n_bulbar (%)
0 11929 ( 71.3)
1 4465 ( 26.7)
2 332 ( 2.0)
n_motor (%)
0 3541 ( 21.2)
1 3955 ( 23.6)
2 2891 ( 17.3)
3 3050 ( 18.2)
4 2199 ( 13.1)
5 932 ( 5.6)
6 158 ( 0.9)
n_total (%)
0 2760 ( 16.5)
1 3745 ( 22.4)
2 2995 ( 17.9)
3 2965 ( 17.7)
4 2282 ( 13.6)
5 1346 ( 8.0)
6 504 ( 3.0)
7 124 ( 0.7)
8 5 ( 0.0)
speech = TRUE (%) 4613 ( 27.6)
swallowing = TRUE (%) 516 ( 3.1)
strength = TRUE (%) 5807 ( 34.7)
gait = TRUE (%) 5036 ( 30.1)
involuntary_movement = TRUE (%) 3960 ( 23.7)
pain = TRUE (%) 9685 ( 57.9)
other = TRUE (%) 7806 ( 46.7)
falls = TRUE (%) 997 ( 6.0)
Stratified by als:lives_in_msa
p test SMD
n
age (median [IQR]) <0.001 nonnorm 0.035
female = TRUE (%) 0.001 0.022
first_year (median [IQR]) 0.041 nonnorm 0.013
last_year (median [IQR]) <0.001 nonnorm 0.076
rate_outpatient_visits (median [IQR]) <0.001 nonnorm 0.332
intensity_outpatient_visits_dx (median [IQR]) <0.001 nonnorm 0.166
rate_inpatient_stays (median [IQR]) <0.001 nonnorm 0.107
intensity_inpatient_stays_los (median [IQR]) <0.001 nonnorm 0.089
elix_CHF = TRUE (%) 0.213 0.011
elix_Valvular = TRUE (%) <0.001 0.079
elix_PHTN = TRUE (%) <0.001 0.035
elix_PVD = TRUE (%) <0.001 0.072
elix_HTN = TRUE (%) <0.001 0.095
elix_HTNcx = TRUE (%) <0.001 0.067
elix_Paralysis = TRUE (%) <0.001 0.253
elix_NeuroOther = TRUE (%) <0.001 0.507
elix_Pulmonary = TRUE (%) <0.001 0.088
elix_DM = TRUE (%) 0.046 0.027
elix_DMcx = TRUE (%) <0.001 0.054
elix_Hypothyroid = TRUE (%) <0.001 0.084
elix_Renal = TRUE (%) <0.001 0.041
elix_Liver = TRUE (%) <0.001 0.037
elix_PUD = TRUE (%) 0.035 0.018
elix_HIV = TRUE (%) <0.001 0.050
elix_Lymphoma = TRUE (%) <0.001 0.039
elix_Mets = TRUE (%) <0.001 0.085
elix_Tumor = TRUE (%) 0.001 0.038
elix_Rheumatic = TRUE (%) <0.001 0.122
elix_Coagulopathy = TRUE (%) <0.001 0.042
elix_Obesity = TRUE (%) 0.047 0.014
elix_WeightLoss = TRUE (%) <0.001 0.167
elix_FluidsLytes = TRUE (%) <0.001 0.071
elix_BloodLoss = TRUE (%) 0.114 0.016
elix_Anemia = TRUE (%) <0.001 0.119
elix_Alcohol = TRUE (%) <0.001 0.043
elix_Drugs = TRUE (%) <0.001 0.040
elix_Psychoses = TRUE (%) <0.001 0.111
elix_Depression = TRUE (%) <0.001 0.123
lives_in_msa = TRUE (%) <0.001 NaN
any_sx = TRUE (%) <0.001 0.533
motor = TRUE (%) <0.001 0.475
bulbar = TRUE (%) <0.001 0.401
n_groups (%) <0.001 0.596
0
1
2
n_bulbar (%) <0.001 0.406
0
1
2
n_motor (%) <0.001 0.662
0
1
2
3
4
5
6
n_total (%) <0.001 0.735
0
1
2
3
4
5
6
7
8
speech = TRUE (%) <0.001 0.413
swallowing = TRUE (%) <0.001 0.067
strength = TRUE (%) <0.001 0.577
gait = TRUE (%) <0.001 0.395
involuntary_movement = TRUE (%) <0.001 0.340
pain = TRUE (%) <0.001 0.210
other = TRUE (%) <0.001 0.540
falls = TRUE (%) <0.001 0.110I want to fit XXXX models:
First, does having any of these codes increase the odds of getting an ALS diagnosis?
any_fml_unadj <- als ~ any_sx * lives_in_msa + strata(stratum)
any_fml_fulladj <- als ~ rate_outpatient_visits + intensity_outpatient_visits_dx +
rate_inpatient_stays + intensity_inpatient_stays_los +
elix_CHF + elix_Valvular + elix_PHTN + elix_PVD + elix_HTN +
elix_HTNcx + elix_Paralysis + elix_NeuroOther + elix_Pulmonary + elix_DM +
elix_DMcx + elix_Hypothyroid + elix_Renal + elix_Liver + elix_PUD +
elix_HIV + elix_Lymphoma + elix_Mets + elix_Tumor + elix_Rheumatic +
elix_Coagulopathy + elix_Obesity + elix_WeightLoss + elix_FluidsLytes + elix_BloodLoss +
elix_Anemia + elix_Alcohol + elix_Drugs + elix_Psychoses + elix_Depression +
any_sx * lives_in_msa + strata(stratum)Second, what is the independent effect of bulbar symptoms?
any_bulbar_unadj <- als ~ bulbar * lives_in_msa + strata(stratum)
any_bulbar_fulladj <- als ~ rate_outpatient_visits + intensity_outpatient_visits_dx +
rate_inpatient_stays + intensity_inpatient_stays_los +
elix_CHF + elix_Valvular + elix_PHTN + elix_PVD + elix_HTN +
elix_HTNcx + elix_Paralysis + elix_NeuroOther + elix_Pulmonary + elix_DM +
elix_DMcx + elix_Hypothyroid + elix_Renal + elix_Liver + elix_PUD +
elix_HIV + elix_Lymphoma + elix_Mets + elix_Tumor + elix_Rheumatic +
elix_Coagulopathy + elix_Obesity + elix_WeightLoss + elix_FluidsLytes + elix_BloodLoss +
elix_Anemia + elix_Alcohol + elix_Drugs + elix_Psychoses + elix_Depression +
bulbar * lives_in_msa + strata(stratum)Third, what is the independent effect of motor symptoms?
any_motor_unadj <- als ~ motor * lives_in_msa + strata(stratum)
any_motor_fulladj <- als ~ rate_outpatient_visits + intensity_outpatient_visits_dx +
rate_inpatient_stays + intensity_inpatient_stays_los +
elix_CHF + elix_Valvular + elix_PHTN + elix_PVD + elix_HTN +
elix_HTNcx + elix_Paralysis + elix_NeuroOther + elix_Pulmonary + elix_DM +
elix_DMcx + elix_Hypothyroid + elix_Renal + elix_Liver + elix_PUD +
elix_HIV + elix_Lymphoma + elix_Mets + elix_Tumor + elix_Rheumatic +
elix_Coagulopathy + elix_Obesity + elix_WeightLoss + elix_FluidsLytes + elix_BloodLoss +
elix_Anemia + elix_Alcohol + elix_Drugs + elix_Psychoses + elix_Depression +
motor * lives_in_msa + strata(stratum)Fourth, what is the effect of symptoms from 0, 1, or 2 affects systems?
