Data Description

The following data are from the CDC WONDER Multiple Cause of Death Database. This is a searchable public-use database of aggregated data for all deaths in the United States. Each death record is extracted from the a death certificate and given a primary uncderlying cause of death (UCOD) and up to 19 additional multiple causes of death (MCOD). These are originally assigned by the physician on the death certificate but are recategorized following a multisystems algorithms by the National Center for Health Statistics.

Data were extracted for 1999-2014 for deaths with MCOD diagnoses for septicemia and influenza & pneumonia codes.

Below we will adhere to the following definitions:

Septicemia = MCOD codes for A40-A41

Influenza and Pneumonia = MCOD codes for J09-J18

Sepsis = MCOD codes for either of the above codes

Citation for Data: Centers for Disease Control and Prevention, National Center for Health Statistics. Multiple Cause of Death 1999-2014 on CDC WONDER Online Database, released 2015. Data are from the Multiple Cause of Death Files, 1999-2014, as compiled from data provided by the 57 vital statistics jurisdictions through the Vital Statistics Cooperative Program. Accessed at http://wonder.cdc.gov/mcd-icd10.html on May 10, 2016 10:17:01 AM

R packages deployed

library(dplyr)
library(ggplot2)
library(knitr)

Data Processing

Results

Septicemia

kable(septicemia, type="markdown")

age.group	Race	MCOD	deaths	population	crude.rate	L95	U95	SE
15-24 years	American Indian or Alaska Native	Septicemia (A40-A41)	185	10787577	1.7	1.5	2.0	0.1
15-24 years	Asian or Pacific Islander	Septicemia (A40-A41)	427	36154211	1.2	1.1	1.3	0.1
15-24 years	Black or African American	Septicemia (A40-A41)	3020	107822451	2.8	2.7	2.9	0.1
15-24 years	White	Septicemia (A40-A41)	8156	522206951	1.6	1.5	1.6	0.0
25-34 years	American Indian or Alaska Native	Septicemia (A40-A41)	517	9053351	5.7	5.2	6.2	0.3
25-34 years	Asian or Pacific Islander	Septicemia (A40-A41)	849	43006670	2.0	1.8	2.1	0.1
25-34 years	Black or African American	Septicemia (A40-A41)	7242	91289236	7.9	7.8	8.1	0.1
25-34 years	White	Septicemia (A40-A41)	17173	504875354	3.4	3.4	3.5	0.0
35-44 years	American Indian or Alaska Native	Septicemia (A40-A41)	1303	8480501	15.4	14.5	16.2	0.4
35-44 years	Asian or Pacific Islander	Septicemia (A40-A41)	1731	39700779	4.4	4.2	4.6	0.1
35-44 years	Black or African American	Septicemia (A40-A41)	18454	91137461	20.2	20.0	20.5	0.1
35-44 years	White	Septicemia (A40-A41)	46627	544960014	8.6	8.5	8.6	0.0
45-54 years	American Indian or Alaska Native	Septicemia (A40-A41)	2669	7356880	36.3	34.9	37.7	0.7
45-54 years	Asian or Pacific Islander	Septicemia (A40-A41)	3880	32492694	11.9	11.6	12.3	0.2
45-54 years	Black or African American	Septicemia (A40-A41)	44571	83283474	53.5	53.0	54.0	0.3
45-54 years	White	Septicemia (A40-A41)	129274	553220646	23.4	23.2	23.5	0.1
55-64 years	American Indian or Alaska Native	Septicemia (A40-A41)	3459	4611773	75.0	72.5	77.5	1.3
55-64 years	Asian or Pacific Islander	Septicemia (A40-A41)	7382	22253840	33.2	32.4	33.9	0.4
55-64 years	Black or African American	Septicemia (A40-A41)	69558	55389764	125.6	124.6	126.5	0.5
55-64 years	White	Septicemia (A40-A41)	246795	432707999	57.0	56.8	57.3	0.1
65-74 years	American Indian or Alaska Native	Septicemia (A40-A41)	3693	2281495	161.9	156.6	167.1	2.7
65-74 years	Asian or Pacific Islander	Septicemia (A40-A41)	11699	12631311	92.6	90.9	94.3	0.9
65-74 years	Black or African American	Septicemia (A40-A41)	84655	31286246	270.6	268.8	272.4	0.9
65-74 years	White	Septicemia (A40-A41)	385175	283869849	135.7	135.3	136.1	0.2
75-84 years	American Indian or Alaska Native	Septicemia (A40-A41)	3410	998396	341.5	330.1	353.0	5.8
75-84 years	Asian or Pacific Islander	Septicemia (A40-A41)	16437	6346595	259.0	255.0	262.9	2.0
75-84 years	Black or African American	Septicemia (A40-A41)	95561	16533737	578.0	574.3	581.6	1.9
75-84 years	White	Septicemia (A40-A41)	601555	183946653	327.0	326.2	327.9	0.4
85+ years	American Indian or Alaska Native	Septicemia (A40-A41)	1952	301745	646.9	618.2	675.6	14.6
85+ years	Asian or Pacific Islander	Septicemia (A40-A41)	13600	1982010	686.2	674.6	697.7	5.9
85+ years	Black or African American	Septicemia (A40-A41)	72733	5796853	1254.7	1245.6	1263.8	4.7
85+ years	White	Septicemia (A40-A41)	546878	72489228	754.4	752.4	756.4	1.0

