COVID Case Series
COVID Study Group
2020-09-22
Introduction
This is an ongoing report of case series describing COVID+ patients at a single center.
Select the code button in this section to see the R code for dataset construction.
Cohort Selection
# bring in covid
load("./Data/covid_master.RData")
# bring in covid1, cleaned set
load("./Data/covid_cleaned.RData")
mytables <- tableby.control(test = F, total = F, digits = 0, digits.pct = 0)
# Daily and weekly data summary for graphing progress
covid.time.series <- covid %>% filter(is.na(sarscov2_status) == F) %>% filter(is.na(sarscov2_collected_date) ==
F) %>% filter(sarscov2_collected_date > "2020-03-08" & sarscov2_collected_date <
"2020-05-18") %>% filter(is.na(delete) == T)
covid.daily <- covid.time.series %>% group_by(sarscov2_collected_date) %>% summarise(N = n(),
Positive = sum(sarscov2_status == "Positive"), Negative = sum(sarscov2_status ==
"Negative"), Percent.positive = round(Positive/N * 100, digits = 1)) %>%
mutate(Cum.N = cumsum(N), Cum.P = cumsum(Positive))
# Weekly data summary for graphing progress and for creating strata for sampling
covid.weekly <- covid.time.series %>% group_by(week) %>% summarise(N = n(), Positive = sum(sarscov2_status ==
"Positive"), Negative = sum(sarscov2_status == "Negative"), Percent.positive = round(Positive/N *
100, digits = 1)) %>% mutate(Cum.N = cumsum(N), Cum.P = cumsum(Positive))As of 2020-09-22 the total number of observations in dataset = 4402
- Exclusions:
- No valid test result (N = 2)
- No valid test date (N = 145)
- Test date < March 9 or after May 17 (N = 52)
- Ambulatory encounter (N = 74)
- Test result not positive for SARS-CoV2 (N = 3950)
- No valid test result (N = 2)
Final cohort for all tests analysis N = 4138
Final cohort for COVID+ analysis N = 372
Figures for all COVID Tests
Daily Total
ggplot(covid.daily, aes(x = sarscov2_collected_date)) + geom_bar(aes(y = N), stat = "identity",
fill = "dark grey", color = "black") + geom_bar(aes(y = Positive), stat = "identity",
fill = "dark red", color = "black") + geom_text(aes(y = N, label = N), nudge_y = 20,
angle = 90) + geom_text(aes(y = 0, label = Positive), nudge_y = -20, color = "dark red",
angle = 90) + theme_bw() + scale_x_date(breaks = "1 week", date_labels = "%b %d") +
labs(title = "Total Daily Tests Performed", x = "Date of SARS-CoV- 2 Test", y = "Number of tests") +
theme(axis.title = element_text(size = 14), axis.text.x = element_text(angle = 60,
hjust = 1, size = 12), axis.text.y = element_text(size = 12))
Daily Cumulative
ggplot(covid.daily, aes(x = sarscov2_collected_date)) + geom_bar(aes(y = Cum.N),
stat = "identity", fill = "dark grey", color = "black") + geom_bar(aes(y = Cum.P),
stat = "identity", fill = "dark red", color = "black") + geom_text(aes(y = Cum.N,
label = Cum.N), nudge_y = 500, angle = 90, color = "black") + geom_text(aes(y = 0,
label = Cum.P), nudge_y = -500, angle = 90, color = "dark red") + theme_bw() +
scale_x_date(breaks = "1 week", date_labels = "%b %d") + labs(title = "Cumulative Number of Tests Performed",
x = "Date of SARS-CoV- 2 Test", y = "Number of tests") + theme(axis.title = element_text(size = 14),
axis.text.x = element_text(angle = 60, hjust = 1, size = 12), axis.text.y = element_text(size = 12))
Daily Percent
ggplot(covid.daily, aes(x = sarscov2_collected_date)) + geom_bar(aes(y = Percent.positive),
stat = "identity", fill = "dark red", color = "black") + geom_text(aes(y = Percent.positive,
label = Percent.positive), nudge_y = 10, angle = 90) + theme_bw() + scale_x_date(breaks = "1 week",
date_labels = "%b %d") + labs(title = "Percent of Daily Tests Performed Resulted Positive",
x = "Date of SARS-CoV- 2 Test", y = "%") + theme(axis.title = element_text(size = 14),
axis.text.x = element_text(angle = 60, hjust = 1, size = 12), axis.text.y = element_text(size = 12))
Weekly Total
ggplot(covid.weekly, aes(x = week)) + geom_bar(aes(y = N), stat = "identity", fill = "dark grey",
color = "black") + geom_bar(aes(y = Positive), stat = "identity", fill = "dark red",
color = "black") + geom_text(aes(y = N, label = N), nudge_y = 30, angle = 90) +
geom_text(aes(y = 0, label = Positive), nudge_y = -30, color = "dark red", angle = 90) +
theme_bw() + # scale_x_date(breaks = '1 week', date_labels = '%b %d')+
labs(title = "Total Weekly Tests Performed", x = "Monday of Week of SARS-CoV- 2 Test",
y = "Number of tests") + theme(axis.title = element_text(size = 14), axis.text.x = element_text(angle = 60,
hjust = 1, size = 12), axis.text.y = element_text(size = 12))
Weekly Cumulative
ggplot(covid.weekly, aes(x = week)) + geom_bar(aes(y = Cum.N), stat = "identity",
fill = "dark grey", color = "black") + geom_bar(aes(y = Cum.P), stat = "identity",
fill = "dark red", color = "black") + geom_text(aes(y = Cum.N, label = Cum.N),
nudge_y = 1000, angle = 90, color = "black") + geom_text(aes(y = 0, label = Cum.P),
nudge_y = -1000, angle = 90, color = "dark red") + theme_bw() + labs(title = "Cumulative Number of Tests Performed",
x = "Monday Date of Week of SARS-CoV- 2 Test", y = "Number of tests") + theme(axis.title = element_text(size = 14),
axis.text.x = element_text(angle = 60, hjust = 1, size = 12), axis.text.y = element_text(size = 12))
Weekly Percent
ggplot(covid.weekly, aes(x = week)) + geom_bar(aes(y = Percent.positive), stat = "identity",
fill = "dark red", color = "black") + geom_text(aes(y = Percent.positive, label = Percent.positive),
nudge_y = 10, angle = 90) + theme_bw() + # scale_x_date(breaks = '1 week', date_labels = '%b %d')+
labs(title = "Percent of Weekly Tests Performed Resulted Positive", x = "Monday Date of Week of SARS-CoV- 2 Test",
y = "%") + theme(axis.title = element_text(size = 14), axis.text.x = element_text(angle = 60,
hjust = 1, size = 12), axis.text.y = element_text(size = 12))
Tables for COVID +
Demographics
summary(tableby(week ~ age + sex + race_adj + ethnic + bmi + bmi_cat + covid_contact +
home, data = covid1, control = mytables))| 03-09 (N=10) | 03-16 (N=23) | 03-23 (N=40) | 03-30 (N=54) | 04-06 (N=46) | 04-13 (N=60) | 04-20 (N=42) | 04-27 (N=44) | 05-04 (N=31) | 05-11 (N=22) | |
|---|---|---|---|---|---|---|---|---|---|---|
| Age, years | ||||||||||
| Mean (SD) | 56 (11) | 53 (15) | 62 (16) | 56 (21) | 59 (15) | 60 (16) | 59 (21) | 61 (22) | 52 (16) | 53 (17) |
| Range | 37 - 71 | 25 - 73 | 28 - 95 | 18 - 90 | 30 - 94 | 18 - 92 | 17 - 98 | 19 - 101 | 22 - 87 | 23 - 90 |
| Sex | ||||||||||
| Female | 6 (60%) | 6 (26%) | 20 (50%) | 28 (52%) | 11 (24%) | 26 (43%) | 20 (48%) | 23 (52%) | 14 (45%) | 12 (55%) |
| Male | 4 (40%) | 17 (74%) | 20 (50%) | 26 (48%) | 35 (76%) | 34 (57%) | 22 (52%) | 21 (48%) | 17 (55%) | 10 (45%) |
| Race | ||||||||||
| N-Miss | 0 | 1 | 0 | 0 | 0 | 1 | 1 | 0 | 7 | 4 |
| Alaskan/Native American | 0 (0%) | 1 (5%) | 1 (2%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Asian/PI | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2%) | 1 (2%) | 1 (2%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Black | 10 (100%) | 17 (77%) | 34 (85%) | 45 (83%) | 36 (78%) | 48 (81%) | 31 (76%) | 35 (80%) | 20 (83%) | 16 (89%) |
| Unknown | 0 (0%) | 2 (9%) | 2 (5%) | 6 (11%) | 6 (13%) | 7 (12%) | 7 (17%) | 4 (9%) | 2 (8%) | 0 (0%) |
| White | 0 (0%) | 2 (9%) | 3 (8%) | 3 (6%) | 3 (7%) | 3 (5%) | 2 (5%) | 5 (11%) | 2 (8%) | 2 (11%) |
| Ethnicity | ||||||||||
| N-Miss | 0 | 1 | 2 | 2 | 3 | 1 | 1 | 1 | 2 | 0 |
| Hispanic | 0 (0%) | 1 (5%) | 0 (0%) | 5 (10%) | 6 (14%) | 8 (14%) | 6 (15%) | 4 (9%) | 6 (21%) | 3 (14%) |
| Non-Hispanic | 10 (100%) | 21 (95%) | 38 (100%) | 47 (90%) | 37 (86%) | 51 (86%) | 35 (85%) | 39 (91%) | 23 (79%) | 19 (86%) |
| BMI,kg/m2 | ||||||||||
| N-Miss | 0 | 1 | 1 | 0 | 1 | 3 | 3 | 0 | 2 | 1 |
| Mean (SD) | 36 (16) | 34 (10) | 33 (35) | 29 (12) | 29 (9) | 29 (7) | 27 (10) | 27 (8) | 27 (10) | 29 (7) |