number_origin_unadj <- als ~ as.factor(I(bulbar + motor)) * lives_in_msa + strata(stratum)
number_origin_fulladj <- als ~ rate_outpatient_visits + intensity_outpatient_visits_dx +
rate_inpatient_stays + intensity_inpatient_stays_los +
elix_CHF + elix_Valvular + elix_PHTN + elix_PVD + elix_HTN +
elix_HTNcx + elix_Paralysis + elix_NeuroOther + elix_Pulmonary + elix_DM +
elix_DMcx + elix_Hypothyroid + elix_Renal + elix_Liver + elix_PUD +
elix_HIV + elix_Lymphoma + elix_Mets + elix_Tumor + elix_Rheumatic +
elix_Coagulopathy + elix_Obesity + elix_WeightLoss + elix_FluidsLytes + elix_BloodLoss +
elix_Anemia + elix_Alcohol + elix_Drugs + elix_Psychoses + elix_Depression +
as.factor(I(bulbar + motor)) * lives_in_msa + strata(stratum)Fifth, what is the effect of the symptom sub-class? This is actually many models…
speech_fml_unadj <- als ~ speech * lives_in_msa + strata(stratum)
speech_fml_fulladj <- als ~ rate_outpatient_visits + intensity_outpatient_visits_dx +
rate_inpatient_stays + intensity_inpatient_stays_los +
elix_CHF + elix_Valvular + elix_PHTN + elix_PVD + elix_HTN +
elix_HTNcx + elix_Paralysis + elix_NeuroOther + elix_Pulmonary + elix_DM +
elix_DMcx + elix_Hypothyroid + elix_Renal + elix_Liver + elix_PUD +
elix_HIV + elix_Lymphoma + elix_Mets + elix_Tumor + elix_Rheumatic +
elix_Coagulopathy + elix_Obesity + elix_WeightLoss + elix_FluidsLytes + elix_BloodLoss +
elix_Anemia + elix_Alcohol + elix_Drugs + elix_Psychoses + elix_Depression +
speech * lives_in_msa + strata(stratum)
swallowing_fml_unadj <- als ~ swallowing * lives_in_msa + strata(stratum)
swallowing_fml_fulladj <- als ~ rate_outpatient_visits + intensity_outpatient_visits_dx +
rate_inpatient_stays + intensity_inpatient_stays_los +
elix_CHF + elix_Valvular + elix_PHTN + elix_PVD + elix_HTN +
elix_HTNcx + elix_Paralysis + elix_NeuroOther + elix_Pulmonary + elix_DM +
elix_DMcx + elix_Hypothyroid + elix_Renal + elix_Liver + elix_PUD +
elix_HIV + elix_Lymphoma + elix_Mets + elix_Tumor + elix_Rheumatic +
elix_Coagulopathy + elix_Obesity + elix_WeightLoss + elix_FluidsLytes + elix_BloodLoss +
elix_Anemia + elix_Alcohol + elix_Drugs + elix_Psychoses + elix_Depression +
swallowing * lives_in_msa + strata(stratum)
strength_fml_unadj <- als ~ strength * lives_in_msa + strata(stratum)
strength_fml_fulladj <- als ~ rate_outpatient_visits + intensity_outpatient_visits_dx +
rate_inpatient_stays + intensity_inpatient_stays_los +
elix_CHF + elix_Valvular + elix_PHTN + elix_PVD + elix_HTN +
elix_HTNcx + elix_Paralysis + elix_NeuroOther + elix_Pulmonary + elix_DM +
elix_DMcx + elix_Hypothyroid + elix_Renal + elix_Liver + elix_PUD +
elix_HIV + elix_Lymphoma + elix_Mets + elix_Tumor + elix_Rheumatic +
elix_Coagulopathy + elix_Obesity + elix_WeightLoss + elix_FluidsLytes + elix_BloodLoss +
elix_Anemia + elix_Alcohol + elix_Drugs + elix_Psychoses + elix_Depression +
strength * lives_in_msa + strata(stratum)
gait_fml_unadj <- als ~ gait * lives_in_msa + strata(stratum)
gait_fml_fulladj <- als ~ rate_outpatient_visits + intensity_outpatient_visits_dx +
rate_inpatient_stays + intensity_inpatient_stays_los +
elix_CHF + elix_Valvular + elix_PHTN + elix_PVD + elix_HTN +
elix_HTNcx + elix_Paralysis + elix_NeuroOther + elix_Pulmonary + elix_DM +
elix_DMcx + elix_Hypothyroid + elix_Renal + elix_Liver + elix_PUD +
elix_HIV + elix_Lymphoma + elix_Mets + elix_Tumor + elix_Rheumatic +
elix_Coagulopathy + elix_Obesity + elix_WeightLoss + elix_FluidsLytes + elix_BloodLoss +
elix_Anemia + elix_Alcohol + elix_Drugs + elix_Psychoses + elix_Depression +
gait * lives_in_msa + strata(stratum)
involuntary_movement_fml_unadj <- als ~ involuntary_movement * lives_in_msa + strata(stratum)
involuntary_movement_fml_fulladj <- als ~ rate_outpatient_visits + intensity_outpatient_visits_dx +
rate_inpatient_stays + intensity_inpatient_stays_los +
elix_CHF + elix_Valvular + elix_PHTN + elix_PVD + elix_HTN +
elix_HTNcx + elix_Paralysis + elix_NeuroOther + elix_Pulmonary + elix_DM +
elix_DMcx + elix_Hypothyroid + elix_Renal + elix_Liver + elix_PUD +
elix_HIV + elix_Lymphoma + elix_Mets + elix_Tumor + elix_Rheumatic +
elix_Coagulopathy + elix_Obesity + elix_WeightLoss + elix_FluidsLytes + elix_BloodLoss +
elix_Anemia + elix_Alcohol + elix_Drugs + elix_Psychoses + elix_Depression +
involuntary_movement * lives_in_msa + strata(stratum)
pain_fml_unadj <- als ~ pain * lives_in_msa + strata(stratum)
pain_fml_fulladj <- als ~ rate_outpatient_visits + intensity_outpatient_visits_dx +
rate_inpatient_stays + intensity_inpatient_stays_los +
elix_CHF + elix_Valvular + elix_PHTN + elix_PVD + elix_HTN +
elix_HTNcx + elix_Paralysis + elix_NeuroOther + elix_Pulmonary + elix_DM +
elix_DMcx + elix_Hypothyroid + elix_Renal + elix_Liver + elix_PUD +
elix_HIV + elix_Lymphoma + elix_Mets + elix_Tumor + elix_Rheumatic +
elix_Coagulopathy + elix_Obesity + elix_WeightLoss + elix_FluidsLytes + elix_BloodLoss +
elix_Anemia + elix_Alcohol + elix_Drugs + elix_Psychoses + elix_Depression +
pain * lives_in_msa + strata(stratum)
other_fml_unadj <- als ~ other * lives_in_msa + strata(stratum)
other_fml_fulladj <- als ~ rate_outpatient_visits + intensity_outpatient_visits_dx +
rate_inpatient_stays + intensity_inpatient_stays_los +
elix_CHF + elix_Valvular + elix_PHTN + elix_PVD + elix_HTN +
elix_HTNcx + elix_Paralysis + elix_NeuroOther + elix_Pulmonary + elix_DM +
elix_DMcx + elix_Hypothyroid + elix_Renal + elix_Liver + elix_PUD +
elix_HIV + elix_Lymphoma + elix_Mets + elix_Tumor + elix_Rheumatic +
elix_Coagulopathy + elix_Obesity + elix_WeightLoss + elix_FluidsLytes + elix_BloodLoss +
elix_Anemia + elix_Alcohol + elix_Drugs + elix_Psychoses + elix_Depression +
other * lives_in_msa + strata(stratum)
falls_fml_unadj <- als ~ falls * lives_in_msa + strata(stratum)
falls_fml_fulladj <- als ~ rate_outpatient_visits + intensity_outpatient_visits_dx +
rate_inpatient_stays + intensity_inpatient_stays_los +
elix_CHF + elix_Valvular + elix_PHTN + elix_PVD + elix_HTN +
elix_HTNcx + elix_Paralysis + elix_NeuroOther + elix_Pulmonary + elix_DM +
elix_DMcx + elix_Hypothyroid + elix_Renal + elix_Liver + elix_PUD +
elix_HIV + elix_Lymphoma + elix_Mets + elix_Tumor + elix_Rheumatic +
elix_Coagulopathy + elix_Obesity + elix_WeightLoss + elix_FluidsLytes + elix_BloodLoss +
elix_Anemia + elix_Alcohol + elix_Drugs + elix_Psychoses + elix_Depression +
falls * lives_in_msa + strata(stratum)Sixth, does the risk increase with each additional symptom?
number_fml_unadj <- als ~ as.factor(n_total) * lives_in_msa + strata(stratum)
number_fml_fulladj <- als ~ rate_outpatient_visits + intensity_outpatient_visits_dx +
rate_inpatient_stays + intensity_inpatient_stays_los +
elix_CHF + elix_Valvular + elix_PHTN + elix_PVD + elix_HTN +
elix_HTNcx + elix_Paralysis + elix_NeuroOther + elix_Pulmonary + elix_DM +
elix_DMcx + elix_Hypothyroid + elix_Renal + elix_Liver + elix_PUD +
elix_HIV + elix_Lymphoma + elix_Mets + elix_Tumor + elix_Rheumatic +
elix_Coagulopathy + elix_Obesity + elix_WeightLoss + elix_FluidsLytes + elix_BloodLoss +
elix_Anemia + elix_Alcohol + elix_Drugs + elix_Psychoses + elix_Depression +
as.factor(n_total) * lives_in_msa + strata(stratum)Quick note: all of these models omit year, age, and sex. This is because the data are matched on age, sex, and enrollment start/end dates. Including the strata accounts for these factors while also properly clustering the errors.
Without adjustment:
clogit(
any_fml_unadj,
model_data
) |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| any_sxTRUE | 7.44 | 6.62 | 8.36 |
| lives_in_msaTRUE | 1.43 | 1.28 | 1.60 |
| any_sxTRUE:lives_in_msaTRUE | 0.84 | 0.75 | 0.96 |
The odds are increased following one or more symptom (OR = 7.44), for those living in MSAs (OR = 1.43), but there is a multiplicative decrease in odds for ALS for those with symptoms living in an MSA (OR = 0.84). The odds are still increased (OR = \(0.84 * 7.44 = 6.25\)) but less than for those who do not live in MSAs.