g0<-
ggplot(septicemia, aes(age.group, crude.rate, group=Race, color=Race))+
    scale_y_continuous(breaks=seq(0, 1500, 100))+
    geom_line(size=.5) +
    geom_point()+
    geom_ribbon(aes(ymin=L95, ymax=U95), alpha=0.2)+
    theme_classic()+
    ggtitle("Septicemia Mortality (A40-A41) by Age and Race, USA 1999-2014")+
    labs(x="Age Group", y = "Crude Mortality per 100,000")

print(g0)

g01<- 
ggplot(septicemia2, aes(age.group, RR, group=Race, color=Race))+
    geom_line(size=.5) +
    geom_point()+
    geom_line(aes(y=1), color='black', linetype="dashed")+
    theme_classic()+
    ggtitle("Septicemia Mortality (A40-A41) by Age and Race, USA 1999-2014")+
    labs(x="Age Group", y = "Risk Ratio to each Age Group's Average")
print(g01)

Influenza & Pneumonia

g1<-
ggplot(pneumonia, aes(age.group, crude.rate, group=Race, color=Race))+
    scale_y_continuous(breaks=seq(0, 1600, 100))+
    geom_line(size=.5) +
    geom_point()+
    geom_ribbon(aes(ymin=L95, ymax=U95), alpha=0.2)+
    theme_classic()+
    ggtitle("Influenza & Pneumonia Mortality (J09-J18) by Age and Race, USA 1999-2014")+
    labs(x="Age Group", y = "Crude Mortality per 100,000")
print(g1)

g2 <-
ggplot(pneumonia2, aes(age.group, RR, group=Race, color=Race))+
    geom_line(size=.5) +
    geom_point()+
    geom_line(aes(y=1), color='black', linetype="dashed")+
    theme_classic()+
    ggtitle("Influenza & Pneumonia Mortality (J09-J18) by Age and Race, USA 1999-2014")+
    labs(x="Age Group", y = "Risk Ratio to each Age Group's Average")
print(g2)

Sepsis

kable(s2, type="markdown")