| Range | 21 - 71 | 23 - 63 | 15 - 239 | 0 - 63 | 17 - 58 | 17 - 52 | 1 - 45 | 0 - 46 | 10 - 52 | 21 - 50 |
| BMI,kg/m2 categories | ||||||||||
| N-Miss | 0 | 1 | 1 | 0 | 1 | 3 | 3 | 0 | 2 | 1 |
| <18.5 | 0 (0%) | 0 (0%) | 3 (8%) | 6 (11%) | 1 (2%) | 3 (5%) | 6 (15%) | 4 (9%) | 5 (17%) | 0 (0%) |
| 18.5-24.9 | 2 (20%) | 2 (9%) | 15 (38%) | 8 (15%) | 15 (33%) | 14 (25%) | 11 (28%) | 16 (36%) | 10 (34%) | 5 (24%) |
| 25-29.9 | 2 (20%) | 9 (41%) | 9 (23%) | 16 (30%) | 14 (31%) | 16 (28%) | 7 (18%) | 13 (30%) | 5 (17%) | 9 (43%) |
| 30+ | 6 (60%) | 11 (50%) | 12 (31%) | 24 (44%) | 15 (33%) | 24 (42%) | 15 (38%) | 11 (25%) | 9 (31%) | 7 (33%) |
| Contact with suspected/confirmed COVID-19 case | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| No | 7 (70%) | 15 (65%) | 29 (72%) | 34 (64%) | 27 (59%) | 36 (60%) | 30 (73%) | 36 (82%) | 23 (74%) | 17 (77%) |
| Yes | 1 (10%) | 5 (22%) | 7 (18%) | 9 (17%) | 12 (26%) | 19 (32%) | 10 (24%) | 7 (16%) | 6 (19%) | 4 (18%) |
| Unknown | 2 (20%) | 3 (13%) | 4 (10%) | 10 (19%) | 7 (15%) | 5 (8%) | 1 (2%) | 1 (2%) | 2 (6%) | 1 (5%) |
| Housing type | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| Correctional facility | 0 (0%) | 2 (9%) | 1 (2%) | 3 (6%) | 2 (4%) | 2 (3%) | 0 (0%) | 0 (0%) | 1 (3%) | 3 (14%) |
| Homeless/shelter | 2 (20%) | 2 (9%) | 3 (8%) | 1 (2%) | 2 (4%) | 2 (3%) | 2 (5%) | 0 (0%) | 2 (6%) | 1 (5%) |
| Long term health facility | 0 (0%) | 1 (4%) | 4 (10%) | 2 (4%) | 1 (2%) | 0 (0%) | 1 (2%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Nursing home | 0 (0%) | 1 (4%) | 4 (10%) | 10 (19%) | 12 (26%) | 24 (40%) | 14 (34%) | 22 (50%) | 6 (19%) | 6 (27%) |
| Stable Home | 8 (80%) | 17 (74%) | 28 (70%) | 37 (70%) | 28 (61%) | 31 (52%) | 24 (59%) | 22 (50%) | 22 (71%) | 12 (55%) |
| Unknown | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2%) | 1 (2%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
Comorbidity
summary(tableby(week ~ htn + diabetes + chf + cad + stroke + dementia + ckd + cirrhosis +
copd + asthma + other_lung + osa + malignancy + transplant + hiv + art + pregnant,
data = covid1, control = mytables))| 03-09 (N=10) | 03-16 (N=23) | 03-23 (N=40) | 03-30 (N=54) | 04-06 (N=46) | 04-13 (N=60) | 04-20 (N=42) | 04-27 (N=44) | 05-04 (N=31) | 05-11 (N=22) | |
|---|---|---|---|---|---|---|---|---|---|---|
| Hypertension | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| No | 2 (20%) | 8 (35%) | 8 (20%) | 24 (45%) | 11 (24%) | 14 (23%) | 14 (33%) | 14 (32%) | 20 (65%) | 10 (45%) |
| Yes | 8 (80%) | 15 (65%) | 32 (80%) | 29 (55%) | 35 (76%) | 46 (77%) | 28 (67%) | 30 (68%) | 11 (35%) | 12 (55%) |
| Diabetes mellitus | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| IDDM | 1 (10%) | 3 (13%) | 7 (18%) | 5 (9%) | 5 (11%) | 10 (17%) | 2 (5%) | 5 (11%) | 4 (13%) | 4 (18%) |
| NIDDM | 2 (20%) | 4 (17%) | 9 (22%) | 12 (23%) | 10 (22%) | 10 (17%) | 10 (24%) | 9 (20%) | 3 (10%) | 2 (9%) |
| No | 7 (70%) | 16 (70%) | 24 (60%) | 35 (66%) | 31 (67%) | 39 (65%) | 29 (71%) | 30 (68%) | 24 (77%) | 16 (73%) |
| Unknown | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2%) | 0 (0%) | 1 (2%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Congestive heart failure | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 0 | 0 |
| No | 8 (80%) | 19 (83%) | 36 (90%) | 46 (87%) | 38 (84%) | 50 (83%) | 34 (83%) | 38 (86%) | 28 (90%) | 16 (73%) |
| Yes | 2 (20%) | 4 (17%) | 4 (10%) | 7 (13%) | 7 (16%) | 10 (17%) | 7 (17%) | 6 (14%) | 3 (10%) | 6 (27%) |
| Coronary artery disease | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 1 |
| No | 9 (90%) | 21 (91%) | 37 (92%) | 47 (89%) | 39 (85%) | 52 (87%) | 39 (95%) | 41 (93%) | 31 (100%) | 18 (86%) |
| Yes | 1 (10%) | 2 (9%) | 3 (8%) | 6 (11%) | 7 (15%) | 8 (13%) | 2 (5%) | 3 (7%) | 0 (0%) | 3 (14%) |
| Stroke | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| No | 9 (90%) | 19 (83%) | 34 (85%) | 43 (81%) | 33 (72%) | 39 (65%) | 32 (76%) | 28 (64%) | 30 (97%) | 13 (59%) |
| Yes | 1 (10%) | 4 (17%) | 6 (15%) | 10 (19%) | 13 (28%) | 21 (35%) | 10 (24%) | 16 (36%) | 1 (3%) | 9 (41%) |
| Dementia | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| No | 10 (100%) | 22 (96%) | 33 (82%) | 41 (77%) | 38 (83%) | 42 (70%) | 30 (71%) | 31 (70%) | 26 (84%) | 18 (82%) |
| Yes | 0 (0%) | 1 (4%) | 7 (18%) | 11 (21%) | 8 (17%) | 18 (30%) | 12 (29%) | 13 (30%) | 5 (16%) | 4 (18%) |
| Unknown | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Chronic kidney disease | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
| No | 9 (90%) | 17 (74%) | 34 (85%) | 47 (89%) | 37 (82%) | 43 (72%) | 37 (88%) | 35 (80%) | 26 (84%) | 18 (82%) |
| Unknown | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Yes | 0 (0%) | 3 (13%) | 3 (8%) | 6 (11%) | 4 (9%) | 11 (18%) | 4 (10%) | 5 (11%) | 3 (10%) | 2 (9%) |
| Yes, on dialysis | 1 (10%) | 3 (13%) | 3 (8%) | 0 (0%) | 4 (9%) | 5 (8%) | 1 (2%) | 4 (9%) | 2 (6%) | 2 (9%) |
| Cirrhosis | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 |
| No | 10 (100%) | 21 (91%) | 40 (100%) | 52 (100%) | 46 (100%) | 59 (98%) | 42 (100%) | 44 (100%) | 30 (97%) | 22 (100%) |
| Yes | 0 (0%) | 2 (9%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2%) | 0 (0%) | 0 (0%) | 1 (3%) | 0 (0%) |
| COPD | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| No | 10 (100%) | 21 (91%) | 38 (95%) | 51 (96%) | 42 (91%) | 54 (90%) | 39 (93%) | 41 (93%) | 30 (97%) | 21 (95%) |
| Yes | 0 (0%) | 2 (9%) | 2 (5%) | 2 (4%) | 4 (9%) | 6 (10%) | 3 (7%) | 3 (7%) | 1 (3%) | 1 (5%) |
| Asthma | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| No | 9 (90%) | 22 (96%) | 35 (88%) | 50 (94%) | 42 (91%) | 57 (95%) | 38 (90%) | 41 (93%) | 27 (87%) | 21 (95%) |
| Yes | 1 (10%) | 1 (4%) | 5 (12%) | 3 (6%) | 4 (9%) | 3 (5%) | 4 (10%) | 3 (7%) | 4 (13%) | 1 (5%) |
| Structural lung disease | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| No | 9 (90%) | 22 (96%) | 40 (100%) | 51 (96%) | 46 (100%) | 58 (97%) | 42 (100%) | 44 (100%) | 31 (100%) | 22 (100%) |
| Yes | 1 (10%) | 1 (4%) | 0 (0%) | 2 (4%) | 0 (0%) | 2 (3%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| OSA/OHS | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 0 | 0 |
| No | 10 (100%) | 19 (83%) | 40 (100%) | 49 (94%) | 44 (98%) | 56 (93%) | 40 (95%) | 42 (95%) | 29 (94%) | 21 (95%) |
| Yes | 0 (0%) | 4 (17%) | 0 (0%) | 2 (4%) | 1 (2%) | 4 (7%) | 2 (5%) | 2 (5%) | 2 (6%) | 1 (5%) |
| Unknown | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Malignancy | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
| Current | 1 (10%) | 2 (9%) | 1 (2%) | 1 (2%) | 2 (4%) | 1 (2%) | 2 (5%) | 1 (2%) | 0 (0%) | 0 (0%) |
| No | 7 (70%) | 21 (91%) | 36 (90%) | 51 (96%) | 42 (93%) | 58 (97%) | 39 (93%) | 42 (95%) | 31 (100%) | 22 (100%) |
| Prior | 2 (20%) | 0 (0%) | 3 (8%) | 1 (2%) | 1 (2%) | 1 (2%) | 1 (2%) | 1 (2%) | 0 (0%) | 0 (0%) |
| Solid organ or stem cell transplant | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| No | 10 (100%) | 23 (100%) | 39 (98%) | 53 (100%) | 46 (100%) | 60 (100%) | 42 (100%) | 44 (100%) | 31 (100%) | 22 (100%) |
| Yes | 0 (0%) | 0 (0%) | 1 (2%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| HIV/AIDs | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| No | 10 (100%) | 21 (91%) | 38 (95%) | 49 (92%) | 44 (96%) | 58 (97%) | 41 (98%) | 44 (100%) | 30 (97%) | 21 (95%) |
| Yes | 0 (0%) | 2 (9%) | 2 (5%) | 4 (8%) | 0 (0%) | 2 (3%) | 1 (2%) | 0 (0%) | 1 (3%) | 1 (5%) |
| Unknown | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 2 (4%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Prescribed antiretroviral therapy | ||||||||||
| N-Miss | 10 | 21 | 38 | 50 | 46 | 58 | 41 | 44 | 30 | 21 |
| No | 0 | 0 (0%) | 0 (0%) | 0 (0%) | 0 | 0 (0%) | 0 (0%) | 0 | 1 (100%) | 0 (0%) |