After adjustment, the story stays the same:
clogit(
any_fml_fulladj,
model_data
) |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| rate_outpatient_visits | 1.02 | 1.02 | 1.03 |
| intensity_outpatient_visits_dx | 1.15 | 1.10 | 1.19 |
| rate_inpatient_stays | 0.78 | 0.74 | 0.82 |
| intensity_inpatient_stays_los | 0.99 | 0.99 | 1.00 |
| elix_CHFTRUE | 0.64 | 0.59 | 0.69 |
| elix_ValvularTRUE | 0.97 | 0.92 | 1.03 |
| elix_PHTNTRUE | 0.99 | 0.90 | 1.09 |
| elix_PVDTRUE | 0.91 | 0.86 | 0.96 |
| elix_HTNTRUE | 0.98 | 0.94 | 1.02 |
| elix_HTNcxTRUE | 0.91 | 0.85 | 0.97 |
| elix_ParalysisTRUE | 3.00 | 2.78 | 3.23 |
| elix_NeuroOtherTRUE | 5.21 | 4.98 | 5.45 |
| elix_PulmonaryTRUE | 0.95 | 0.91 | 1.00 |
| elix_DMTRUE | 0.86 | 0.82 | 0.91 |
| elix_DMcxTRUE | 0.80 | 0.74 | 0.86 |
| elix_HypothyroidTRUE | 1.11 | 1.05 | 1.16 |
| elix_RenalTRUE | 0.60 | 0.55 | 0.65 |
| elix_LiverTRUE | 0.94 | 0.87 | 1.02 |
| elix_PUDTRUE | 1.00 | 0.80 | 1.25 |
| elix_HIVTRUE | 0.98 | 0.68 | 1.40 |
| elix_LymphomaTRUE | 1.20 | 1.05 | 1.38 |
| elix_MetsTRUE | 0.33 | 0.29 | 0.38 |
| elix_TumorTRUE | 0.86 | 0.81 | 0.92 |
| elix_RheumaticTRUE | 1.24 | 1.17 | 1.32 |
| elix_CoagulopathyTRUE | 0.85 | 0.78 | 0.93 |
| elix_ObesityTRUE | 0.83 | 0.78 | 0.88 |
| elix_WeightLossTRUE | 1.69 | 1.59 | 1.81 |
| elix_FluidsLytesTRUE | 0.80 | 0.75 | 0.85 |
| elix_BloodLossTRUE | 0.70 | 0.61 | 0.79 |
| elix_AnemiaTRUE | 1.05 | 0.99 | 1.10 |
| elix_AlcoholTRUE | 0.83 | 0.74 | 0.93 |
| elix_DrugsTRUE | 0.82 | 0.72 | 0.94 |
| elix_PsychosesTRUE | 0.82 | 0.77 | 0.87 |
| elix_DepressionTRUE | 0.97 | 0.92 | 1.02 |
| any_sxTRUE | 4.92 | 4.36 | 5.56 |
| lives_in_msaTRUE | 1.44 | 1.28 | 1.61 |
| any_sxTRUE:lives_in_msaTRUE | 0.83 | 0.73 | 0.94 |
Bulbar symptoms alone increases the odds before adjustment:
clogit(
any_bulbar_unadj,
model_data
) |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| bulbarTRUE | 6.39 | 5.74 | 7.11 |
| lives_in_msaTRUE | 1.30 | 1.23 | 1.37 |
| bulbarTRUE:lives_in_msaTRUE | 0.84 | 0.75 | 0.94 |
And unsurprisingly adjustment does not change the story:
clogit(
any_bulbar_fulladj,
model_data
) |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| rate_outpatient_visits | 1.03 | 1.03 | 1.03 |
| intensity_outpatient_visits_dx | 1.29 | 1.25 | 1.34 |
| rate_inpatient_stays | 0.78 | 0.74 | 0.83 |
| intensity_inpatient_stays_los | 0.99 | 0.99 | 1.00 |
| elix_CHFTRUE | 0.60 | 0.55 | 0.65 |
| elix_ValvularTRUE | 0.94 | 0.89 | 1.00 |
| elix_PHTNTRUE | 0.94 | 0.85 | 1.04 |
| elix_PVDTRUE | 0.92 | 0.87 | 0.98 |
| elix_HTNTRUE | 1.03 | 0.99 | 1.08 |
| elix_HTNcxTRUE | 0.88 | 0.82 | 0.94 |
| elix_ParalysisTRUE | 3.00 | 2.77 | 3.24 |
| elix_NeuroOtherTRUE | 5.23 | 4.99 | 5.47 |
| elix_PulmonaryTRUE | 0.93 | 0.89 | 0.97 |
| elix_DMTRUE | 0.85 | 0.80 | 0.90 |
| elix_DMcxTRUE | 0.80 | 0.74 | 0.87 |
| elix_HypothyroidTRUE | 1.10 | 1.04 | 1.15 |
| elix_RenalTRUE | 0.55 | 0.50 | 0.60 |
| elix_LiverTRUE | 0.95 | 0.88 | 1.03 |
| elix_PUDTRUE | 0.92 | 0.72 | 1.16 |
| elix_HIVTRUE | 0.85 | 0.59 | 1.22 |
| elix_LymphomaTRUE | 1.15 | 1.00 | 1.32 |
| elix_MetsTRUE | 0.30 | 0.26 | 0.34 |
| elix_TumorTRUE | 0.84 | 0.79 | 0.89 |
| elix_RheumaticTRUE | 1.36 | 1.27 | 1.45 |
| elix_CoagulopathyTRUE | 0.83 | 0.76 | 0.91 |
| elix_ObesityTRUE | 0.84 | 0.79 | 0.90 |
| elix_WeightLossTRUE | 1.57 | 1.47 | 1.67 |
| elix_FluidsLytesTRUE | 0.77 | 0.73 | 0.82 |
| elix_BloodLossTRUE | 0.65 | 0.57 | 0.74 |
| elix_AnemiaTRUE | 1.05 | 1.00 | 1.11 |
| elix_AlcoholTRUE | 0.88 | 0.78 | 0.99 |
| elix_DrugsTRUE | 0.83 | 0.72 | 0.96 |
| elix_PsychosesTRUE | 0.79 | 0.74 | 0.84 |
| elix_DepressionTRUE | 0.96 | 0.91 | 1.02 |
| bulbarTRUE | 3.80 | 3.37 | 4.29 |
| lives_in_msaTRUE | 1.27 | 1.20 | 1.35 |
| bulbarTRUE:lives_in_msaTRUE | 0.84 | 0.74 | 0.95 |
The same is true of motor symptoms
clogit(
any_motor_unadj,
model_data
) |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| motorTRUE | 5.64 | 5.07 | 6.27 |
| lives_in_msaTRUE | 1.42 | 1.29 | 1.57 |
| motorTRUE:lives_in_msaTRUE | 0.84 | 0.75 | 0.94 |
and with adjustment:
clogit(
any_motor_fulladj,
model_data
) |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| rate_outpatient_visits | 1.03 | 1.02 | 1.03 |
| intensity_outpatient_visits_dx | 1.19 | 1.15 | 1.23 |
| rate_inpatient_stays | 0.78 | 0.74 | 0.82 |
| intensity_inpatient_stays_los | 1.00 | 0.99 | 1.00 |
| elix_CHFTRUE | 0.63 | 0.58 | 0.68 |
| elix_ValvularTRUE | 0.97 | 0.92 | 1.02 |
| elix_PHTNTRUE | 0.98 | 0.89 | 1.08 |
| elix_PVDTRUE | 0.91 | 0.86 | 0.96 |
| elix_HTNTRUE | 0.98 | 0.94 | 1.02 |
| elix_HTNcxTRUE | 0.91 | 0.85 | 0.96 |
| elix_ParalysisTRUE | 3.03 | 2.81 | 3.27 |
| elix_NeuroOtherTRUE | 5.42 | 5.18 | 5.67 |
| elix_PulmonaryTRUE | 0.97 | 0.93 | 1.01 |
| elix_DMTRUE | 0.86 | 0.81 | 0.90 |
| elix_DMcxTRUE | 0.79 | 0.73 | 0.85 |
| elix_HypothyroidTRUE | 1.12 | 1.06 | 1.17 |
| elix_RenalTRUE | 0.59 | 0.54 | 0.64 |
| elix_LiverTRUE | 0.94 | 0.87 | 1.02 |
| elix_PUDTRUE | 1.02 | 0.82 | 1.28 |
| elix_HIVTRUE | 0.99 | 0.69 | 1.41 |
| elix_LymphomaTRUE | 1.19 | 1.04 | 1.36 |
| elix_MetsTRUE | 0.33 | 0.29 | 0.37 |
| elix_TumorTRUE | 0.86 | 0.81 | 0.91 |
| elix_RheumaticTRUE | 1.25 | 1.17 | 1.33 |
| elix_CoagulopathyTRUE | 0.84 | 0.77 | 0.92 |
| elix_ObesityTRUE | 0.83 | 0.78 | 0.88 |
| elix_WeightLossTRUE | 1.73 | 1.62 | 1.84 |
| elix_FluidsLytesTRUE | 0.80 | 0.75 | 0.84 |
| elix_BloodLossTRUE | 0.69 | 0.61 | 0.79 |
| elix_AnemiaTRUE | 1.04 | 0.99 | 1.09 |
| elix_AlcoholTRUE | 0.83 | 0.74 | 0.94 |
| elix_DrugsTRUE | 0.81 | 0.71 | 0.93 |
| elix_PsychosesTRUE | 0.81 | 0.76 | 0.86 |
| elix_DepressionTRUE | 0.97 | 0.92 | 1.02 |
| motorTRUE | 3.75 | 3.35 | 4.19 |
| lives_in_msaTRUE | 1.43 | 1.29 | 1.58 |
| motorTRUE:lives_in_msaTRUE | 0.82 | 0.73 | 0.92 |
Without adjustment:
clogit(
number_origin_unadj,
model_data
) |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| as.factor(I(bulbar + motor))1 | 5.98 | 5.30 | 6.74 |
| as.factor(I(bulbar + motor))2 | 26.38 | 22.68 | 30.67 |
| lives_in_msaTRUE | 1.45 | 1.30 | 1.62 |
| as.factor(I(bulbar + motor))1:lives_in_msaTRUE | 0.88 | 0.78 | 1.00 |
| as.factor(I(bulbar + motor))2:lives_in_msaTRUE | 0.71 | 0.61 | 0.84 |
And with adjustment
clogit(
number_origin_fulladj,
model_data
) |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| rate_outpatient_visits | 1.02 | 1.02 | 1.02 |
| intensity_outpatient_visits_dx | 1.13 | 1.09 | 1.17 |
| rate_inpatient_stays | 0.79 | 0.74 | 0.84 |
| intensity_inpatient_stays_los | 0.99 | 0.99 | 1.00 |
| elix_CHFTRUE | 0.63 | 0.59 | 0.68 |
| elix_ValvularTRUE | 0.95 | 0.90 | 1.01 |
| elix_PHTNTRUE | 0.98 | 0.88 | 1.08 |