age.group	Race	deaths	population	crude.rate	L95	U95	SE	RR1	RR2
15-24 years	American Indian or Alaska Native	334	10787577	3.1	2.8	3.4	0.2	1.00	1.63
15-24 years	Asian or Pacific Islander	677	36154211	1.9	1.7	2.0	0.1	0.61	1.00
15-24 years	Black or African American	4749	107822451	4.4	4.3	4.5	0.1	1.42	2.32
15-24 years	White	15674	522206951	3.0	3.0	3.0	0.0	0.97	1.58
25-34 years	American Indian or Alaska Native	800	9053351	8.8	8.2	9.4	0.3	1.19	3.03
25-34 years	Asian or Pacific Islander	1257	43006670	2.9	2.8	3.1	0.1	0.39	1.00
25-34 years	Black or African American	10954	91289236	12.0	11.8	12.2	0.1	1.62	4.14
25-34 years	White	29761	504875354	5.9	5.8	6.0	0.0	0.80	2.03
35-44 years	American Indian or Alaska Native	1969	8480501	23.2	22.2	24.2	0.5	1.27	3.68
35-44 years	Asian or Pacific Islander	2505	39700779	6.3	6.1	6.6	0.1	0.35	1.00
35-44 years	Black or African American	27020	91137461	29.6	29.3	30.0	0.2	1.62	4.70
35-44 years	White	75420	544960014	13.8	13.7	13.9	0.1	0.76	2.19
45-54 years	American Indian or Alaska Native	3795	7356880	51.6	49.9	53.2	0.8	1.14	2.93
45-54 years	Asian or Pacific Islander	5723	32492694	17.6	17.2	18.1	0.2	0.39	1.00
45-54 years	Black or African American	62706	83283474	75.3	74.7	75.9	0.3	1.67	4.28
45-54 years	White	201500	553220646	36.4	36.3	36.6	0.1	0.80	2.07
55-64 years	American Indian or Alaska Native	5150	4611773	111.7	108.6	114.7	1.6	1.05	2.24
55-64 years	Asian or Pacific Islander	11102	22253840	49.9	49.0	50.8	0.5	0.47	1.00
55-64 years	Black or African American	96046	55389764	173.4	172.3	174.5	0.6	1.63	3.47
55-64 years	White	388578	432707999	89.8	89.5	90.1	0.1	0.85	1.80
65-74 years	American Indian or Alaska Native	6081	2281495	266.5	259.8	273.2	3.4	1.02	1.74
65-74 years	Asian or Pacific Islander	19355	12631311	153.2	151.1	155.4	1.1	0.58	1.00
65-74 years	Black or African American	122361	31286246	391.1	388.9	393.3	1.1	1.49	2.55
65-74 years	White	676174	283869849	238.2	237.6	238.8	0.3	0.91	1.55
75-84 years	American Indian or Alaska Native	6725	998396	673.6	657.5	689.7	8.2	0.96	1.28
75-84 years	Asian or Pacific Islander	33370	6346595	525.8	520.2	531.4	2.9	0.75	1.00
75-84 years	Black or African American	150522	16533737	910.4	905.8	915.0	2.3	1.30	1.73
75-84 years	White	1286803	183946653	699.6	698.3	700.8	0.6	1.00	1.33
85+ years	American Indian or Alaska Native	5214	301745	1727.9	1681.0	1774.9	23.9	0.87	1.00
85+ years	Asian or Pacific Islander	36424	1982010	1837.7	1818.9	1856.6	9.6	0.93	1.06
85+ years	Black or African American	130921	5796853	2258.5	2246.3	2270.7	6.2	1.14	1.31
85+ years	White	1538209	72489228	2122.0	2118.6	2125.3	1.7	1.07	1.23

We will plot crude rate by age-group and race.

g3 <-
ggplot(s2, aes(age.group, crude.rate, group=Race, color=Race))+
    scale_y_continuous(breaks=seq(0, 2500, 200))+
    geom_line(size=.5) +
    geom_point()+
    geom_ribbon(aes(ymin=L95, ymax=U95), alpha=0.2)+
    theme_classic()+
    ggtitle("Sepsis Mortality by Age and Race, USA 1999-2014")+
    labs(x="Age Group", y = "Crude Mortality per 100,000")
print(g3)

Now we will plot the risk ratio of each race within each age-group. Here we will make the referent within each age-group the average crude rate of the the age-group.

g4 <- 
ggplot(s2, aes(age.group, RR1, group=Race, color=Race))+
    geom_line(size=.5) +
    geom_point()+
    geom_line(aes(y=1), color='black', linetype="dashed")+
    theme_classic()+
    ggtitle("Sepsis by Age and Race, USA 1999-2014")+
    labs(x="Age Group", y = "Risk Ratio to each Age Group's Average")
print(g4)

Now we will plot the risk ratio of each race within each age-group. Here we will make the referent within each age-group the minimum crude rate of the the age-group. This is the Asian/Pacific Islander group for every age-group except the >/= 85 years-old age-group.

g5<-
ggplot(s2, aes(age.group, RR2, group=Race, color=Race))+
    geom_line(size=.5) +
    geom_point()+
    theme_classic()+
    theme(legend.justification = c(1,1), legend.position=c(1,1), 
        legend.title = element_blank(), text = element_text(size = 18))+
    ggtitle("Sepsis Mortality Risk by Age and Race, USA 1999-2014")+
    labs(x="Age Group", y ="Risk Ratio")
print(g5)

Sepsis Mortality in US

Jordan A. Kempker, MD, MSc

2016-05-12