| Yes | 0 | 2 (100%) | 2 (100%) | 4 (100%) | 0 | 2 (100%) | 1 (100%) | 0 | 0 (0%) | 1 (100%) |
| Pregnant | ||||||||||
| N-Miss | 4 | 17 | 20 | 27 | 35 | 34 | 22 | 21 | 17 | 10 |
| No | 6 (100%) | 6 (100%) | 20 (100%) | 27 (100%) | 10 (91%) | 26 (100%) | 19 (95%) | 19 (83%) | 11 (79%) | 11 (92%) |
| Yes | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (9%) | 0 (0%) | 1 (5%) | 4 (17%) | 3 (21%) | 1 (8%) |
Symptoms
summary(tableby(week ~ fever + cough + sob + myalgias + chills + fatigue + sore_throat +
diarrhea + nausea + vomit + headache + anosmia + ageusia + abdominal_pain + ams,
data = covid1, control = mytables))| 03-09 (N=10) | 03-16 (N=23) | 03-23 (N=40) | 03-30 (N=54) | 04-06 (N=46) | 04-13 (N=60) | 04-20 (N=42) | 04-27 (N=44) | 05-04 (N=31) | 05-11 (N=22) | |
|---|---|---|---|---|---|---|---|---|---|---|
| Fever | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 0 | 0 | 1 | 0 | 0 | 0 |
| No | 2 (20%) | 4 (17%) | 13 (32%) | 16 (31%) | 12 (26%) | 27 (45%) | 23 (56%) | 26 (59%) | 14 (45%) | 12 (55%) |
| Yes | 8 (80%) | 18 (78%) | 23 (58%) | 32 (62%) | 30 (65%) | 25 (42%) | 13 (32%) | 11 (25%) | 14 (45%) | 7 (32%) |
| Unknown | 0 (0%) | 1 (4%) | 4 (10%) | 4 (8%) | 4 (9%) | 8 (13%) | 5 (12%) | 7 (16%) | 3 (10%) | 3 (14%) |
| Cough | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| No | 1 (10%) | 2 (9%) | 8 (20%) | 10 (19%) | 11 (24%) | 21 (35%) | 16 (39%) | 19 (43%) | 10 (32%) | 11 (50%) |
| Yes | 9 (90%) | 20 (87%) | 28 (70%) | 39 (74%) | 30 (65%) | 28 (47%) | 21 (51%) | 17 (39%) | 16 (52%) | 8 (36%) |
| Unknown | 0 (0%) | 1 (4%) | 4 (10%) | 4 (8%) | 5 (11%) | 11 (18%) | 4 (10%) | 8 (18%) | 5 (16%) | 3 (14%) |
| Dyspnea | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 0 | 0 |
| No | 4 (40%) | 7 (30%) | 16 (40%) | 19 (36%) | 18 (40%) | 27 (45%) | 19 (46%) | 23 (52%) | 15 (48%) | 8 (36%) |
| Yes | 6 (60%) | 15 (65%) | 20 (50%) | 31 (58%) | 22 (49%) | 23 (38%) | 16 (39%) | 17 (39%) | 12 (39%) | 14 (64%) |
| Unknown | 0 (0%) | 1 (4%) | 4 (10%) | 3 (6%) | 5 (11%) | 10 (17%) | 6 (15%) | 4 (9%) | 4 (13%) | 0 (0%) |
| Myalgias | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 0 | 0 |
| No | 6 (60%) | 5 (22%) | 22 (55%) | 31 (58%) | 23 (51%) | 33 (55%) | 25 (61%) | 29 (66%) | 16 (52%) | 14 (64%) |
| Yes | 4 (40%) | 16 (70%) | 13 (32%) | 17 (32%) | 16 (36%) | 13 (22%) | 10 (24%) | 6 (14%) | 10 (32%) | 3 (14%) |
| Unknown | 0 (0%) | 2 (9%) | 5 (12%) | 5 (9%) | 6 (13%) | 14 (23%) | 6 (15%) | 9 (20%) | 5 (16%) | 5 (23%) |
| Chills | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| No | 3 (30%) | 13 (57%) | 22 (55%) | 27 (51%) | 27 (59%) | 38 (63%) | 29 (71%) | 33 (75%) | 13 (42%) | 15 (68%) |
| Yes | 7 (70%) | 9 (39%) | 13 (32%) | 22 (42%) | 13 (28%) | 8 (13%) | 6 (15%) | 3 (7%) | 12 (39%) | 3 (14%) |
| Unknown | 0 (0%) | 1 (4%) | 5 (12%) | 4 (8%) | 6 (13%) | 14 (23%) | 6 (15%) | 8 (18%) | 6 (19%) | 4 (18%) |
| Fatigue | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| No | 5 (50%) | 6 (26%) | 22 (55%) | 28 (53%) | 22 (48%) | 32 (53%) | 29 (71%) | 25 (57%) | 12 (39%) | 12 (55%) |
| Yes | 5 (50%) | 15 (65%) | 13 (32%) | 20 (38%) | 18 (39%) | 14 (23%) | 6 (15%) | 10 (23%) | 14 (45%) | 5 (23%) |
| Unknown | 0 (0%) | 2 (9%) | 5 (12%) | 5 (9%) | 6 (13%) | 14 (23%) | 6 (15%) | 9 (20%) | 5 (16%) | 5 (23%) |
| Sore throat | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| No | 7 (70%) | 18 (78%) | 32 (80%) | 41 (77%) | 38 (83%) | 44 (73%) | 32 (78%) | 31 (70%) | 23 (74%) | 14 (64%) |
| Yes | 3 (30%) | 3 (13%) | 3 (8%) | 7 (13%) | 2 (4%) | 2 (3%) | 3 (7%) | 4 (9%) | 3 (10%) | 3 (14%) |
| Unknown | 0 (0%) | 2 (9%) | 5 (12%) | 5 (9%) | 6 (13%) | 14 (23%) | 6 (15%) | 9 (20%) | 5 (16%) | 5 (23%) |
| Diarrhea | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| No | 8 (80%) | 15 (65%) | 20 (50%) | 33 (62%) | 24 (52%) | 38 (63%) | 31 (76%) | 32 (73%) | 22 (71%) | 12 (55%) |
| Yes | 2 (20%) | 7 (30%) | 15 (38%) | 16 (30%) | 16 (35%) | 9 (15%) | 4 (10%) | 4 (9%) | 4 (13%) | 7 (32%) |
| Unknown | 0 (0%) | 1 (4%) | 5 (12%) | 4 (8%) | 6 (13%) | 13 (22%) | 6 (15%) | 8 (18%) | 5 (16%) | 3 (14%) |
| Nausea | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| No | 9 (90%) | 16 (70%) | 23 (58%) | 41 (77%) | 33 (72%) | 39 (65%) | 32 (78%) | 27 (61%) | 18 (58%) | 14 (64%) |
| Yes | 1 (10%) | 6 (26%) | 12 (30%) | 8 (15%) | 8 (17%) | 7 (12%) | 3 (7%) | 9 (20%) | 8 (26%) | 4 (18%) |
| Unknown | 0 (0%) | 1 (4%) | 5 (12%) | 4 (8%) | 5 (11%) | 14 (23%) | 6 (15%) | 8 (18%) | 5 (16%) | 4 (18%) |
| Vomiting | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| No | 10 (100%) | 21 (91%) | 27 (68%) | 40 (75%) | 35 (76%) | 43 (72%) | 33 (80%) | 30 (68%) | 19 (61%) | 15 (68%) |
| Yes | 0 (0%) | 1 (4%) | 8 (20%) | 9 (17%) | 5 (11%) | 4 (7%) | 2 (5%) | 7 (16%) | 7 (23%) | 3 (14%) |
| Unknown | 0 (0%) | 1 (4%) | 5 (12%) | 4 (8%) | 6 (13%) | 13 (22%) | 6 (15%) | 7 (16%) | 5 (16%) | 4 (18%) |
| Headache | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 0 | 0 |
| No | 7 (70%) | 16 (70%) | 28 (70%) | 38 (72%) | 35 (78%) | 37 (62%) | 32 (78%) | 32 (73%) | 21 (68%) | 15 (68%) |
| Yes | 3 (30%) | 5 (22%) | 7 (18%) | 10 (19%) | 4 (9%) | 9 (15%) | 3 (7%) | 3 (7%) | 5 (16%) | 2 (9%) |
| Unknown | 0 (0%) | 2 (9%) | 5 (12%) | 5 (9%) | 6 (13%) | 14 (23%) | 6 (15%) | 9 (20%) | 5 (16%) | 5 (23%) |
| Loss of smell | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| No | 10 (100%) | 21 (91%) | 34 (85%) | 45 (85%) | 37 (80%) | 43 (72%) | 30 (73%) | 33 (75%) | 22 (71%) | 18 (82%) |
| Yes | 0 (0%) | 0 (0%) | 1 (2%) | 3 (6%) | 3 (7%) | 1 (2%) | 5 (12%) | 2 (5%) | 3 (10%) | 0 (0%) |
| Unknown | 0 (0%) | 2 (9%) | 5 (12%) | 5 (9%) | 6 (13%) | 16 (27%) | 6 (15%) | 9 (20%) | 6 (19%) | 4 (18%) |
| Loss of taste | ||||||||||
| N-Miss | 0 | 0 | 1 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| No | 10 (100%) | 21 (91%) | 33 (85%) | 40 (75%) | 37 (80%) | 43 (72%) | 29 (71%) | 33 (75%) | 21 (68%) | 18 (82%) |
| Yes | 0 (0%) | 0 (0%) | 1 (3%) | 8 (15%) | 3 (7%) | 1 (2%) | 6 (15%) | 2 (5%) | 4 (13%) | 1 (5%) |
| Unknown | 0 (0%) | 2 (9%) | 5 (13%) | 5 (9%) | 6 (13%) | 16 (27%) | 6 (15%) | 9 (20%) | 6 (19%) | 3 (14%) |
| Abdominal pain | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 1 | 0 | 1 | 0 | 0 | 0 |
| No | 10 (100%) | 18 (78%) | 32 (80%) | 39 (75%) | 37 (82%) | 41 (68%) | 31 (76%) | 29 (66%) | 20 (65%) | 14 (64%) |
| Yes | 0 (0%) | 4 (17%) | 3 (8%) | 8 (15%) | 2 (4%) | 7 (12%) | 4 (10%) | 6 (14%) | 6 (19%) | 3 (14%) |
| Unknown | 0 (0%) | 1 (4%) | 5 (12%) | 5 (10%) | 6 (13%) | 12 (20%) | 6 (15%) | 9 (20%) | 5 (16%) | 5 (23%) |
| Altered mental status on presentation | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| No | 9 (90%) | 18 (78%) | 27 (68%) | 43 (81%) | 37 (80%) | 39 (65%) | 31 (76%) | 25 (57%) | 25 (81%) | 17 (77%) |
| Yes | 1 (10%) | 4 (17%) | 12 (30%) | 10 (19%) | 9 (20%) | 21 (35%) | 10 (24%) | 19 (43%) | 6 (19%) | 5 (23%) |
| Unknown | 0 (0%) | 1 (4%) | 1 (2%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
Initial Values
summary(tableby(week ~ temp_max + temp_min + hr_max + hr_min + sbp_min + max_map +
min_map + rr_max + rr_min + sao2_min + sao2_fio2 + dopamine_sofa + dobutamine_sofa +
epinepherine_sofa + norepinephrine_sofa + na + k + creatinine + alt + ast + tbili +
lactate + wbc + hgb + hct + platelets + lymphocytes + abg_pao2 + abg_paco2 +
abg_spo2 + abg_ph, data = covid1, control = mytables))| 03-09 (N=10) | 03-16 (N=23) | 03-23 (N=40) | 03-30 (N=54) | 04-06 (N=46) | 04-13 (N=60) | 04-20 (N=42) | 04-27 (N=44) | 05-04 (N=31) | 05-11 (N=22) | |
|---|---|---|---|---|---|---|---|---|---|---|
| Temperature maximum, °C | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 1 | 0 |
| Mean (SD) | 39 (1) | 38 (1) | 38 (1) | 38 (1) | 41 (13) | 38 (1) | 37 (4) | 38 (1) | 38 (1) | 38 (1) |