| elix_PVDTRUE | 0.89 | 0.84 | 0.95 |
| elix_HTNTRUE | 0.98 | 0.94 | 1.02 |
| elix_HTNcxTRUE | 0.90 | 0.84 | 0.96 |
| elix_ParalysisTRUE | 2.77 | 2.56 | 2.99 |
| elix_NeuroOtherTRUE | 4.75 | 4.54 | 4.97 |
| elix_PulmonaryTRUE | 0.92 | 0.88 | 0.96 |
| elix_DMTRUE | 0.86 | 0.81 | 0.91 |
| elix_DMcxTRUE | 0.80 | 0.74 | 0.87 |
| elix_HypothyroidTRUE | 1.09 | 1.04 | 1.14 |
| elix_RenalTRUE | 0.60 | 0.55 | 0.66 |
| elix_LiverTRUE | 0.94 | 0.87 | 1.02 |
| elix_PUDTRUE | 0.95 | 0.75 | 1.20 |
| elix_HIVTRUE | 1.02 | 0.70 | 1.46 |
| elix_LymphomaTRUE | 1.19 | 1.04 | 1.37 |
| elix_MetsTRUE | 0.33 | 0.29 | 0.38 |
| elix_TumorTRUE | 0.86 | 0.80 | 0.91 |
| elix_RheumaticTRUE | 1.22 | 1.15 | 1.30 |
| elix_CoagulopathyTRUE | 0.85 | 0.78 | 0.93 |
| elix_ObesityTRUE | 0.81 | 0.76 | 0.86 |
| elix_WeightLossTRUE | 1.57 | 1.47 | 1.68 |
| elix_FluidsLytesTRUE | 0.78 | 0.74 | 0.83 |
| elix_BloodLossTRUE | 0.68 | 0.60 | 0.78 |
| elix_AnemiaTRUE | 1.05 | 0.99 | 1.10 |
| elix_AlcoholTRUE | 0.85 | 0.75 | 0.96 |
| elix_DrugsTRUE | 0.84 | 0.73 | 0.97 |
| elix_PsychosesTRUE | 0.81 | 0.76 | 0.86 |
| elix_DepressionTRUE | 0.94 | 0.89 | 0.99 |
| as.factor(I(bulbar + motor))1 | 4.37 | 3.85 | 4.95 |
| as.factor(I(bulbar + motor))2 | 13.11 | 11.14 | 15.43 |
| lives_in_msaTRUE | 1.44 | 1.29 | 1.62 |
| as.factor(I(bulbar + motor))1:lives_in_msaTRUE | 0.87 | 0.76 | 0.99 |
| as.factor(I(bulbar + motor))2:lives_in_msaTRUE | 0.70 | 0.59 | 0.83 |
speech_unadjusted <- clogit(
speech_fml_unadj,
model_data
)
speech_unadjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| speechTRUE | 7.33 | 6.57 | 8.19 |
| lives_in_msaTRUE | 1.30 | 1.23 | 1.37 |
| speechTRUE:lives_in_msaTRUE | 0.83 | 0.74 | 0.93 |
speech_adjusted <- clogit(
speech_fml_fulladj,
model_data
)
speech_adjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| rate_outpatient_visits | 1.03 | 1.03 | 1.03 |
| intensity_outpatient_visits_dx | 1.29 | 1.25 | 1.34 |
| rate_inpatient_stays | 0.78 | 0.73 | 0.83 |
| intensity_inpatient_stays_los | 0.99 | 0.99 | 1.00 |
| elix_CHFTRUE | 0.59 | 0.55 | 0.64 |
| elix_ValvularTRUE | 0.94 | 0.89 | 1.00 |
| elix_PHTNTRUE | 0.93 | 0.84 | 1.03 |
| elix_PVDTRUE | 0.92 | 0.87 | 0.98 |
| elix_HTNTRUE | 1.04 | 0.99 | 1.08 |
| elix_HTNcxTRUE | 0.88 | 0.83 | 0.94 |
| elix_ParalysisTRUE | 2.96 | 2.74 | 3.20 |
| elix_NeuroOtherTRUE | 5.15 | 4.92 | 5.39 |
| elix_PulmonaryTRUE | 0.93 | 0.89 | 0.97 |
| elix_DMTRUE | 0.85 | 0.80 | 0.90 |
| elix_DMcxTRUE | 0.80 | 0.74 | 0.87 |
| elix_HypothyroidTRUE | 1.10 | 1.05 | 1.16 |
| elix_RenalTRUE | 0.55 | 0.50 | 0.60 |
| elix_LiverTRUE | 0.95 | 0.88 | 1.03 |
| elix_PUDTRUE | 0.90 | 0.71 | 1.14 |
| elix_HIVTRUE | 0.87 | 0.60 | 1.24 |
| elix_LymphomaTRUE | 1.16 | 1.01 | 1.33 |
| elix_MetsTRUE | 0.30 | 0.26 | 0.34 |
| elix_TumorTRUE | 0.84 | 0.79 | 0.89 |
| elix_RheumaticTRUE | 1.36 | 1.28 | 1.45 |
| elix_CoagulopathyTRUE | 0.83 | 0.76 | 0.91 |
| elix_ObesityTRUE | 0.85 | 0.80 | 0.90 |
| elix_WeightLossTRUE | 1.55 | 1.45 | 1.66 |
| elix_FluidsLytesTRUE | 0.77 | 0.73 | 0.82 |
| elix_BloodLossTRUE | 0.65 | 0.57 | 0.74 |
| elix_AnemiaTRUE | 1.05 | 1.00 | 1.11 |
| elix_AlcoholTRUE | 0.87 | 0.77 | 0.98 |
| elix_DrugsTRUE | 0.83 | 0.72 | 0.96 |
| elix_PsychosesTRUE | 0.79 | 0.74 | 0.84 |
| elix_DepressionTRUE | 0.96 | 0.91 | 1.02 |
| speechTRUE | 4.28 | 3.78 | 4.85 |
| lives_in_msaTRUE | 1.27 | 1.20 | 1.35 |
| speechTRUE:lives_in_msaTRUE | 0.83 | 0.72 | 0.94 |
swallowing_unadjusted <- clogit(
swallowing_fml_unadj,
model_data
)
swallowing_unadjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| swallowingTRUE | 1.68 | 1.24 | 2.26 |
| lives_in_msaTRUE | 1.23 | 1.17 | 1.28 |
| swallowingTRUE:lives_in_msaTRUE | 1.22 | 0.89 | 1.67 |
swallowing_adjusted <- clogit(
swallowing_fml_fulladj,
model_data
)
swallowing_adjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| rate_outpatient_visits | 1.03 | 1.03 | 1.04 |
| intensity_outpatient_visits_dx | 1.33 | 1.29 | 1.37 |
| rate_inpatient_stays | 0.77 | 0.73 | 0.82 |
| intensity_inpatient_stays_los | 1.00 | 0.99 | 1.00 |
| elix_CHFTRUE | 0.60 | 0.56 | 0.65 |
| elix_ValvularTRUE | 0.96 | 0.91 | 1.02 |
| elix_PHTNTRUE | 0.95 | 0.86 | 1.05 |
| elix_PVDTRUE | 0.94 | 0.88 | 0.99 |
| elix_HTNTRUE | 1.03 | 0.99 | 1.07 |
| elix_HTNcxTRUE | 0.89 | 0.84 | 0.95 |
| elix_ParalysisTRUE | 3.30 | 3.06 | 3.56 |
| elix_NeuroOtherTRUE | 5.99 | 5.73 | 6.26 |
| elix_PulmonaryTRUE | 0.98 | 0.94 | 1.03 |
| elix_DMTRUE | 0.85 | 0.80 | 0.90 |
| elix_DMcxTRUE | 0.78 | 0.73 | 0.85 |
| elix_HypothyroidTRUE | 1.13 | 1.07 | 1.18 |
| elix_RenalTRUE | 0.54 | 0.50 | 0.59 |
| elix_LiverTRUE | 0.95 | 0.88 | 1.03 |
| elix_PUDTRUE | 1.01 | 0.80 | 1.26 |
| elix_HIVTRUE | 0.85 | 0.59 | 1.21 |
| elix_LymphomaTRUE | 1.16 | 1.01 | 1.33 |
| elix_MetsTRUE | 0.30 | 0.27 | 0.34 |
| elix_TumorTRUE | 0.84 | 0.80 | 0.90 |
| elix_RheumaticTRUE | 1.37 | 1.29 | 1.46 |
| elix_CoagulopathyTRUE | 0.83 | 0.76 | 0.91 |
| elix_ObesityTRUE | 0.86 | 0.81 | 0.91 |
| elix_WeightLossTRUE | 1.75 | 1.64 | 1.86 |
| elix_FluidsLytesTRUE | 0.80 | 0.75 | 0.84 |
| elix_BloodLossTRUE | 0.67 | 0.58 | 0.76 |
| elix_AnemiaTRUE | 1.05 | 1.00 | 1.10 |
| elix_AlcoholTRUE | 0.86 | 0.76 | 0.97 |
| elix_DrugsTRUE | 0.80 | 0.70 | 0.92 |
| elix_PsychosesTRUE | 0.80 | 0.75 | 0.85 |
| elix_DepressionTRUE | 1.00 | 0.95 | 1.05 |
| swallowingTRUE | 1.23 | 0.87 | 1.73 |
| lives_in_msaTRUE | 1.21 | 1.15 | 1.28 |
| swallowingTRUE:lives_in_msaTRUE | 1.20 | 0.84 | 1.72 |
strength_unadjusted <- clogit(
strength_fml_unadj,
model_data
)
strength_unadjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| strengthTRUE | 16.13 | 14.34 | 18.14 |
| lives_in_msaTRUE | 1.33 | 1.25 | 1.40 |
| strengthTRUE:lives_in_msaTRUE | 0.74 | 0.66 | 0.84 |
strength_adjusted <- clogit(
strength_fml_fulladj,
model_data
)
strength_adjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| rate_outpatient_visits | 1.03 | 1.03 | 1.03 |
| intensity_outpatient_visits_dx | 1.22 | 1.17 | 1.26 |
| rate_inpatient_stays | 0.77 | 0.72 | 0.81 |
| intensity_inpatient_stays_los | 0.99 | 0.99 | 1.00 |
| elix_CHFTRUE | 0.57 | 0.53 | 0.62 |
| elix_ValvularTRUE | 0.98 | 0.92 | 1.03 |
| elix_PHTNTRUE | 0.91 | 0.82 | 1.02 |
| elix_PVDTRUE | 0.88 | 0.82 | 0.93 |
| elix_HTNTRUE | 1.05 | 1.00 | 1.09 |
| elix_HTNcxTRUE | 0.91 | 0.85 | 0.97 |
| elix_ParalysisTRUE | 2.33 | 2.14 | 2.53 |
| elix_NeuroOtherTRUE | 5.05 | 4.82 | 5.30 |
| elix_PulmonaryTRUE | 1.00 | 0.96 | 1.05 |
| elix_DMTRUE | 0.87 | 0.82 | 0.92 |
| elix_DMcxTRUE | 0.75 | 0.69 | 0.81 |
| elix_HypothyroidTRUE | 1.14 | 1.08 | 1.20 |
| elix_RenalTRUE | 0.52 | 0.47 | 0.57 |
| elix_LiverTRUE | 0.97 | 0.89 | 1.05 |
| elix_PUDTRUE | 1.06 | 0.83 | 1.36 |
| elix_HIVTRUE | 0.94 | 0.64 | 1.38 |
| elix_LymphomaTRUE | 1.17 | 1.01 | 1.35 |
| elix_MetsTRUE | 0.30 | 0.26 | 0.35 |
| elix_TumorTRUE | 0.86 | 0.80 | 0.91 |
| elix_RheumaticTRUE | 1.28 | 1.19 | 1.36 |
| elix_CoagulopathyTRUE | 0.80 | 0.73 | 0.88 |
| elix_ObesityTRUE | 0.83 | 0.78 | 0.89 |
| elix_WeightLossTRUE | 1.61 | 1.51 | 1.73 |
| elix_FluidsLytesTRUE | 0.75 | 0.70 | 0.80 |
| elix_BloodLossTRUE | 0.61 | 0.53 | 0.70 |
| elix_AnemiaTRUE | 1.03 | 0.98 | 1.09 |
| elix_AlcoholTRUE | 0.88 | 0.77 | 1.00 |
| elix_DrugsTRUE | 0.83 | 0.72 | 0.97 |
| elix_PsychosesTRUE | 0.81 | 0.76 | 0.87 |
| elix_DepressionTRUE | 0.95 | 0.90 | 1.01 |
| strengthTRUE | 10.47 | 9.18 | 11.93 |
| lives_in_msaTRUE | 1.31 | 1.24 | 1.39 |
| strengthTRUE:lives_in_msaTRUE | 0.74 | 0.64 | 0.85 |
gait_unadjusted <- clogit(
gait_fml_unadj,
model_data
)
gait_unadjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| gaitTRUE | 6.37 | 5.71 | 7.11 |
| lives_in_msaTRUE | 1.25 | 1.18 | 1.32 |
| gaitTRUE:lives_in_msaTRUE | 0.86 | 0.77 | 0.97 |
gait_adjusted <- clogit(
gait_fml_fulladj,
model_data
)
gait_adjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| rate_outpatient_visits | 1.03 | 1.03 | 1.03 |
| intensity_outpatient_visits_dx | 1.29 | 1.25 | 1.34 |
| rate_inpatient_stays | 0.74 | 0.70 | 0.79 |
| intensity_inpatient_stays_los | 0.99 | 0.99 | 1.00 |
| elix_CHFTRUE | 0.59 | 0.55 | 0.64 |
| elix_ValvularTRUE | 0.97 | 0.92 | 1.03 |
| elix_PHTNTRUE | 0.92 | 0.83 | 1.02 |
| elix_PVDTRUE | 0.89 | 0.84 | 0.94 |
| elix_HTNTRUE | 1.02 | 0.98 | 1.07 |
| elix_HTNcxTRUE | 0.88 | 0.83 | 0.94 |
| elix_ParalysisTRUE | 2.69 | 2.48 | 2.91 |
| elix_NeuroOtherTRUE | 5.20 | 4.97 | 5.44 |
| elix_PulmonaryTRUE | 1.00 | 0.96 | 1.05 |
| elix_DMTRUE | 0.86 | 0.82 | 0.91 |
| elix_DMcxTRUE | 0.76 | 0.71 | 0.83 |
| elix_HypothyroidTRUE | 1.14 | 1.08 | 1.20 |
| elix_RenalTRUE | 0.55 | 0.50 | 0.60 |
| elix_LiverTRUE | 0.97 | 0.90 | 1.05 |
| elix_PUDTRUE | 1.06 | 0.84 | 1.33 |
| elix_HIVTRUE | 0.87 | 0.61 | 1.25 |
| elix_LymphomaTRUE | 1.18 | 1.03 | 1.36 |
| elix_MetsTRUE | 0.30 | 0.27 | 0.35 |
| elix_TumorTRUE | 0.85 | 0.80 | 0.91 |
| elix_RheumaticTRUE | 1.32 | 1.24 | 1.41 |
| elix_CoagulopathyTRUE | 0.82 | 0.75 | 0.89 |
| elix_ObesityTRUE | 0.83 | 0.78 | 0.88 |
| elix_WeightLossTRUE | 1.72 | 1.61 | 1.84 |
| elix_FluidsLytesTRUE | 0.77 | 0.72 | 0.81 |
| elix_BloodLossTRUE | 0.65 | 0.57 | 0.75 |
| elix_AnemiaTRUE | 1.03 | 0.97 | 1.08 |
| elix_AlcoholTRUE | 0.85 | 0.76 | 0.96 |
| elix_DrugsTRUE | 0.80 | 0.70 | 0.93 |
| elix_PsychosesTRUE | 0.77 | 0.72 | 0.82 |
| elix_DepressionTRUE | 0.98 | 0.92 | 1.03 |
| gaitTRUE | 3.22 | 2.84 | 3.65 |
| lives_in_msaTRUE | 1.24 | 1.17 | 1.31 |
| gaitTRUE:lives_in_msaTRUE | 0.90 | 0.79 | 1.02 |
involuntary_movements_unadjusted <- clogit(
involuntary_movement_fml_unadj,
model_data
)
involuntary_movements_unadjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| involuntary_movementTRUE | 5.06 | 4.51 | 5.67 |
| lives_in_msaTRUE | 1.26 | 1.19 | 1.32 |
| involuntary_movementTRUE:lives_in_msaTRUE | 0.97 | 0.85 | 1.09 |
involuntary_movements_adjusted <- clogit(
involuntary_movement_fml_fulladj,
model_data
)
involuntary_movements_adjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| rate_outpatient_visits | 1.03 | 1.03 | 1.03 |
| intensity_outpatient_visits_dx | 1.28 | 1.23 | 1.32 |
| rate_inpatient_stays | 0.79 | 0.75 | 0.84 |
| intensity_inpatient_stays_los | 1.00 | 0.99 | 1.00 |
| elix_CHFTRUE | 0.61 | 0.57 | 0.66 |
| elix_ValvularTRUE | 0.97 | 0.91 | 1.02 |
| elix_PHTNTRUE | 0.96 | 0.87 | 1.06 |
| elix_PVDTRUE | 0.94 | 0.88 | 0.99 |
| elix_HTNTRUE | 1.02 | 0.98 | 1.07 |
| elix_HTNcxTRUE | 0.89 | 0.84 | 0.95 |
| elix_ParalysisTRUE | 3.11 | 2.87 | 3.36 |
| elix_NeuroOtherTRUE | 5.57 | 5.33 | 5.83 |
| elix_PulmonaryTRUE | 0.97 | 0.93 | 1.02 |
| elix_DMTRUE | 0.86 | 0.82 | 0.91 |
| elix_DMcxTRUE | 0.80 | 0.74 | 0.86 |
| elix_HypothyroidTRUE | 1.12 | 1.07 | 1.18 |
| elix_RenalTRUE | 0.55 | 0.50 | 0.60 |
| elix_LiverTRUE | 0.93 | 0.86 | 1.01 |
| elix_PUDTRUE | 0.95 | 0.75 | 1.20 |
| elix_HIVTRUE | 0.94 | 0.66 | 1.34 |
| elix_LymphomaTRUE | 1.19 | 1.03 | 1.36 |
| elix_MetsTRUE | 0.31 | 0.27 | 0.35 |
| elix_TumorTRUE | 0.86 | 0.80 | 0.91 |
| elix_RheumaticTRUE | 1.30 | 1.22 | 1.39 |
| elix_CoagulopathyTRUE | 0.84 | 0.77 | 0.92 |
| elix_ObesityTRUE | 0.86 | 0.81 | 0.91 |
| elix_WeightLossTRUE | 1.72 | 1.61 | 1.84 |
| elix_FluidsLytesTRUE | 0.79 | 0.74 | 0.84 |
| elix_BloodLossTRUE | 0.67 | 0.59 | 0.76 |
| elix_AnemiaTRUE | 1.05 | 1.00 | 1.10 |
| elix_AlcoholTRUE | 0.85 | 0.76 | 0.96 |
| elix_DrugsTRUE | 0.74 | 0.64 | 0.86 |
| elix_PsychosesTRUE | 0.78 | 0.73 | 0.84 |
| elix_DepressionTRUE | 0.97 | 0.92 | 1.02 |
| involuntary_movementTRUE | 3.23 | 2.83 | 3.68 |
| lives_in_msaTRUE | 1.24 | 1.17 | 1.31 |
| involuntary_movementTRUE:lives_in_msaTRUE | 0.96 | 0.83 | 1.10 |
pain_unadjusted <- clogit(
pain_fml_unadj,
model_data
)
pain_unadjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| painTRUE | 2.11 | 1.94 | 2.30 |
| lives_in_msaTRUE | 1.29 | 1.20 | 1.38 |
| painTRUE:lives_in_msaTRUE | 0.93 | 0.85 | 1.02 |
pain_adjusted <- clogit(
pain_fml_fulladj,
model_data
)
pain_adjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| rate_outpatient_visits | 1.03 | 1.03 | 1.03 |
| intensity_outpatient_visits_dx | 1.30 | 1.26 | 1.35 |
| rate_inpatient_stays | 0.77 | 0.73 | 0.82 |
| intensity_inpatient_stays_los | 1.00 | 0.99 | 1.00 |
| elix_CHFTRUE | 0.61 | 0.56 | 0.65 |
| elix_ValvularTRUE | 0.96 | 0.91 | 1.02 |
| elix_PHTNTRUE | 0.95 | 0.86 | 1.05 |
| elix_PVDTRUE | 0.92 | 0.87 | 0.98 |
| elix_HTNTRUE | 1.02 | 0.98 | 1.06 |
| elix_HTNcxTRUE | 0.89 | 0.84 | 0.95 |
| elix_ParalysisTRUE | 3.27 | 3.03 | 3.53 |
| elix_NeuroOtherTRUE | 5.97 | 5.71 | 6.24 |
| elix_PulmonaryTRUE | 0.98 | 0.93 | 1.02 |
| elix_DMTRUE | 0.85 | 0.80 | 0.90 |
| elix_DMcxTRUE | 0.78 | 0.72 | 0.84 |
| elix_HypothyroidTRUE | 1.12 | 1.07 | 1.18 |
| elix_RenalTRUE | 0.55 | 0.50 | 0.60 |
| elix_LiverTRUE | 0.95 | 0.88 | 1.03 |
| elix_PUDTRUE | 1.01 | 0.80 | 1.27 |
| elix_HIVTRUE | 0.89 | 0.62 | 1.27 |
| elix_LymphomaTRUE | 1.16 | 1.02 | 1.34 |
| elix_MetsTRUE | 0.31 | 0.27 | 0.35 |
| elix_TumorTRUE | 0.85 | 0.80 | 0.90 |
| elix_RheumaticTRUE | 1.32 | 1.24 | 1.41 |
| elix_CoagulopathyTRUE | 0.83 | 0.76 | 0.91 |
| elix_ObesityTRUE | 0.85 | 0.80 | 0.90 |
| elix_WeightLossTRUE | 1.76 | 1.65 | 1.87 |
| elix_FluidsLytesTRUE | 0.80 | 0.75 | 0.84 |
| elix_BloodLossTRUE | 0.67 | 0.59 | 0.76 |
| elix_AnemiaTRUE | 1.04 | 0.99 | 1.10 |
| elix_AlcoholTRUE | 0.85 | 0.76 | 0.96 |