| Range | 37 - 40 | 37 - 40 | 37 - 40 | 36 - 40 | 37 - 101 | 36 - 40 | 15 - 40 | 36 - 40 | 36 - 39 | 36 - 40 |
| Temperature minimum, °C | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 2 | 0 | 1 | 0 |
| Mean (SD) | 37 (0) | 37 (1) | 37 (1) | 37 (1) | 38 (9) | 37 (0) | 37 (1) | 36 (1) | 37 (1) | 37 (1) |
| Range | 37 - 37 | 35 - 37 | 33 - 38 | 35 - 39 | 35 - 99 | 36 - 38 | 34 - 38 | 34 - 38 | 34 - 38 | 35 - 37 |
| Heart rate maximum, bpm | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 1 | 0 |
| Mean (SD) | 104 (13) | 101 (16) | 103 (17) | 105 (16) | 98 (20) | 101 (17) | 99 (20) | 109 (27) | 102 (18) | 106 (21) |
| Range | 81 - 132 | 82 - 142 | 66 - 142 | 81 - 147 | 56 - 151 | 71 - 158 | 36 - 140 | 64 - 168 | 70 - 136 | 71 - 141 |
| Heart rate minimum, bpm | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 2 | 0 | 1 | 0 |
| Mean (SD) | 78 (14) | 74 (17) | 73 (15) | 76 (13) | 74 (15) | 75 (13) | 80 (13) | 72 (14) | 75 (16) | 77 (16) |
| Range | 58 - 100 | 44 - 127 | 43 - 101 | 46 - 107 | 35 - 108 | 46 - 106 | 54 - 105 | 46 - 112 | 44 - 105 | 41 - 103 |
| Systolic blood pressure minimum, mm Hg | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 1 | 0 |
| Mean (SD) | 108 (25) | 108 (17) | 109 (16) | 113 (18) | 115 (19) | 109 (18) | 112 (19) | 106 (25) | 112 (21) | 107 (17) |
| Range | 64 - 134 | 77 - 144 | 71 - 165 | 70 - 175 | 63 - 151 | 64 - 151 | 78 - 151 | 32 - 180 | 71 - 160 | 78 - 142 |
| Mean arterial pressure maximum, mm Hg | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 0 | 0 | 2 | 0 | 1 | 0 |
| Mean (SD) | 101 (14) | 105 (8) | 109 (14) | 112 (16) | 106 (13) | 109 (19) | 107 (21) | 111 (17) | 106 (24) | 104 (17) |
| Range | 86 - 118 | 89 - 117 | 83 - 158 | 75 - 148 | 65 - 134 | 71 - 166 | 75 - 157 | 79 - 145 | 72 - 196 | 76 - 137 |
| Mean arterial pressure minimum, mm Hg | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 1 | 0 | 2 | 0 | 1 | 0 |
| Mean (SD) | 73 (13) | 74 (13) | 76 (14) | 78 (12) | 81 (12) | 77 (13) | 78 (11) | 76 (18) | 79 (15) | 71 (15) |
| Range | 52 - 92 | 44 - 94 | 54 - 136 | 52 - 125 | 50 - 110 | 44 - 105 | 54 - 100 | 27 - 113 | 55 - 115 | 34 - 103 |
| Respiratory rate maximum, bpm | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 1 | 0 |
| Mean (SD) | 29 (6) | 27 (8) | 26 (7) | 28 (8) | 25 (6) | 25 (7) | 24 (7) | 28 (8) | 26 (9) | 28 (8) |
| Range | 20 - 37 | 18 - 50 | 18 - 47 | 18 - 54 | 15 - 37 | 11 - 51 | 16 - 44 | 14 - 48 | 18 - 48 | 17 - 48 |
| Respiratory rate minimum, bpm | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 2 | 0 | 1 | 0 |
| Mean (SD) | 16 (3) | 16 (4) | 18 (17) | 16 (3) | 16 (2) | 15 (3) | 16 (3) | 16 (4) | 16 (3) | 15 (3) |
| Range | 12 - 22 | 9 - 25 | 11 - 124 | 8 - 23 | 11 - 22 | 9 - 24 | 9 - 26 | 10 - 34 | 10 - 22 | 5 - 18 |
| Oxygen saturation minimum, % | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 1 | 0 |
| Mean (SD) | 93 (2) | 89 (9) | 93 (3) | 93 (5) | 92 (5) | 92 (6) | 93 (5) | 92 (5) | 94 (6) | 91 (6) |
| Range | 89 - 96 | 55 - 97 | 87 - 98 | 80 - 100 | 77 - 100 | 64 - 100 | 78 - 100 | 78 - 100 | 75 - 100 | 75 - 99 |
| FiO2 at saturation minimum, decimal | ||||||||||
| N-Miss | 1 | 0 | 0 | 1 | 2 | 0 | 2 | 0 | 1 | 0 |
| Mean (SD) | 0 (0) | 5 (21) | 3 (16) | 0 (0) | 2 (11) | 2 (13) | 1 (6) | 4 (17) | 0 (0) | 0 (0) |
| Range | 0 - 1 | 0 - 100 | 0 - 100 | 0 - 0 | 0 - 70 | 0 - 100 | 0 - 40 | 0 - 100 | 0 - 1 | 0 - 1 |
| Dopamine | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 2 | 2 | 2 | 1 | 0 |
| No | 10 (100%) | 23 (100%) | 40 (100%) | 53 (100%) | 45 (100%) | 58 (100%) | 40 (100%) | 42 (100%) | 30 (100%) | 22 (100%) |
| Dobutamine | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 1 | 2 | 2 | 1 | 0 |
| No | 10 (100%) | 23 (100%) | 40 (100%) | 53 (100%) | 45 (100%) | 59 (100%) | 40 (100%) | 42 (100%) | 30 (100%) | 22 (100%) |
| Epinepherine | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 1 | 2 | 1 | 1 | 0 |
| No | 10 (100%) | 23 (100%) | 39 (98%) | 53 (100%) | 45 (100%) | 59 (100%) | 40 (100%) | 41 (95%) | 29 (97%) | 22 (100%) |
| Yes | 0 (0%) | 0 (0%) | 1 (2%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 2 (5%) | 1 (3%) | 0 (0%) |
| Norepinephrine | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 1 | 2 | 1 | 1 | 0 |
| No | 9 (90%) | 20 (87%) | 37 (92%) | 53 (100%) | 43 (96%) | 58 (98%) | 38 (95%) | 39 (91%) | 30 (100%) | 20 (91%) |
| Yes | 1 (10%) | 3 (13%) | 3 (8%) | 0 (0%) | 2 (4%) | 1 (2%) | 2 (5%) | 4 (9%) | 0 (0%) | 2 (9%) |
| Initial Sodium, meql/L | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 2 | 2 | 9 | 2 | 4 | 1 |
| Mean (SD) | 136 (5) | 137 (3) | 138 (6) | 138 (7) | 139 (6) | 140 (6) | 141 (7) | 140 (8) | 137 (6) | 139 (4) |
| Range | 127 - 143 | 130 - 144 | 119 - 160 | 127 - 167 | 121 - 155 | 130 - 162 | 128 - 160 | 121 - 168 | 123 - 149 | 127 - 151 |
| Initial Potassium, meq/L | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 2 | 2 | 9 | 2 | 4 | 1 |
| Mean (SD) | 4 (0) | 4 (1) | 4 (1) | 4 (1) | 6 (15) | 4 (1) | 4 (0) | 5 (1) | 4 (1) | 4 (1) |
| Range | 4 - 5 | 3 - 6 | 3 - 6 | 3 - 5 | 3 - 103 | 2 - 7 | 3 - 5 | 3 - 8 | 2 - 6 | 3 - 7 |
| Initial Creatinine, mg/dL | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 2 | 2 | 9 | 2 | 4 | 1 |
| Mean (SD) | 1 (0) | 2 (1) | 2 (3) | 1 (1) | 2 (2) | 2 (3) | 2 (3) | 3 (4) | 2 (3) | 2 (4) |
| Range | 0 - 2 | 1 - 7 | 1 - 13 | 0 - 5 | 0 - 11 | 0 - 15 | 1 - 13 | 0 - 15 | 1 - 14 | 0 - 18 |
| ALT initial, IU/L | ||||||||||
| N-Miss | 0 | 0 | 0 | 5 | 2 | 2 | 10 | 2 | 4 | 1 |
| Mean (SD) | 31 (19) | 44 (56) | 31 (47) | 30 (32) | 36 (33) | 28 (21) | 28 (26) | 47 (77) | 34 (26) | 25 (16) |
| Range | 15 - 76 | 3 - 233 | 4 - 310 | 8 - 177 | 8 - 159 | 6 - 94 | 7 - 134 | 6 - 452 | 6 - 116 | 7 - 64 |
| AST initial, IU/L | ||||||||||
| N-Miss | 0 | 0 | 0 | 5 | 2 | 2 | 10 | 2 | 4 | 1 |
| Mean (SD) | 33 (14) | 103 (252) | 49 (88) | 41 (44) | 46 (37) | 38 (31) | 39 (25) | 53 (62) | 48 (39) | 35 (18) |
| Range | 16 - 57 | 10 - 1197 | 5 - 578 | 10 - 266 | 12 - 169 | 9 - 163 | 15 - 114 | 10 - 341 | 9 - 163 | 15 - 87 |
| Total bilirubin initial, mg/dL | ||||||||||
| N-Miss | 0 | 0 | 0 | 5 | 2 | 2 | 10 | 2 | 4 | 1 |
| Mean (SD) | 0 (0) | 1 (0) | 1 (0) | 1 (0) | 1 (0) | 1 (0) | 1 (0) | 1 (1) | 1 (0) | 1 (0) |
| Range | 0 - 1 | 0 - 1 | 0 - 2 | 0 - 2 | 0 - 2 | 0 - 2 | 0 - 2 | 0 - 3 | 0 - 2 | 0 - 2 |
| Lactate initial, mmol/L | ||||||||||
| N-Miss | 3 | 5 | 19 | 27 | 20 | 33 | 24 | 17 | 18 | 10 |
| Mean (SD) | 2 (1) | 2 (2) | 3 (3) | 2 (1) | 2 (1) | 3 (1) | 2 (1) | 3 (3) | 2 (1) | 2 (1) |
| Range | 1 - 3 | 0 - 10 | 1 - 15 | 1 - 7 | 1 - 3 | 1 - 6 | 1 - 4 | 1 - 14 | 1 - 3 | 0 - 5 |
| WBC count initial, K/mcL | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 2 | 2 | 9 | 0 | 4 | 0 |
| Mean (SD) | 6 (2) | 7 (5) | 7 (4) | 7 (3) | 7 (3) | 8 (4) | 9 (11) | 8 (3) | 6 (3) | 8 (4) |
| Range | 3 - 9 | 1 - 28 | 2 - 17 | 2 - 18 | 3 - 23 | 3 - 19 | 3 - 65 | 3 - 18 | 2 - 15 | 3 - 20 |
| Hemoglobin initial, g/dL | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 2 | 2 | 9 | 0 | 4 | 0 |
| Mean (SD) | 12 (2) | 13 (2) | 12 (2) | 12 (2) | 13 (2) | 13 (2) | 13 (3) | 12 (2) | 12 (2) | 13 (2) |
| Range | 8 - 16 | 7 - 15 | 6 - 16 | 7 - 17 | 8 - 17 | 8 - 17 | 5 - 17 | 6 - 17 | 8 - 17 | 8 - 16 |
| Hematocrit initial, % | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 2 | 2 | 9 | 0 | 4 | 0 |
| Mean (SD) | 38 (7) | 40 (6) | 38 (7) | 38 (7) | 39 (7) | 39 (6) | 38 (8) | 37 (7) | 38 (6) | 39 (6) |
| Range | 24 - 48 | 25 - 48 | 20 - 49 | 11 - 50 | 10 - 53 | 23 - 50 | 15 - 51 | 17 - 54 | 24 - 50 | 26 - 49 |
| Platelet Count initial, K/mcL | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 2 | 2 | 9 | 0 | 4 | 0 |
| Mean (SD) | 228 (69) | 194 (66) | 226 (110) | 244 (103) | 213 (69) | 239 (97) | 231 (98) | 247 (107) | 236 (92) | 240 (122) |