| elix_DrugsTRUE | 0.80 | 0.69 | 0.91 |
| elix_PsychosesTRUE | 0.80 | 0.75 | 0.85 |
| elix_DepressionTRUE | 0.99 | 0.94 | 1.04 |
| painTRUE | 1.47 | 1.33 | 1.62 |
| lives_in_msaTRUE | 1.29 | 1.20 | 1.39 |
| painTRUE:lives_in_msaTRUE | 0.91 | 0.82 | 1.00 |
falls_unadjusted <- clogit(
falls_fml_unadj,
model_data
)
falls_unadjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| fallsTRUE | 2.46 | 2.02 | 2.99 |
| lives_in_msaTRUE | 1.24 | 1.18 | 1.29 |
| fallsTRUE:lives_in_msaTRUE | 1.02 | 0.83 | 1.26 |
falls_adjusted <- clogit(
falls_fml_fulladj,
model_data
)
falls_adjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| rate_outpatient_visits | 1.03 | 1.03 | 1.04 |
| intensity_outpatient_visits_dx | 1.33 | 1.28 | 1.37 |
| rate_inpatient_stays | 0.77 | 0.73 | 0.81 |
| intensity_inpatient_stays_los | 1.00 | 0.99 | 1.00 |
| elix_CHFTRUE | 0.60 | 0.56 | 0.65 |
| elix_ValvularTRUE | 0.97 | 0.91 | 1.02 |
| elix_PHTNTRUE | 0.95 | 0.86 | 1.05 |
| elix_PVDTRUE | 0.94 | 0.88 | 0.99 |
| elix_HTNTRUE | 1.03 | 0.99 | 1.07 |
| elix_HTNcxTRUE | 0.89 | 0.84 | 0.95 |
| elix_ParalysisTRUE | 3.26 | 3.03 | 3.52 |
| elix_NeuroOtherTRUE | 5.96 | 5.70 | 6.23 |
| elix_PulmonaryTRUE | 0.98 | 0.94 | 1.03 |
| elix_DMTRUE | 0.85 | 0.81 | 0.90 |
| elix_DMcxTRUE | 0.78 | 0.72 | 0.84 |
| elix_HypothyroidTRUE | 1.13 | 1.08 | 1.19 |
| elix_RenalTRUE | 0.54 | 0.50 | 0.59 |
| elix_LiverTRUE | 0.95 | 0.88 | 1.03 |
| elix_PUDTRUE | 1.01 | 0.81 | 1.27 |
| elix_HIVTRUE | 0.85 | 0.60 | 1.22 |
| elix_LymphomaTRUE | 1.16 | 1.01 | 1.33 |
| elix_MetsTRUE | 0.30 | 0.27 | 0.34 |
| elix_TumorTRUE | 0.85 | 0.80 | 0.90 |
| elix_RheumaticTRUE | 1.37 | 1.29 | 1.46 |
| elix_CoagulopathyTRUE | 0.83 | 0.76 | 0.90 |
| elix_ObesityTRUE | 0.86 | 0.81 | 0.91 |
| elix_WeightLossTRUE | 1.75 | 1.64 | 1.87 |
| elix_FluidsLytesTRUE | 0.79 | 0.75 | 0.84 |
| elix_BloodLossTRUE | 0.67 | 0.58 | 0.76 |
| elix_AnemiaTRUE | 1.05 | 1.00 | 1.10 |
| elix_AlcoholTRUE | 0.85 | 0.76 | 0.96 |
| elix_DrugsTRUE | 0.80 | 0.69 | 0.92 |
| elix_PsychosesTRUE | 0.79 | 0.75 | 0.85 |
| elix_DepressionTRUE | 0.99 | 0.94 | 1.05 |
| fallsTRUE | 1.20 | 0.95 | 1.51 |
| lives_in_msaTRUE | 1.22 | 1.16 | 1.28 |
| fallsTRUE:lives_in_msaTRUE | 1.04 | 0.81 | 1.33 |
other_unadjusted <- clogit(
other_fml_unadj,
model_data
)
other_unadjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| otherTRUE | 7.13 | 6.50 | 7.83 |
| lives_in_msaTRUE | 1.35 | 1.27 | 1.44 |
| otherTRUE:lives_in_msaTRUE | 0.81 | 0.74 | 0.90 |
other_adjusted <- clogit(
other_fml_fulladj,
model_data
)
other_adjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| rate_outpatient_visits | 1.03 | 1.02 | 1.03 |
| intensity_outpatient_visits_dx | 1.23 | 1.19 | 1.27 |
| rate_inpatient_stays | 0.80 | 0.76 | 0.85 |
| intensity_inpatient_stays_los | 1.00 | 0.99 | 1.00 |
| elix_CHFTRUE | 0.61 | 0.57 | 0.66 |
| elix_ValvularTRUE | 0.96 | 0.91 | 1.02 |
| elix_PHTNTRUE | 0.96 | 0.86 | 1.06 |
| elix_PVDTRUE | 0.90 | 0.85 | 0.96 |
| elix_HTNTRUE | 1.03 | 0.99 | 1.07 |
| elix_HTNcxTRUE | 0.90 | 0.84 | 0.96 |
| elix_ParalysisTRUE | 2.68 | 2.47 | 2.90 |
| elix_NeuroOtherTRUE | 5.36 | 5.12 | 5.61 |
| elix_PulmonaryTRUE | 0.98 | 0.94 | 1.03 |
| elix_DMTRUE | 0.86 | 0.82 | 0.91 |
| elix_DMcxTRUE | 0.77 | 0.71 | 0.83 |
| elix_HypothyroidTRUE | 1.11 | 1.06 | 1.17 |
| elix_RenalTRUE | 0.56 | 0.51 | 0.61 |
| elix_LiverTRUE | 0.94 | 0.87 | 1.02 |
| elix_PUDTRUE | 0.99 | 0.78 | 1.25 |
| elix_HIVTRUE | 0.93 | 0.64 | 1.35 |
| elix_LymphomaTRUE | 1.21 | 1.05 | 1.40 |
| elix_MetsTRUE | 0.33 | 0.29 | 0.38 |
| elix_TumorTRUE | 0.86 | 0.81 | 0.92 |
| elix_RheumaticTRUE | 1.24 | 1.16 | 1.32 |
| elix_CoagulopathyTRUE | 0.83 | 0.76 | 0.91 |
| elix_ObesityTRUE | 0.82 | 0.77 | 0.87 |
| elix_WeightLossTRUE | 1.69 | 1.59 | 1.81 |
| elix_FluidsLytesTRUE | 0.77 | 0.72 | 0.81 |
| elix_BloodLossTRUE | 0.65 | 0.57 | 0.75 |
| elix_AnemiaTRUE | 1.04 | 0.99 | 1.10 |
| elix_AlcoholTRUE | 0.89 | 0.78 | 1.00 |
| elix_DrugsTRUE | 0.78 | 0.67 | 0.90 |
| elix_PsychosesTRUE | 0.81 | 0.76 | 0.87 |
| elix_DepressionTRUE | 0.97 | 0.91 | 1.02 |
| otherTRUE | 4.77 | 4.31 | 5.28 |
| lives_in_msaTRUE | 1.34 | 1.26 | 1.43 |
| otherTRUE:lives_in_msaTRUE | 0.81 | 0.73 | 0.90 |
To summarize these in a practical way:
list(
speech_unadjusted,
swallowing_unadjusted,
strength_unadjusted,
gait_unadjusted,
involuntary_movements_unadjusted,
pain_unadjusted,
falls_unadjusted,
other_unadjusted
) |>
lapply(
broom::tidy,
exponentiate = TRUE,
conf.int = TRUE
) |>
enframe() |>
mutate(
symptom = c("Speech", "Swallowing", "Muscle",
"Gait", "Involuntary\nMovements", "Pain", "Falls",
"Other Motor")
) |>
unnest(cols = value) |>
mutate(
variable = rep(c("Symptom", "Lives in Urban Area", "Symptom x Lives in Urban Area"), 8)
) |>
mutate(
symptom = forcats::fct_relevel(
symptom,
"Speech", "Swallowing", "Muscle",
"Gait", "Involuntary\nMovements", "Pain", "Falls",
"Other Motor"
),
variable = forcats::fct_relevel(
variable,
"Symptom", "Lives in Urban Area", "Symptom x Lives in Urban Area"
)
) |>
ggplot(
aes(
x = symptom,
y = estimate,
ymin = conf.low,
ymax = conf.high
)
) +
geom_point() +
geom_linerange() +
facet_grid(rows = vars(variable), scale = "free_y") +
geom_hline(yintercept = 1, linetype = 2) +
labs(x = "", y = "Odds Ratio\n(95% CI)") +
theme_bw()
list(
speech_adjusted,
swallowing_adjusted,
strength_adjusted,
gait_adjusted,
involuntary_movements_adjusted,
pain_adjusted,
falls_adjusted,
other_adjusted
) |>
lapply(
broom::tidy,
exponentiate = TRUE,
conf.int = TRUE
) |>
enframe() |>
mutate(
symptom = c("Speech", "Swallowing", "Muscle",
"Gait", "Involuntary\nMovements", "Pain", "Falls",
"Other Motor")
) |>
unnest(cols = value) |>
group_by(symptom) |>
filter(row_number() >= 35) |>
ungroup() |>
mutate(
variable = rep(c("Symptom", "Lives in Urban Area", "Symptom x Lives in Urban Area"), 8)
) |>
mutate(
symptom = forcats::fct_relevel(
symptom,
"Speech", "Swallowing", "Muscle",
"Gait", "Involuntary\nMovements", "Pain", "Falls",
"Other Motor"
),
variable = forcats::fct_relevel(
variable,
"Symptom", "Lives in Urban Area", "Symptom x Lives in Urban Area"
)
) |>
ggplot(
aes(
x = symptom,
y = estimate,
ymin = conf.low,
ymax = conf.high
)
) +
geom_point() +
geom_linerange() +
facet_grid(rows = vars(variable), scale = "free_y") +
geom_hline(yintercept = 1, linetype = 2) +
labs(x = "", y = "Odds Ratio\n(95% CI)") +
theme_bw() +
scale_y_log10()
ggsave("~/projects/als-sx/fig_1.svg", width = 8, height = 8)n_symptoms_unadjusted <- clogit(
number_fml_unadj,
model_data
)
n_symptoms_unadjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| as.factor(n_total)1 | 3.00 | 2.61 | 3.46 |