| Range | 143 - 359 | 80 - 369 | 55 - 441 | 80 - 607 | 87 - 413 | 63 - 675 | 13 - 480 | 108 - 742 | 23 - 469 | 98 - 622 |
| Lymphocytes initial, K/mcL | ||||||||||
| N-Miss | 0 | 0 | 0 | 4 | 2 | 2 | 10 | 6 | 4 | 1 |
| Mean (SD) | 1 (1) | 1 (2) | 1 (1) | 1 (1) | 1 (1) | 1 (1) | 1 (0) | 1 (1) | 1 (1) | 1 (1) |
| Range | 0 - 4 | 0 - 9 | 0 - 3 | 0 - 3 | 0 - 5 | 0 - 4 | 0 - 2 | 0 - 3 | 0 - 3 | 1 - 3 |
| PA02 initial, mm Hg | ||||||||||
| N-Miss | 9 | 15 | 33 | 44 | 39 | 50 | 34 | 34 | 28 | 16 |
| Mean (SD) | 95 (NA) | 76 (19) | 132 (77) | 122 (59) | 100 (50) | 77 (46) | 95 (50) | 175 (81) | 102 (17) | 93 (27) |
| Range | 95 - 95 | 43 - 101 | 53 - 243 | 57 - 234 | 47 - 193 | 33 - 198 | 55 - 210 | 77 - 346 | 84 - 116 | 58 - 137 |
| PAC02 initial, mm Hg | ||||||||||
| N-Miss | 9 | 15 | 33 | 44 | 39 | 50 | 34 | 34 | 28 | 16 |
| Mean (SD) | 36 (NA) | 44 (13) | 40 (13) | 35 (9) | 37 (7) | 37 (11) | 36 (11) | 37 (12) | 32 (6) | 38 (6) |
| Range | 36 - 36 | 32 - 68 | 27 - 60 | 27 - 55 | 28 - 51 | 20 - 52 | 26 - 56 | 21 - 56 | 27 - 39 | 32 - 46 |
| Arterial SpO2 initial, % | ||||||||||
| N-Miss | 9 | 17 | 33 | 44 | 39 | 50 | 34 | 35 | 28 | 16 |
| Mean (SD) | 97 (NA) | 91 (7) | 95 (4) | 96 (2) | 92 (8) | 86 (14) | 94 (4) | 96 (2) | 96 (1) | 94 (3) |
| Range | 97 - 97 | 77 - 97 | 89 - 98 | 92 - 98 | 74 - 97 | 50 - 99 | 88 - 98 | 93 - 99 | 95 - 97 | 89 - 98 |
| pH initial | ||||||||||
| N-Miss | 9 | 15 | 33 | 44 | 39 | 50 | 34 | 34 | 28 | 16 |
| Mean (SD) | 7 (NA) | 7 (0) | 7 (0) | 7 (0) | 7 (0) | 7 (0) | 7 (0) | 7 (0) | 7 (0) | 7 (0) |
| Range | 7 - 7 | 7 - 7 | 7 - 7 | 7 - 8 | 7 - 8 | 7 - 8 | 7 - 8 | 7 - 8 | 7 - 8 | 7 - 7 |
Extreme Values
summary(tableby(week ~ max_creat + cpk_max + troponin_max + bnp_max + crp_max + ldh_max +
hgb_a1c_max + ferritin_max + alt_max + ast_max + lactate_max + min_lymp + ddimer_max,
data = covid1, control = mytables))| 03-09 (N=10) | 03-16 (N=23) | 03-23 (N=40) | 03-30 (N=54) | 04-06 (N=46) | 04-13 (N=60) | 04-20 (N=42) | 04-27 (N=44) | 05-04 (N=31) | 05-11 (N=22) | |
|---|---|---|---|---|---|---|---|---|---|---|
| Creatinine maximum, mg/dL | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 2 | 2 | 9 | 2 | 4 | 1 |
| Mean (SD) | 1 (0) | 3 (3) | 2 (3) | 2 (1) | 2 (3) | 3 (3) | 2 (3) | 3 (4) | 2 (3) | 3 (4) |
| Range | 0 - 2 | 1 - 10 | 1 - 13 | 0 - 8 | 0 - 14 | 0 - 15 | 1 - 14 | 0 - 18 | 1 - 14 | 0 - 18 |
| CPK maximum, U/L | ||||||||||
| N-Miss | 7 | 15 | 23 | 38 | 26 | 43 | 30 | 28 | 23 | 14 |
| Mean (SD) | 56 (96) | 7714 (17329) | 1164 (1692) | 826 (1501) | 949 (1110) | 593 (1602) | 299 (438) | 1044 (1737) | 456 (706) | 286 (257) |
| Range | 0 - 166 | 70 - 50000 | 50 - 6049 | 60 - 5925 | 41 - 4084 | 0 - 6774 | 18 - 1507 | 29 - 5925 | 53 - 2139 | 62 - 752 |
| Troponin-I maximum, ng/mL | ||||||||||
| N-Miss | 2 | 13 | 8 | 20 | 10 | 18 | 16 | 13 | 17 | 8 |
| Mean (SD) | 0 (0) | 0 (0) | 0 (1) | 0 (0) | 0 (0) | 0 (0) | 0 (2) | 0 (1) | 0 (0) | 2 (4) |
| Range | 0 - 0 | 0 - 0 | 0 - 4 | 0 - 0 | 0 - 1 | 0 - 1 | 0 - 8 | 0 - 4 | 0 - 0 | 0 - 16 |
| BNP maximum, pg/mL | ||||||||||
| N-Miss | 3 | 12 | 20 | 28 | 26 | 34 | 26 | 23 | 23 | 13 |
| Mean (SD) | 26 (13) | 218 (461) | 166 (336) | 180 (265) | 672 (1516) | 912 (2029) | 285 (573) | 138 (108) | 539 (1181) | 466 (1188) |
| Range | 14 - 51 | 9 - 1577 | 7 - 1400 | 14 - 1033 | 19 - 5958 | 6 - 7906 | 8 - 2274 | 7 - 413 | 8 - 3419 | 10 - 3622 |
| HS-CRP maximum, mg/L | ||||||||||
| N-Miss | 9 | 20 | 22 | 30 | 22 | 25 | 26 | 20 | 19 | 6 |
| Mean (SD) | 0 (NA) | 171 (60) | 116 (84) | 137 (86) | 150 (81) | 103 (79) | 153 (97) | 129 (101) | 108 (99) | 94 (95) |
| Range | 0 - 0 | 134 - 240 | 0 - 240 | 23 - 240 | 10 - 240 | 0 - 240 | 3 - 240 | 1 - 240 | 2 - 240 | 0 - 240 |
| Lactate dehydrogenase maximum, U/L | ||||||||||
| N-Miss | 7 | 15 | 26 | 21 | 15 | 15 | 18 | 15 | 14 | 9 |
| Mean (SD) | 122 (112) | 403 (217) | 338 (180) | 353 (162) | 361 (162) | 323 (130) | 876 (2357) | 445 (287) | 372 (218) | 365 (151) |
| Range | 0 - 220 | 128 - 784 | 0 - 658 | 150 - 800 | 171 - 857 | 150 - 785 | 124 - 11894 | 113 - 1518 | 170 - 1021 | 176 - 640 |
| Hemoglobin A1c maximum, % | ||||||||||
| N-Miss | 6 | 14 | 24 | 34 | 32 | 31 | 26 | 27 | 19 | 14 |
| Mean (SD) | 6 (4) | 10 (3) | 8 (3) | 7 (3) | 8 (3) | 7 (3) | 6 (1) | 6 (2) | 7 (2) | 7 (3) |
| Range | 0 - 9 | 5 - 15 | 5 - 17 | 0 - 13 | 5 - 14 | 0 - 14 | 5 - 10 | 0 - 11 | 5 - 11 | 5 - 12 |
| Ferritin maximum, ng/mL | ||||||||||
| N-Miss | 7 | 16 | 23 | 31 | 22 | 36 | 25 | 19 | 22 | 12 |
| Mean (SD) | 46 (76) | 1370 (1308) | 755 (752) | 635 (1111) | 920 (1101) | 1321 (3091) | 2044 (3956) | 1468 (1986) | 632 (645) | 1277 (1843) |
| Range | 0 - 134 | 81 - 3947 | 24 - 2338 | 10 - 5514 | 24 - 4234 | 41 - 15000 | 24 - 15000 | 13 - 9751 | 33 - 1976 | 5 - 5324 |
| ALT maximum, IU/L | ||||||||||
| N-Miss | 0 | 0 | 0 | 5 | 2 | 2 | 9 | 2 | 4 | 1 |
| Mean (SD) | 44 (32) | 74 (91) | 248 (1081) | 55 (95) | 52 (77) | 44 (49) | 493 (1808) | 72 (111) | 35 (26) | 220 (851) |
| Range | 15 - 105 | 6 - 343 | 10 - 6776 | 9 - 622 | 10 - 491 | 6 - 272 | 9 - 7500 | 6 - 491 | 6 - 116 | 10 - 3928 |
| AST maximum, IU/L | ||||||||||
| N-Miss | 0 | 0 | 0 | 5 | 2 | 2 | 9 | 2 | 4 | 1 |
| Mean (SD) | 46 (30) | 148 (267) | 551 (2661) | 71 (104) | 71 (106) | 58 (59) | 421 (1944) | 94 (143) | 51 (40) | 515 (2151) |
| Range | 16 - 98 | 18 - 1197 | 8 - 16762 | 11 - 636 | 12 - 675 | 11 - 316 | 16 - 11216 | 13 - 660 | 9 - 163 | 16 - 9902 |
| Lactate maximum, mmol/L | ||||||||||
| N-Miss | 3 | 3 | 16 | 24 | 20 | 31 | 23 | 16 | 18 | 11 |
| Mean (SD) | 2 (1) | 3 (2) | 3 (3) | 3 (2) | 2 (1) | 3 (2) | 4 (4) | 4 (4) | 2 (1) | 5 (8) |
| Range | 1 - 3 | 1 - 10 | 1 - 15 | 1 - 14 | 1 - 4 | 1 - 8 | 1 - 13 | 1 - 15 | 1 - 3 | 1 - 30 |
| Lymphocytes minimum, K/mcL | ||||||||||
| N-Miss | 0 | 0 | 0 | 4 | 2 | 2 | 10 | 5 | 4 | 1 |
| Mean (SD) | 1 (1) | 1 (0) | 1 (1) | 1 (1) | 1 (1) | 1 (1) | 1 (1) | 1 (1) | 1 (1) | 1 (1) |
| Range | 0 - 4 | 0 - 2 | 0 - 3 | 0 - 2 | 0 - 5 | 0 - 2 | 0 - 2 | 0 - 3 | 0 - 2 | 0 - 3 |
| D-dimer maximum, ng/mL | ||||||||||
| N-Miss | 7 | 19 | 23 | 33 | 21 | 20 | 18 | 10 | 15 | 3 |
| Mean (SD) | 580 (151) | 2850 (2580) | 11046 (27163) | 7084 (13493) | 7421 (13077) | 5113 (16504) | 12012 (25984) | 19310 (35957) | 3064 (4846) | 4482 (7947) |
| Range | 479 - 754 | 1261 - 6686 | 0 - 113990 | 250 - 52889 | 296 - 60889 | 250 - 105488 | 250 - 128000 | 250 - 128000 | 324 - 19721 | 250 - 32153 |
Radiology
summary(tableby(week ~ cxr_done + cxr_abnormal + cxr_atelectasis + cxr_bilateral +
cxr_cavity + cxr_consolidation + cxr_interstital + cxr_mass + cxr_multifocal +
cxr_effusion + cxr_nodule + ct_done + us_done + vq_done + tte_done, data = covid1,
control = mytables))| 03-09 (N=10) | 03-16 (N=23) | 03-23 (N=40) | 03-30 (N=54) | 04-06 (N=46) | 04-13 (N=60) | 04-20 (N=42) | 04-27 (N=44) | 05-04 (N=31) | 05-11 (N=22) | |
|---|---|---|---|---|---|---|---|---|---|---|
| CXR performed | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
| No | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 2 (4%) | 4 (7%) | 6 (14%) | 6 (14%) | 3 (10%) | 1 (5%) |
| Yes | 10 (100%) | 23 (100%) | 40 (100%) | 53 (100%) | 43 (96%) | 56 (93%) | 36 (86%) | 38 (86%) | 28 (90%) | 21 (95%) |
| CXR abnormal | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 4 | 4 | 6 | 7 | 3 | 1 |
| No | 3 (30%) | 5 (22%) | 13 (32%) | 11 (21%) | 9 (21%) | 18 (32%) | 13 (36%) | 13 (35%) | 11 (39%) | 9 (43%) |
| Yes | 7 (70%) | 18 (78%) | 27 (68%) | 41 (79%) | 33 (79%) | 38 (68%) | 23 (64%) | 24 (65%) | 17 (61%) | 12 (57%) |
| Atelectasis | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 4 | 4 | 6 | 6 | 3 | 1 |
| No | 7 (70%) | 17 (74%) | 27 (68%) | 38 (72%) | 24 (57%) | 45 (80%) | 25 (69%) | 27 (71%) | 19 (68%) | 15 (71%) |
| Yes | 3 (30%) | 6 (26%) | 13 (32%) | 15 (28%) | 18 (43%) | 11 (20%) | 11 (31%) | 11 (29%) | 9 (32%) | 6 (29%) |
| Bilateral Opacities, not effusions | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 3 | 4 | 6 | 6 | 3 | 1 |
| No | 5 (50%) | 10 (43%) | 27 (68%) | 26 (49%) | 19 (44%) | 28 (50%) | 28 (78%) | 23 (61%) | 15 (54%) | 13 (62%) |
| Yes | 5 (50%) | 13 (57%) | 13 (32%) | 27 (51%) | 24 (56%) | 28 (50%) | 8 (22%) | 15 (39%) | 13 (46%) | 8 (38%) |
| Cavity/abscess | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 3 | 4 | 6 | 6 | 3 | 1 |
| No | 10 (100%) | 23 (100%) | 40 (100%) | 53 (100%) | 43 (100%) | 56 (100%) | 36 (100%) | 38 (100%) | 28 (100%) | 21 (100%) |
| Consolidation | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 3 | 4 | 6 | 6 | 3 | 1 |
| No | 9 (90%) | 22 (96%) | 34 (85%) | 48 (91%) | 40 (93%) | 53 (95%) | 35 (97%) | 34 (89%) | 27 (96%) | 21 (100%) |
| Yes | 1 (10%) | 1 (4%) | 6 (15%) | 5 (9%) | 3 (7%) | 3 (5%) | 1 (3%) | 4 (11%) | 1 (4%) | 0 (0%) |
| Interstitial | ||||||||||
| N-Miss | 0 | 1 | 0 | 1 | 3 | 4 | 6 | 6 | 3 | 1 |
| No | 7 (70%) | 19 (86%) | 39 (98%) | 46 (87%) | 43 (100%) | 48 (86%) | 30 (83%) | 33 (87%) | 25 (89%) | 20 (95%) |
| Yes | 3 (30%) | 3 (14%) | 1 (2%) | 7 (13%) | 0 (0%) | 8 (14%) | 6 (17%) | 5 (13%) | 3 (11%) | 1 (5%) |
| Mass/mass-like | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 3 | 4 | 6 | 6 | 3 | 1 |
| No | 10 (100%) | 23 (100%) | 40 (100%) | 53 (100%) | 43 (100%) | 56 (100%) | 36 (100%) | 38 (100%) | 28 (100%) | 21 (100%) |
| Multifocal | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 3 | 4 | 6 | 6 | 3 | 1 |
| No | 10 (100%) | 15 (65%) | 23 (58%) | 46 (87%) | 39 (91%) | 46 (82%) | 34 (94%) | 32 (84%) | 27 (96%) | 20 (95%) |
| Yes | 0 (0%) | 8 (35%) | 17 (42%) | 7 (13%) | 4 (9%) | 10 (18%) | 2 (6%) | 6 (16%) | 1 (4%) | 1 (5%) |
| Pleural effusion | ||||||||||
| N-Miss | 1 | 0 | 0 | 1 | 3 | 4 | 6 | 6 | 3 | 1 |
| No | 9 (100%) | 23 (100%) | 38 (95%) | 50 (94%) | 42 (98%) | 47 (84%) | 34 (94%) | 35 (92%) | 26 (93%) | 19 (90%) |
| Yes | 0 (0%) | 0 (0%) | 2 (5%) | 3 (6%) | 1 (2%) | 9 (16%) | 2 (6%) | 3 (8%) | 2 (7%) | 2 (10%) |
| Reticulonodular | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 4 | 5 | 6 | 6 | 3 | 2 |
| No | 10 (100%) | 21 (91%) | 40 (100%) | 53 (100%) | 42 (100%) | 55 (100%) | 35 (97%) | 37 (97%) | 27 (96%) | 19 (95%) |
| Yes | 0 (0%) | 2 (9%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (3%) | 1 (3%) | 1 (4%) | 1 (5%) |
| Chest CT performed | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
| No | 5 (50%) | 15 (65%) | 28 (70%) | 39 (74%) | 39 (87%) | 49 (82%) | 34 (81%) | 31 (70%) | 26 (84%) | 14 (64%) |
| Yes, with IV contrast | 4 (40%) | 4 (17%) | 9 (22%) | 8 (15%) | 3 (7%) | 9 (15%) | 8 (19%) | 10 (23%) | 3 (10%) | 7 (32%) |
| Yes, without IV contrast | 1 (10%) | 4 (17%) | 3 (8%) | 6 (11%) | 3 (7%) | 2 (3%) | 0 (0%) | 3 (7%) | 2 (6%) | 1 (5%) |
| Ultrasound of extremities performed | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 0 |
| No | 10 (100%) | 20 (87%) | 34 (85%) | 45 (85%) | 39 (87%) | 50 (83%) | 33 (79%) | 36 (82%) | 28 (93%) | 16 (73%) |
| Yes | 0 (0%) | 3 (13%) | 6 (15%) | 8 (15%) | 6 (13%) | 10 (17%) | 9 (21%) | 8 (18%) | 2 (7%) | 6 (27%) |
| VQ scan performed | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 0 | 0 |
| No | 10 (100%) | 23 (100%) | 40 (100%) | 53 (100%) | 45 (100%) | 60 (100%) | 41 (100%) | 44 (100%) | 31 (100%) | 22 (100%) |
| TTE performed | ||||||||||
| N-Miss | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
| No | 8 (89%) | 17 (74%) | 31 (78%) | 41 (77%) | 35 (78%) | 45 (75%) | 26 (62%) | 35 (80%) | 27 (87%) | 13 (59%) |
| Yes | 1 (11%) | 6 (26%) | 9 (22%) | 12 (23%) | 10 (22%) | 15 (25%) | 16 (38%) | 9 (20%) | 4 (13%) | 9 (41%) |
Microbiology
summary(tableby(week ~ sars_samples + blood_cx + resp_cx + procal_72 + influenza +
legionella + hiv_test_alt + hiv_vl + cd4, data = covid1, control = mytables))| 03-09 (N=10) | 03-16 (N=23) | 03-23 (N=40) | 03-30 (N=54) | 04-06 (N=46) | 04-13 (N=60) | 04-20 (N=42) | 04-27 (N=44) | 05-04 (N=31) | 05-11 (N=22) | |
|---|---|---|---|---|---|---|---|---|---|---|
| Number of SARS-CoV-2 tests | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 1 | 0 | 0 | 0 | 0 |
| Mean (SD) | 2 (1) | 2 (2) | 2 (2) | 3 (3) | 2 (2) | 2 (2) | 2 (2) | 2 (2) | 1 (1) | 2 (2) |
| Range | 1 - 3 | 1 - 10 | 0 - 9 | 1 - 15 | 1 - 11 | 1 - 7 | 1 - 7 | 1 - 10 | 1 - 8 | 1 - 9 |
| Blood cultures in first 48 hours | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 2 | 1 | 0 | 0 | 0 | 0 |
| Negative | 7 (70%) | 18 (78%) | 22 (55%) | 24 (45%) | 21 (48%) | 19 (32%) | 12 (29%) | 19 (43%) | 11 (35%) | 7 (32%) |
| Not done | 3 (30%) | 5 (22%) | 15 (38%) | 27 (51%) | 22 (50%) | 35 (59%) | 28 (67%) | 22 (50%) | 19 (61%) | 11 (50%) |
| Positive | 0 (0%) | 0 (0%) | 3 (8%) | 2 (4%) | 1 (2%) | 5 (8%) | 2 (5%) | 3 (7%) | 1 (3%) | 4 (18%) |
| Respiratory cultures in first 48 hours | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 2 | 3 | 0 | 0 | 0 | 0 |
| Negative | 6 (60%) | 5 (22%) | 4 (10%) | 4 (8%) | 4 (9%) | 3 (5%) | 1 (2%) | 0 (0%) | 0 (0%) | 2 (9%) |
| Not done | 4 (40%) | 18 (78%) | 35 (88%) | 48 (91%) | 40 (91%) | 54 (95%) | 39 (93%) | 40 (91%) | 31 (100%) | 19 (86%) |
| Positive | 0 (0%) | 0 (0%) | 1 (2%) | 1 (2%) | 0 (0%) | 0 (0%) | 2 (5%) | 4 (9%) | 0 (0%) | 1 (5%) |
| Procalcitonin initial (48h), ng/mL | ||||||||||
| N-Miss | 6 | 13 | 28 | 35 | 31 | 23 | 21 | 22 | 18 | 10 |
| Mean (SD) | 0 (0) | 2 (5) | 3 (8) | 0 (1) | 1 (3) | 1 (2) | 1 (1) | 11 (35) | 6 (20) | 0 (1) |
| Range | 0 - 1 | 0 - 16 | 0 - 28 | 0 - 5 | 0 - 11 | 0 - 9 | 0 - 5 | 0 - 164 | 0 - 72 | 0 - 2 |
| Influenza PCR | ||||||||||
| N-Miss | 0 | 1 | 1 | 3 | 2 | 1 | 0 | 0 | 0 | 0 |
| A/B+ | 10 (100%) | 22 (100%) | 37 (95%) | 16 (31%) | 3 (7%) | 1 (2%) | 1 (2%) | 1 (2%) | 1 (3%) | 2 (9%) |
| Not Done | 0 (0%) | 0 (0%) | 2 (5%) | 35 (69%) | 41 (93%) | 58 (98%) | 41 (98%) | 43 (98%) | 30 (97%) | 20 (91%) |
| Legionella urine antigen | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
| Negative | 3 (30%) | 7 (30%) | 8 (20%) | 7 (13%) | 3 (7%) | 6 (10%) | 2 (5%) | 1 (2%) | 2 (6%) | 2 (9%) |
| Not done | 7 (70%) | 16 (70%) | 32 (80%) | 46 (87%) | 42 (93%) | 54 (90%) | 40 (95%) | 43 (98%) | 29 (94%) | 20 (91%) |
| HIV test | ||||||||||
| N-Miss | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
| Current or Prior negative < 1 year | 3 (33%) | 12 (52%) | 21 (52%) | 23 (43%) | 22 (49%) | 20 (33%) | 11 (26%) | 17 (39%) | 13 (42%) | 11 (50%) |
| Current or Prior Positive | 0 (0%) | 2 (9%) | 2 (5%) | 4 (8%) | 0 (0%) | 1 (2%) | 1 (2%) | 0 (0%) | 1 (3%) | 1 (5%) |
| Not done, no prior | 6 (67%) | 9 (39%) | 17 (42%) | 26 (49%) | 23 (51%) | 39 (65%) | 30 (71%) | 27 (61%) | 17 (55%) | 10 (45%) |
| Viral load undetectable | ||||||||||
| N-Miss | 10 | 21 | 38 | 50 | 46 | 59 | 41 | 44 | 30 | 21 |
| No | 0 | 1 (50%) | 1 (50%) | 1 (25%) | 0 | 1 (100%) | 1 (100%) | 0 | 0 (0%) | 1 (100%) |
| Yes | 0 | 1 (50%) | 1 (50%) | 3 (75%) | 0 | 0 (0%) | 0 (0%) | 0 | 0 (0%) | 0 (0%) |
| Not done | 0 | 0 (0%) | 0 (0%) | 0 (0%) | 0 | 0 (0%) | 0 (0%) | 0 | 1 (100%) | 0 (0%) |
| CD4, K/L | ||||||||||
| N-Miss | 10 | 21 | 38 | 51 | 46 | 59 | 41 | 44 | 31 | 21 |
| Mean (SD) | NA | 610 (373) | 252 (157) | 243 (275) | NA | 507 (NA) | 90 (NA) | NA | NA | 86 (NA) |
| Range | NA | 346 - 874 | 141 - 363 | 75 - 560 | NA | 507 - 507 | 90 - 90 | NA | NA | 86 - 86 |
Drugs
summary(tableby(week ~ covid_tx___1 + covid_tx___2 + covid_tx___3 + covid_tx___4 +
covid_tx___5 + covid_tx___0 + abx_received___1 + abx_received___2 + abx_received___3 +
abx_received___4 + abx_received___5 + abx_received___6 + abx_received___7 + abx_other +
steroid_type___1 + steroid_type___2 + steroid_type___3 + steroid_type___4 + steroid_type___5 +