| as.factor(n_total)2 | 9.61 | 8.27 | 11.17 |
| as.factor(n_total)3 | 21.46 | 18.27 | 25.22 |
| as.factor(n_total)4 | 42.06 | 34.82 | 50.80 |
| as.factor(n_total)5 | 66.20 | 50.74 | 86.37 |
| as.factor(n_total)6 | 57.26 | 39.58 | 82.82 |
| as.factor(n_total)7 | 43.86 | 22.42 | 85.83 |
| as.factor(n_total)8 | 26.13 | 8.41 | 81.21 |
| lives_in_msaTRUE | 1.47 | 1.31 | 1.64 |
| as.factor(n_total)1:lives_in_msaTRUE | 0.98 | 0.84 | 1.14 |
| as.factor(n_total)2:lives_in_msaTRUE | 0.80 | 0.68 | 0.94 |
| as.factor(n_total)3:lives_in_msaTRUE | 0.76 | 0.64 | 0.90 |
| as.factor(n_total)4:lives_in_msaTRUE | 0.71 | 0.58 | 0.87 |
| as.factor(n_total)5:lives_in_msaTRUE | 0.62 | 0.47 | 0.82 |
| as.factor(n_total)6:lives_in_msaTRUE | 0.77 | 0.52 | 1.15 |
| as.factor(n_total)7:lives_in_msaTRUE | 1.10 | 0.54 | 2.26 |
| as.factor(n_total)8:lives_in_msaTRUE | NA | NA | NA |
n_symptoms_adjusted <- clogit(
number_fml_fulladj,
model_data
)
n_symptoms_adjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
select(term, estimate, conf.low, conf.high) |>
knitr::kable(digits = 2)| term | estimate | conf.low | conf.high |
|---|---|---|---|
| rate_outpatient_visits | 1.02 | 1.01 | 1.02 |
| intensity_outpatient_visits_dx | 1.06 | 1.02 | 1.10 |
| rate_inpatient_stays | 0.79 | 0.74 | 0.84 |
| intensity_inpatient_stays_los | 0.99 | 0.99 | 1.00 |
| elix_CHFTRUE | 0.64 | 0.59 | 0.69 |
| elix_ValvularTRUE | 0.96 | 0.90 | 1.02 |
| elix_PHTNTRUE | 0.99 | 0.89 | 1.09 |
| elix_PVDTRUE | 0.84 | 0.79 | 0.89 |
| elix_HTNTRUE | 0.98 | 0.94 | 1.03 |
| elix_HTNcxTRUE | 0.90 | 0.84 | 0.96 |
| elix_ParalysisTRUE | 2.21 | 2.04 | 2.39 |
| elix_NeuroOtherTRUE | 4.14 | 3.94 | 4.34 |
| elix_PulmonaryTRUE | 0.94 | 0.90 | 0.99 |
| elix_DMTRUE | 0.89 | 0.84 | 0.94 |
| elix_DMcxTRUE | 0.77 | 0.71 | 0.84 |
| elix_HypothyroidTRUE | 1.09 | 1.03 | 1.15 |
| elix_RenalTRUE | 0.61 | 0.56 | 0.67 |
| elix_LiverTRUE | 0.93 | 0.85 | 1.01 |
| elix_PUDTRUE | 0.98 | 0.77 | 1.25 |
| elix_HIVTRUE | 1.13 | 0.78 | 1.66 |
| elix_LymphomaTRUE | 1.24 | 1.08 | 1.43 |
| elix_MetsTRUE | 0.35 | 0.30 | 0.40 |
| elix_TumorTRUE | 0.87 | 0.82 | 0.93 |
| elix_RheumaticTRUE | 1.11 | 1.03 | 1.18 |
| elix_CoagulopathyTRUE | 0.84 | 0.77 | 0.92 |
| elix_ObesityTRUE | 0.78 | 0.73 | 0.83 |
| elix_WeightLossTRUE | 1.55 | 1.45 | 1.66 |
| elix_FluidsLytesTRUE | 0.74 | 0.70 | 0.79 |
| elix_BloodLossTRUE | 0.67 | 0.58 | 0.76 |
| elix_AnemiaTRUE | 1.02 | 0.96 | 1.07 |
| elix_AlcoholTRUE | 0.86 | 0.76 | 0.98 |
| elix_DrugsTRUE | 0.80 | 0.69 | 0.92 |
| elix_PsychosesTRUE | 0.80 | 0.75 | 0.85 |
| elix_DepressionTRUE | 0.90 | 0.85 | 0.95 |
| as.factor(n_total)1 | 2.63 | 2.28 | 3.04 |
| as.factor(n_total)2 | 7.42 | 6.35 | 8.68 |
| as.factor(n_total)3 | 15.17 | 12.79 | 17.99 |
| as.factor(n_total)4 | 26.65 | 21.72 | 32.70 |
| as.factor(n_total)5 | 33.20 | 24.80 | 44.44 |
| as.factor(n_total)6 | 22.63 | 14.96 | 34.23 |
| as.factor(n_total)7 | 16.36 | 7.78 | 34.41 |
| as.factor(n_total)8 | 7.66 | 2.29 | 25.58 |
| lives_in_msaTRUE | 1.46 | 1.30 | 1.63 |
| as.factor(n_total)1:lives_in_msaTRUE | 0.97 | 0.84 | 1.14 |
| as.factor(n_total)2:lives_in_msaTRUE | 0.79 | 0.67 | 0.93 |
| as.factor(n_total)3:lives_in_msaTRUE | 0.75 | 0.63 | 0.90 |
| as.factor(n_total)4:lives_in_msaTRUE | 0.73 | 0.59 | 0.91 |
| as.factor(n_total)5:lives_in_msaTRUE | 0.67 | 0.49 | 0.90 |
| as.factor(n_total)6:lives_in_msaTRUE | 0.91 | 0.58 | 1.40 |
| as.factor(n_total)7:lives_in_msaTRUE | 1.38 | 0.62 | 3.06 |
| as.factor(n_total)8:lives_in_msaTRUE | NA | NA | NA |
n_symptoms_adjusted |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
filter(!stringr::str_detect(term, "msa"), stringr::str_detect(term, "as.factor")) |>
mutate(
variable = 1:8
) |>
ggplot(aes(x = variable,
y = estimate,
ymin = conf.low,
ymax = conf.high)) +
geom_point() +
geom_linerange() +
labs(x = "Number of Symptoms", y = "ORs Compared to Having No Symptoms\n(95% CI)") +
theme_bw()
Require the exposure to have occurred at least \(i\) days before the ALS diagnosis or data exit date where \(i\) ranges from 0 days to 5 years.
Since this difference is only defined for people who had a symptom, retain any people who are symptom free if they’re possibly still included in the data (e.g., if the time between the enrollment date and the end date is less than \(i\) days).
First, a couple specific models:
delay_30 <- clogit(
any_fml_fulladj,
model_data |>
filter(is.na(first_symptom_date) | (first_symptom_date < (end_date - 30))) |>
filter(first_date < (end_date - 30)) |>
mutate(
across(
is_logical,
as.numeric
)
)
)Warning: There was 1 warning in `mutate()`.
ℹ In argument: `across(is_logical, as.numeric)`.
Caused by warning:
! Use of bare predicate functions was deprecated in tidyselect 1.1.0.
ℹ Please use wrap predicates in `where()` instead.
# Was:
data %>% select(is_logical)
# Now:
data %>% select(where(is_logical))delay_60 <- clogit(
any_fml_fulladj,
model_data |>
filter(is.na(first_symptom_date) | (first_symptom_date < (end_date - 60))) |>
filter(first_date < (end_date - 60)) |>
mutate(
across(
is_logical,
as.numeric
)
)
)
delay_90 <- clogit(
any_fml_fulladj,
model_data |>
filter(is.na(first_symptom_date) | (first_symptom_date < (end_date - 90))) |>
filter(first_date < (end_date - 90)) |>
mutate(
across(
is_logical,
as.numeric
)
)
)
delay_180 <- clogit(
any_fml_fulladj,
model_data |>
filter(is.na(first_symptom_date) | (first_symptom_date < (end_date - 180))) |>
filter(first_date < (end_date - 180)) |>
mutate(
across(
is_logical,
as.numeric
)
)
)
delay_365 <- clogit(
any_fml_fulladj,
model_data |>
filter(is.na(first_symptom_date) | (first_symptom_date < (end_date - 365))) |>
filter(first_date < (end_date - 365)) |>
mutate(
across(
is_logical,
as.numeric
)
)
)
glance_vars <- c("nobs","nevent", "concordance", "r.squared")
tbl_merge(
tbls = list(
tbl_regression(delay_30, exponentiate = TRUE) |> add_glance_table(glance_vars),
tbl_regression(delay_60, exponentiate = TRUE) |> add_glance_table(glance_vars),
tbl_regression(delay_90, exponentiate = TRUE) |> add_glance_table(glance_vars),
tbl_regression(delay_180, exponentiate = TRUE) |> add_glance_table(glance_vars),
tbl_regression(delay_365, exponentiate = TRUE) |> add_glance_table(glance_vars)
),
tab_spanner = c("**30 Day Delay**", "**60 Day Delay**", "**90 Day Delay**",
"**180 Day Delay**", "**365 Day Delay**")
) |>
modify_column_hide(columns = c(p.value_1, p.value_2, p.value_3, p.value_4))Warning: Using an external vector in selections was deprecated in tidyselect 1.1.0.
ℹ Please use `all_of()` or `any_of()` instead.