steroid_type___0 + anticoagulation, data = covid1, control = mytables))| 03-09 (N=10) | 03-16 (N=23) | 03-23 (N=40) | 03-30 (N=54) | 04-06 (N=46) | 04-13 (N=60) | 04-20 (N=42) | 04-27 (N=44) | 05-04 (N=31) | 05-11 (N=22) | |
|---|---|---|---|---|---|---|---|---|---|---|
| Redesmivir, on clinical trial | ||||||||||
| No | 10 (100%) | 23 (100%) | 40 (100%) | 53 (98%) | 40 (87%) | 57 (95%) | 42 (100%) | 44 (100%) | 31 (100%) | 19 (86%) |
| Yes | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2%) | 6 (13%) | 3 (5%) | 0 (0%) | 0 (0%) | 0 (0%) | 3 (14%) |
| Redesmivir, not on clinical trial | ||||||||||
| No | 10 (100%) | 23 (100%) | 40 (100%) | 54 (100%) | 46 (100%) | 60 (100%) | 42 (100%) | 44 (100%) | 31 (100%) | 21 (95%) |
| Yes | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (5%) |
| Lopinavir/ritonavir | ||||||||||
| No | 10 (100%) | 22 (96%) | 40 (100%) | 54 (100%) | 46 (100%) | 60 (100%) | 42 (100%) | 44 (100%) | 31 (100%) | 22 (100%) |
| Yes | 0 (0%) | 1 (4%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Hydroxycloroquine | ||||||||||
| No | 7 (70%) | 14 (61%) | 27 (68%) | 40 (74%) | 41 (89%) | 57 (95%) | 42 (100%) | 42 (95%) | 30 (97%) | 22 (100%) |
| Yes | 3 (30%) | 9 (39%) | 13 (32%) | 14 (26%) | 5 (11%) | 3 (5%) | 0 (0%) | 2 (5%) | 1 (3%) | 0 (0%) |
| Tocilizumab | ||||||||||
| No | 10 (100%) | 23 (100%) | 40 (100%) | 54 (100%) | 46 (100%) | 60 (100%) | 41 (98%) | 44 (100%) | 31 (100%) | 21 (95%) |
| Yes | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2%) | 0 (0%) | 0 (0%) | 1 (5%) |
| No SARS-CoV-2 Therapies | ||||||||||
| Mean (SD) | 1 (0) | 1 (1) | 1 (0) | 1 (0) | 1 (0) | 1 (0) | 1 (0) | 1 (0) | 1 (0) | 1 (0) |
| Range | 0 - 1 | 0 - 1 | 0 - 1 | 0 - 1 | 0 - 1 | 0 - 1 | 0 - 1 | 0 - 1 | 0 - 1 | 0 - 1 |
| Azithromycin | ||||||||||
| No | 5 (50%) | 6 (26%) | 16 (40%) | 34 (63%) | 32 (70%) | 46 (77%) | 30 (71%) | 32 (73%) | 24 (77%) | 19 (86%) |
| Yes | 5 (50%) | 17 (74%) | 24 (60%) | 20 (37%) | 14 (30%) | 14 (23%) | 12 (29%) | 12 (27%) | 7 (23%) | 3 (14%) |
| Ceftriaxone | ||||||||||
| No | 6 (60%) | 7 (30%) | 18 (45%) | 34 (63%) | 28 (61%) | 43 (72%) | 32 (76%) | 34 (77%) | 25 (81%) | 19 (86%) |
| Yes | 4 (40%) | 16 (70%) | 22 (55%) | 20 (37%) | 18 (39%) | 17 (28%) | 10 (24%) | 10 (23%) | 6 (19%) | 3 (14%) |
| Doxycycline | ||||||||||
| No | 10 (100%) | 22 (96%) | 36 (90%) | 50 (93%) | 43 (93%) | 57 (95%) | 41 (98%) | 44 (100%) | 31 (100%) | 21 (95%) |
| Yes | 0 (0%) | 1 (4%) | 4 (10%) | 4 (7%) | 3 (7%) | 3 (5%) | 1 (2%) | 0 (0%) | 0 (0%) | 1 (5%) |
| ESBLactam | ||||||||||
| No | 7 (70%) | 19 (83%) | 30 (75%) | 44 (81%) | 42 (91%) | 47 (78%) | 32 (76%) | 33 (75%) | 26 (84%) | 16 (73%) |
| Yes | 3 (30%) | 4 (17%) | 10 (25%) | 10 (19%) | 4 (9%) | 13 (22%) | 10 (24%) | 11 (25%) | 5 (16%) | 6 (27%) |
| Fluoroquinolone | ||||||||||
| No | 10 (100%) | 23 (100%) | 39 (98%) | 53 (98%) | 46 (100%) | 60 (100%) | 40 (95%) | 44 (100%) | 31 (100%) | 22 (100%) |
| Yes | 0 (0%) | 0 (0%) | 1 (2%) | 1 (2%) | 0 (0%) | 0 (0%) | 2 (5%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Vancomycin | ||||||||||
| No | 7 (70%) | 17 (74%) | 27 (68%) | 44 (81%) | 39 (85%) | 46 (77%) | 32 (76%) | 31 (70%) | 27 (87%) | 16 (73%) |
| Yes | 3 (30%) | 6 (26%) | 13 (32%) | 10 (19%) | 7 (15%) | 14 (23%) | 10 (24%) | 13 (30%) | 4 (13%) | 6 (27%) |
| Other Antibiotic | ||||||||||
| No | 8 (80%) | 19 (83%) | 35 (88%) | 52 (96%) | 38 (83%) | 52 (87%) | 41 (98%) | 42 (95%) | 27 (87%) | 19 (86%) |
| Yes | 2 (20%) | 4 (17%) | 5 (12%) | 2 (4%) | 8 (17%) | 8 (13%) | 1 (2%) | 2 (5%) | 4 (13%) | 3 (14%) |
| Other Antibiotics description | ||||||||||
| N-Miss | 8 | 19 | 36 | 52 | 40 | 52 | 41 | 42 | 27 | 19 |
| Acyclovir | 0 (0%) | 1 (25%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| acyclovir (home med) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (12%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| amoxicillin | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (25%) | 0 (0%) |
| Amoxicillin-clavulanate | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (25%) | 0 (0%) |
| ampicillin | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (33%) |
| ampicillin-sulbactam | 0 (0%) | 0 (0%) | 0 (0%) | 1 (50%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Augmentin | 1 (50%) | 0 (0%) | 1 (25%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| aztreonam | 1 (50%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Bactrim | 0 (0%) | 1 (25%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Bactrim (HIV prophylactic dose) | 0 (0%) | 0 (0%) | 1 (25%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Cefazolin | 0 (0%) | 1 (25%) | 1 (25%) | 0 (0%) | 0 (0%) | 2 (25%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| cefazolin (peri-op) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (12%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| cefazolin, cefoxitin | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (17%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Cefepime | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (33%) |
| Cefuroxime | 0 (0%) | 0 (0%) | 1 (25%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Dapsone | 0 (0%) | 0 (0%) | 0 (0%) | 1 (50%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| flagyl (empiric treatment for STIs, pyuria) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (12%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Linezolid, clindamycin, Tobramycin | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (12%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| metronidazole | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (50%) | 2 (50%) | 1 (33%) |
| Metronidazole | 0 (0%) | 1 (25%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (100%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Nitrofurantoin | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (12%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| PIP-TAZO | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (17%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| piperacillin-tazobactam | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (17%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Piperacillin-tazobactam | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (17%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| tobramycin | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (50%) | 0 (0%) | 0 (0%) |
| Tobramycin | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (17%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| tobramycin, aztrenam | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (17%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Zosyn | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (12%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| Hydrocortisone | ||||||||||
| No | 10 (100%) | 22 (96%) | 39 (98%) | 51 (94%) | 43 (93%) | 59 (98%) | 38 (90%) | 41 (93%) | 30 (97%) | 19 (86%) |
| Yes | 0 (0%) | 1 (4%) | 1 (2%) | 3 (6%) | 3 (7%) | 1 (2%) | 4 (10%) | 3 (7%) | 1 (3%) | 3 (14%) |
| Methylprednisolone | ||||||||||
| No | 10 (100%) | 21 (91%) | 39 (98%) | 51 (94%) | 45 (98%) | 56 (93%) | 37 (88%) | 41 (93%) | 30 (97%) | 21 (95%) |
| Yes | 0 (0%) | 2 (9%) | 1 (2%) | 3 (6%) | 1 (2%) | 4 (7%) | 5 (12%) | 3 (7%) | 1 (3%) | 1 (5%) |
| Prednisone | ||||||||||
| No | 8 (80%) | 23 (100%) | 39 (98%) | 51 (94%) | 45 (98%) | 57 (95%) | 39 (93%) | 43 (98%) | 31 (100%) | 21 (95%) |
| Yes | 2 (20%) | 0 (0%) | 1 (2%) | 3 (6%) | 1 (2%) | 3 (5%) | 3 (7%) | 1 (2%) | 0 (0%) | 1 (5%) |
| Fludrocortisone | ||||||||||
| No | 10 (100%) | 23 (100%) | 40 (100%) | 54 (100%) | 46 (100%) | 60 (100%) | 42 (100%) | 44 (100%) | 31 (100%) | 22 (100%) |
| Dexamethasone | ||||||||||
| No | 10 (100%) | 23 (100%) | 38 (95%) | 53 (98%) | 45 (98%) | 60 (100%) | 41 (98%) | 41 (93%) | 31 (100%) | 22 (100%) |