# Was:
data %>% select(glance_vars)
# Now:
data %>% select(all_of(glance_vars))
See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.| Characteristic | 30 Day Delay | 60 Day Delay | 90 Day Delay | 180 Day Delay | 365 Day Delay | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| OR1 | 95% CI1 | OR1 | 95% CI1 | OR1 | 95% CI1 | OR1 | 95% CI1 | OR1 | 95% CI1 | p-value | |
| rate_outpatient_visits | 1.02 | 1.02, 1.03 | 1.03 | 1.02, 1.03 | 1.03 | 1.03, 1.03 | 1.03 | 1.03, 1.03 | 1.03 | 1.03, 1.03 | <0.001 |
| intensity_outpatient_visits_dx | 1.14 | 1.09, 1.18 | 1.14 | 1.10, 1.19 | 1.14 | 1.10, 1.19 | 1.13 | 1.08, 1.17 | 1.11 | 1.06, 1.16 | <0.001 |
| rate_inpatient_stays | 0.78 | 0.74, 0.83 | 0.78 | 0.73, 0.83 | 0.78 | 0.73, 0.83 | 0.78 | 0.73, 0.83 | 0.79 | 0.73, 0.85 | <0.001 |
| intensity_inpatient_stays_los | 1.00 | 0.99, 1.00 | 1.00 | 0.99, 1.00 | 1.00 | 0.99, 1.00 | 1.00 | 0.99, 1.00 | 1.00 | 0.99, 1.01 | >0.9 |
| elix_CHF | 0.63 | 0.59, 0.68 | 0.64 | 0.59, 0.69 | 0.63 | 0.58, 0.68 | 0.63 | 0.58, 0.68 | 0.64 | 0.59, 0.70 | <0.001 |
| elix_Valvular | 0.97 | 0.92, 1.03 | 0.97 | 0.91, 1.02 | 0.97 | 0.92, 1.03 | 0.97 | 0.91, 1.03 | 0.98 | 0.92, 1.04 | 0.5 |
| elix_PHTN | 0.98 | 0.89, 1.09 | 0.98 | 0.89, 1.09 | 0.99 | 0.90, 1.10 | 1.01 | 0.91, 1.12 | 0.98 | 0.88, 1.10 | 0.8 |
| elix_PVD | 0.92 | 0.87, 0.98 | 0.94 | 0.88, 0.99 | 0.94 | 0.88, 1.0 | 0.92 | 0.87, 0.98 | 0.91 | 0.86, 0.98 | 0.008 |
| elix_HTN | 0.99 | 0.95, 1.03 | 1.00 | 0.95, 1.04 | 1.00 | 0.96, 1.05 | 1.01 | 0.97, 1.06 | 1.01 | 0.96, 1.07 | 0.6 |
| elix_HTNcx | 0.91 | 0.85, 0.97 | 0.91 | 0.86, 0.97 | 0.91 | 0.85, 0.97 | 0.91 | 0.85, 0.97 | 0.91 | 0.84, 0.97 | 0.007 |
| elix_Paralysis | 2.99 | 2.77, 3.23 | 2.95 | 2.72, 3.19 | 2.94 | 2.72, 3.19 | 2.93 | 2.70, 3.18 | 2.89 | 2.65, 3.16 | <0.001 |
| elix_NeuroOther | 5.28 | 5.05, 5.53 | 5.33 | 5.09, 5.58 | 5.33 | 5.09, 5.59 | 5.26 | 5.00, 5.52 | 5.09 | 4.83, 5.37 | <0.001 |
| elix_Pulmonary | 0.96 | 0.91, 1.00 | 0.95 | 0.91, 1.00 | 0.96 | 0.91, 1.00 | 0.97 | 0.93, 1.02 | 0.99 | 0.94, 1.04 | 0.8 |
| elix_DM | 0.87 | 0.82, 0.92 | 0.88 | 0.83, 0.93 | 0.89 | 0.84, 0.94 | 0.89 | 0.84, 0.95 | 0.91 | 0.86, 0.97 | 0.004 |
| elix_DMcx | 0.79 | 0.73, 0.86 | 0.79 | 0.73, 0.85 | 0.78 | 0.72, 0.85 | 0.78 | 0.72, 0.85 | 0.77 | 0.70, 0.84 | <0.001 |
| elix_Hypothyroid | 1.11 | 1.05, 1.16 | 1.10 | 1.05, 1.16 | 1.09 | 1.04, 1.15 | 1.09 | 1.03, 1.15 | 1.10 | 1.04, 1.16 | 0.001 |
| elix_Renal | 0.58 | 0.53, 0.64 | 0.58 | 0.53, 0.63 | 0.58 | 0.53, 0.63 | 0.59 | 0.53, 0.65 | 0.58 | 0.53, 0.65 | <0.001 |
| elix_Liver | 0.93 | 0.86, 1.01 | 0.93 | 0.86, 1.01 | 0.94 | 0.86, 1.02 | 0.92 | 0.85, 1.01 | 0.95 | 0.86, 1.04 | 0.2 |
| elix_PUD | 1.01 | 0.80, 1.27 | 1.01 | 0.80, 1.27 | 0.96 | 0.76, 1.21 | 1.00 | 0.79, 1.27 | 0.99 | 0.77, 1.27 | >0.9 |
| elix_HIV | 1.01 | 0.70, 1.45 | 1.02 | 0.71, 1.48 | 1.07 | 0.74, 1.55 | 1.04 | 0.72, 1.52 | 1.07 | 0.72, 1.58 | 0.7 |
| elix_Lymphoma | 1.24 | 1.08, 1.42 | 1.18 | 1.03, 1.36 | 1.19 | 1.03, 1.38 | 1.21 | 1.04, 1.40 | 1.18 | 1.01, 1.38 | 0.033 |
| elix_Mets | 0.33 | 0.29, 0.38 | 0.34 | 0.30, 0.39 | 0.34 | 0.30, 0.39 | 0.35 | 0.31, 0.41 | 0.39 | 0.34, 0.45 | <0.001 |
| elix_Tumor | 0.86 | 0.81, 0.91 | 0.86 | 0.81, 0.92 | 0.88 | 0.82, 0.93 | 0.89 | 0.83, 0.95 | 0.89 | 0.83, 0.95 | <0.001 |
| elix_Rheumatic | 1.25 | 1.17, 1.33 | 1.26 | 1.18, 1.35 | 1.26 | 1.19, 1.35 | 1.26 | 1.18, 1.35 | 1.27 | 1.19, 1.36 | <0.001 |
| elix_Coagulopathy | 0.85 | 0.78, 0.93 | 0.85 | 0.78, 0.93 | 0.85 | 0.78, 0.93 | 0.86 | 0.78, 0.94 | 0.84 | 0.76, 0.92 | <0.001 |
| elix_Obesity | 0.83 | 0.79, 0.89 | 0.85 | 0.80, 0.90 | 0.86 | 0.80, 0.91 | 0.86 | 0.81, 0.92 | 0.87 | 0.81, 0.93 | <0.001 |
| elix_WeightLoss | 1.65 | 1.55, 1.76 | 1.62 | 1.52, 1.73 | 1.63 | 1.52, 1.74 | 1.58 | 1.48, 1.70 | 1.54 | 1.43, 1.66 | <0.001 |
| elix_FluidsLytes | 0.79 | 0.75, 0.84 | 0.80 | 0.76, 0.85 | 0.80 | 0.75, 0.85 | 0.81 | 0.76, 0.86 | 0.81 | 0.76, 0.86 | <0.001 |
| elix_BloodLoss | 0.70 | 0.61, 0.79 | 0.69 | 0.61, 0.79 | 0.70 | 0.62, 0.80 | 0.72 | 0.63, 0.82 | 0.73 | 0.63, 0.83 | <0.001 |
| elix_Anemia | 1.05 | 1.00, 1.11 | 1.06 | 1.00, 1.11 | 1.06 | 1.00, 1.11 | 1.05 | 1.00, 1.11 | 1.06 | 1.00, 1.12 | 0.057 |
| elix_Alcohol | 0.83 | 0.73, 0.93 | 0.83 | 0.74, 0.94 | 0.84 | 0.74, 0.95 | 0.85 | 0.75, 0.97 | 0.85 | 0.74, 0.97 | 0.016 |
| elix_Drugs | 0.82 | 0.71, 0.94 | 0.82 | 0.71, 0.95 | 0.82 | 0.71, 0.95 | 0.82 | 0.71, 0.96 | 0.81 | 0.69, 0.95 | 0.008 |
| elix_Psychoses | 0.82 | 0.77, 0.87 | 0.82 | 0.76, 0.87 | 0.82 | 0.77, 0.88 | 0.83 | 0.78, 0.89 | 0.84 | 0.78, 0.90 | <0.001 |
| elix_Depression | 0.98 | 0.92, 1.03 | 0.98 | 0.93, 1.04 | 0.98 | 0.93, 1.03 | 0.97 | 0.92, 1.03 | 0.98 | 0.93, 1.05 | 0.6 |
| any_sx | 4.49 | 3.97, 5.07 | 4.20 | 3.71, 4.75 | 3.98 | 3.51, 4.50 | 3.56 | 3.14, 4.04 | 3.08 | 2.70, 3.51 | <0.001 |
| lives_in_msa | 1.42 | 1.27, 1.60 | 1.42 | 1.27, 1.59 | 1.42 | 1.26, 1.59 | 1.41 | 1.26, 1.58 | 1.40 | 1.25, 1.58 | <0.001 |
| any_sx * lives_in_msa | 0.83 | 0.73, 0.95 | 0.83 | 0.73, 0.95 | 0.83 | 0.73, 0.95 | 0.84 | 0.73, 0.96 | 0.85 | 0.74, 0.97 | 0.017 |
| No. Obs. | 113,827 | 112,410 | 111,062 | 107,147 | 98,850 | ||||||
| N events | 18,342 | 17,615 | 17,016 | 15,574 | 13,418 | ||||||
| c-index | 0.795 | 0.794 | 0.793 | 0.789 | 0.778 | ||||||
| R² | 0.150 | 0.146 | 0.142 | 0.133 | 0.117 | ||||||
| 1 OR = Odds Ratio, CI = Confidence Interval | |||||||||||
And then with all the lags up to 5 years:
lags <- round(seq(0, 2, by = 1/12) * 365)
results <- vector("list", length(lags))
j <- 1
p <- progress::progress_bar$new(
total = length(lags),
format = "[:bar] :percent in :elapsed with :eta remaining"
)
for (i in lags) {
results[[j]] <- clogit(
any_fml_fulladj,
model_data |>
filter(is.na(first_symptom_date) | (first_symptom_date < (end_date - i))) |>
filter(first_date < (end_date - i))
) |>
broom::tidy(exponentiate = TRUE, conf.int = TRUE) |>
mutate(i = i) |>
select(i, term, estimate, conf.low, conf.high)
j <- j + 1
p$tick()
}
results |>
bind_rows() |>
filter(
stringr::str_detect(term, "Neuro")
) |>
ggplot(aes(x = i / 365,
y = estimate,
ymin = conf.low,
ymax = conf.high)) +
geom_point() +
geom_linerange() +
labs(x = "Lead-in Period by Years",
y = "Odds Ratio for Elixhauser Neurological CMs") +
theme_bw()
ggsave("~/projects/als-sx/neuro_series.svg", width = 16/2, height = 9/2)
results |>
bind_rows() |>
filter(
stringr::str_detect(term, "sx") | stringr::str_detect(term, "msa")
) |>
mutate(
term = case_when(
term == "any_sxTRUE" ~ "Has Symptom",
term == "lives_in_msaTRUE" ~ "Lives in MSA",
term == "any_sxTRUE:lives_in_msaTRUE" ~ "Symptom x MSA"
),
term = forcats::fct_relevel(term,
"Has Symptom", "Lives in MSA")
) |>
ggplot(
aes(
x = i / 365,
y = estimate,
ymin = conf.low,
ymax = conf.high
)
) +
geom_point() +
geom_linerange() +
facet_grid(rows = vars(term), scales = "free_y") +
labs(x = "Years Between Symptom and ALS Date", y = "Odds Ratio") +
theme_bw()
ggsave("~/projects/als-sx/symptom_series.svg", width = 16/2, height = 9/2)