| Yes | 0 (0%) | 0 (0%) | 2 (5%) | 1 (2%) | 1 (2%) | 0 (0%) | 1 (2%) | 3 (7%) | 0 (0%) | 0 (0%) |
| No steroids | ||||||||||
| No | 2 (20%) | 3 (13%) | 4 (10%) | 8 (15%) | 5 (11%) | 6 (10%) | 9 (21%) | 9 (20%) | 2 (6%) | 3 (14%) |
| Yes | 8 (80%) | 20 (87%) | 36 (90%) | 46 (85%) | 41 (89%) | 54 (90%) | 33 (79%) | 35 (80%) | 29 (94%) | 19 (86%) |
| Therapeutic anticoagulation | ||||||||||
| N-Miss | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| No | 10 (100%) | 21 (91%) | 32 (82%) | 44 (83%) | 41 (89%) | 45 (75%) | 25 (60%) | 27 (61%) | 27 (87%) | 14 (64%) |
| Yes, chronic | 0 (0%) | 1 (4%) | 1 (3%) | 3 (6%) | 3 (7%) | 6 (10%) | 4 (10%) | 4 (9%) | 1 (3%) | 2 (9%) |
| Yes, new | 0 (0%) | 1 (4%) | 6 (15%) | 6 (11%) | 2 (4%) | 9 (15%) | 13 (31%) | 13 (30%) | 3 (10%) | 6 (27%) |
Other Tx & Dispo
summary(tableby(week ~ patient_location + admit_loc + admit_service + fu_loc + hfnc +
niv + ett + extubated + rrt + arrest + discharge_hai + discharge_disposition +
discharge_o2 + discharge_hd, data = covid1, control = mytables))| 03-09 (N=10) | 03-16 (N=23) | 03-23 (N=40) | 03-30 (N=54) | 04-06 (N=46) | 04-13 (N=60) | 04-20 (N=42) | 04-27 (N=44) | 05-04 (N=31) | 05-11 (N=22) | |
|---|---|---|---|---|---|---|---|---|---|---|
| SARS-CoV-2 Location | ||||||||||
| ECC/Hospital | 10 (100%) | 23 (100%) | 40 (100%) | 54 (100%) | 45 (98%) | 60 (100%) | 40 (95%) | 43 (98%) | 31 (100%) | 22 (100%) |
| Outpatient | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2%) | 0 (0%) | 2 (5%) | 1 (2%) | 0 (0%) | 0 (0%) |
| Admission Level of Care | ||||||||||
| N-Miss | 0 | 0 | 0 | 0 | 1 | 0 | 2 | 1 | 0 | 2 |
| Discharged from ED | 0 (0%) | 1 (4%) | 1 (2%) | 9 (17%) | 9 (20%) | 11 (18%) | 15 (38%) | 5 (12%) | 13 (42%) | 1 (5%) |
| General | 7 (70%) | 17 (74%) | 30 (75%) | 33 (61%) | 27 (60%) | 36 (60%) | 15 (38%) | 23 (53%) | 14 (45%) | 9 (45%) |
| Intensive | 1 (10%) | 5 (22%) | 3 (8%) | 3 (6%) | 2 (4%) | 9 (15%) | 6 (15%) | 8 (19%) | 2 (6%) | 3 (15%) |
| Intermediate | 2 (20%) | 0 (0%) | 6 (15%) | 9 (17%) | 7 (16%) | 4 (7%) | 4 (10%) | 7 (16%) | 2 (6%) | 7 (35%) |
| Admission Service | ||||||||||
| N-Miss | 0 | 1 | 1 | 9 | 11 | 11 | 17 | 6 | 13 | 3 |
| Medical | 10 (100%) | 22 (100%) | 37 (95%) | 43 (96%) | 34 (97%) | 46 (94%) | 23 (92%) | 31 (82%) | 15 (83%) | 17 (89%) |
| Neurology | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (6%) | 0 (0%) |
| Other | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 2 (8%) | 3 (8%) | 1 (6%) | 1 (5%) |
| Surgical | 0 (0%) | 0 (0%) | 2 (5%) | 2 (4%) | 1 (3%) | 3 (6%) | 0 (0%) | 4 (11%) | 1 (6%) | 1 (5%) |
| Highest Level of Care | ||||||||||
| N-Miss | 0 | 2 | 1 | 9 | 10 | 12 | 17 | 6 | 13 | 3 |
| General | 7 (70%) | 14 (67%) | 29 (74%) | 30 (67%) | 22 (61%) | 31 (65%) | 10 (40%) | 16 (42%) | 12 (67%) | 9 (47%) |
| Intensive | 2 (20%) | 6 (29%) | 6 (15%) | 7 (16%) | 7 (19%) | 12 (25%) | 12 (48%) | 14 (37%) | 3 (17%) | 4 (21%) |
| Intermediate | 1 (10%) | 1 (5%) | 4 (10%) | 8 (18%) | 7 (19%) | 5 (10%) | 3 (12%) | 8 (21%) | 3 (17%) | 6 (32%) |
| High flow nasal cannula | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 3 | 0 | 0 | 0 | 0 | 0 |
| No | 9 (90%) | 22 (96%) | 37 (92%) | 48 (91%) | 36 (84%) | 55 (92%) | 33 (79%) | 34 (77%) | 29 (94%) | 19 (86%) |
| Yes | 1 (10%) | 1 (4%) | 3 (8%) | 5 (9%) | 7 (16%) | 5 (8%) | 9 (21%) | 10 (23%) | 2 (6%) | 3 (14%) |
| Non-invasive ventilation | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 3 | 0 | 0 | 0 | 0 | 0 |
| Mean (SD) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) |
| Range | 0 - 1 | 0 - 1 | 0 - 1 | 0 - 0 | 0 - 1 | 0 - 0 | 0 - 1 | 0 - 0 | 0 - 0 | 0 - 0 |
| Endotracheal intubation | ||||||||||
| N-Miss | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
| No | 8 (80%) | 16 (70%) | 35 (88%) | 47 (89%) | 41 (91%) | 55 (92%) | 34 (81%) | 32 (73%) | 28 (90%) | 18 (82%) |
| Yes | 2 (20%) | 7 (30%) | 5 (12%) | 6 (11%) | 4 (9%) | 5 (8%) | 8 (19%) | 12 (27%) | 3 (10%) | 4 (18%) |
| Disposition of ETT | ||||||||||
| N-Miss | 8 | 16 | 36 | 49 | 42 | 57 | 34 | 32 | 28 | 18 |
| Discharged with ETT | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (8%) | 1 (33%) | 0 (0%) |
| Extubated < 24 hours before death/hospice | 0 (0%) | 0 (0%) | 0 (0%) | 1 (20%) | 0 (0%) | 0 (0%) | 2 (25%) | 0 (0%) | 1 (33%) | 1 (25%) |
| Other | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (8%) | 0 (0%) | 0 (0%) |
| Present at death | 0 (0%) | 4 (57%) | 2 (50%) | 0 (0%) | 1 (25%) | 1 (33%) | 3 (38%) | 3 (25%) | 0 (0%) | 1 (25%) |
| Removed for tracheostomy | 0 (0%) | 0 (0%) | 0 (0%) | 2 (40%) | 1 (25%) | 0 (0%) | 0 (0%) | 1 (8%) | 0 (0%) | 0 (0%) |
| To spontaneous breathing | 2 (100%) | 3 (43%) | 2 (50%) | 2 (40%) | 2 (50%) | 2 (67%) | 3 (38%) | 6 (50%) | 1 (33%) | 2 (50%) |
| Renal replacement therapy | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 0 | 0 |
| Continuous | 0 (0%) | 2 (9%) | 2 (5%) | 1 (2%) | 0 (0%) | 0 (0%) | 2 (5%) | 1 (2%) | 0 (0%) | 1 (5%) |
| Intermittent | 0 (0%) | 1 (4%) | 0 (0%) | 2 (4%) | 1 (2%) | 4 (7%) | 1 (2%) | 4 (9%) | 0 (0%) | 1 (5%) |
| No | 10 (100%) | 20 (87%) | 38 (95%) | 49 (94%) | 44 (98%) | 56 (93%) | 39 (93%) | 39 (89%) | 31 (100%) | 20 (91%) |
| Cardiac Arrest | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 1 | 0 | 2 | 1 | 1 | 0 |
| No | 10 (100%) | 20 (87%) | 38 (95%) | 52 (100%) | 41 (91%) | 58 (97%) | 36 (90%) | 41 (95%) | 29 (97%) | 22 (100%) |
| Yes | 0 (0%) | 3 (13%) | 2 (5%) | 0 (0%) | 4 (9%) | 2 (3%) | 4 (10%) | 2 (5%) | 1 (3%) | 0 (0%) |
| Hospital-Acquired Infection | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 1 | 0 | 2 | 1 | 1 | 0 |
| No | 10 (100%) | 22 (96%) | 37 (92%) | 42 (81%) | 42 (93%) | 52 (87%) | 37 (92%) | 36 (84%) | 27 (90%) | 21 (95%) |
| Yes | 0 (0%) | 1 (4%) | 3 (8%) | 7 (13%) | 2 (4%) | 2 (3%) | 1 (2%) | 6 (14%) | 3 (10%) | 1 (5%) |
| Unknown | 0 (0%) | 0 (0%) | 0 (0%) | 3 (6%) | 1 (2%) | 6 (10%) | 2 (5%) | 1 (2%) | 0 (0%) | 0 (0%) |
| Discharge disposition | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 1 | 0 | 2 | 0 | 0 | 1 |
| AMA | 1 (10%) | 0 (0%) | 0 (0%) | 1 (2%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2%) | 1 (3%) | 0 (0%) |
| Died | 0 (0%) | 4 (17%) | 2 (5%) | 4 (8%) | 5 (11%) | 1 (2%) | 6 (15%) | 5 (11%) | 2 (6%) | 2 (10%) |
| Home | 9 (90%) | 18 (78%) | 27 (68%) | 38 (73%) | 26 (58%) | 36 (60%) | 21 (52%) | 21 (48%) | 24 (77%) | 15 (71%) |
| Hospice | 0 (0%) | 0 (0%) | 1 (2%) | 1 (2%) | 3 (7%) | 7 (12%) | 4 (10%) | 4 (9%) | 1 (3%) | 1 (5%) |
| Long-term Acute Care (LTAC) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2%) | 1 (2%) | 0 (0%) | 0 (0%) | 1 (2%) | 0 (0%) | 0 (0%) |
| Nursing Home/Rehabilitation Facility | 0 (0%) | 1 (4%) | 8 (20%) | 7 (13%) | 9 (20%) | 16 (27%) | 9 (22%) | 10 (23%) | 3 (10%) | 3 (14%) |
| Transfer to the hospital | 0 (0%) | 0 (0%) | 2 (5%) | 0 (0%) | 1 (2%) | 0 (0%) | 0 (0%) | 2 (5%) | 0 (0%) | 0 (0%) |
| New or increased oxygen requirement at discharge/death | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 1 | 0 | 2 | 0 | 1 | 1 |
| No | 9 (90%) | 19 (83%) | 37 (92%) | 44 (85%) | 37 (82%) | 51 (85%) | 30 (75%) | 33 (75%) | 26 (87%) | 16 (76%) |
| Yes | 1 (10%) | 4 (17%) | 3 (8%) | 8 (15%) | 8 (18%) | 8 (13%) | 10 (25%) | 9 (20%) | 4 (13%) | 5 (24%) |
| Unknown | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (2%) | 0 (0%) | 2 (5%) | 0 (0%) | 0 (0%) |
| New HD requirement at discharge/death | ||||||||||
| N-Miss | 0 | 0 | 0 | 2 | 1 | 0 | 2 | 0 | 1 | 1 |
| No | 10 (100%) | 22 (96%) | 38 (95%) | 51 (98%) | 44 (98%) | 59 (98%) | 39 (98%) | 43 (98%) | 30 (100%) | 21 (100%) |
| Yes | 0 (0%) | 1 (4%) | 1 (2%) | 1 (2%) | 1 (2%) | 1 (2%) | 1 (2%) | 1 (2%) | 0 (0%) | 0 (0%) |
| Unknown | 0 (0%) | 0 (0%) | 1 (2%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |