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New files from NEU DC
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Fatemeh Kazemi committed Jul 25, 2022
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3 changes: 2 additions & 1 deletion .gitignore
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Expand Up @@ -40,4 +40,5 @@ vignettes/*.pdf

# Data
data/
output/
output/
notes/
139 changes: 106 additions & 33 deletions code/data-analysis/output-cleaning.Rmd
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
---
title: "Analysis Output files"
title: "Ozone Paper Analysis output files"
author: "Fatemeh Kazemi"
date: "6-11-2022"
---

https://cran.r-project.org/web/packages/forestplot/vignettes/forestplot.html
Expand All @@ -14,9 +16,6 @@ library(tidyverse)
library(here)
```

```{r Load data}
```

```{r Outcome to Cause }
Outcome.to.Cause <- tribble(
~Cause, ~Outcome,
Expand Down Expand Up @@ -55,7 +54,7 @@ cuz <- c("All-Cause", "Non-Accidental", "Accidental", "Cardiovascular",
```{r Output Base}
out.base.t = data.frame()
for (i in 1:4){
load(here('output','analysis', 'New folder', paste('out-base-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-base-',i,'.RDa', sep= "")))
out.base.t <- rbind(out.base.t, out.base) %>% drop_na()
}
Expand All @@ -76,7 +75,7 @@ rm(out.base.t)
```{r Output State}
out.state.t = data.frame()
for (i in 1:4){
load(here('output','analysis', 'New folder', paste('out-state-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-state-',i,'.RDa', sep= "")))
out.state.t <- rbind(out.state.t, out.state) %>% drop_na()
}
Expand All @@ -97,7 +96,7 @@ rm(out.state.t)
```{r Output SES}
out.ses.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder', paste('out-ses-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-ses-',i,'.RDa', sep= "")))
out.ses.t <- rbind(out.ses.t, out.ses) %>% drop_na()
}
Expand All @@ -118,7 +117,7 @@ rm(out.ses.t)
```{r Output PM}
out.pm25.t = data.frame()
for (i in 1:4){
load(here('output','analysis', 'New folder', paste('out-pm-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-pm-',i,'.RDa', sep= "")))
out.pm25.t <- rbind(out.pm25.t, out.pm) %>% drop_na()
}
Expand All @@ -139,7 +138,7 @@ rm(out.pm25.t, out.pm)
```{r Output NO2}
out.no2.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder', paste('out-no2-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-no2-',i,'.RDa', sep= "")))
out.no2.t <- rbind(out.no2.t, out.no2) %>% drop_na()
}
Expand Down Expand Up @@ -174,13 +173,13 @@ save(out.main, file = here('output','analysis','out-main.RDa'))
```{r Output Age}
out.le.t = data.frame()
for (i in 1:4){
load(here('output','analysis', 'New folder', paste('out-le-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-le-',i,'.RDa', sep= "")))
out.le.t <- rbind(out.le.t, age.le) %>% drop_na()
}
out.mt.t = data.frame()
for (i in 1:4){
load(here('output','analysis', 'New folder', paste('out-mt-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-mt-',i,'.RDa', sep= "")))
out.mt.t <- rbind(out.mt.t, age.mt) %>% drop_na()
}
Expand Down Expand Up @@ -209,13 +208,13 @@ rm(out.le.t, out.mt.t, out.age.t, age.le, age.mt)
```{r Output Sex}
out.f.t = data.frame()
for (i in 1:4){
load(here('output','analysis', 'New folder', paste('out-sexF-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-sexF-',i,'.RDa', sep= "")))
out.f.t <- rbind(out.f.t, sex.F) %>% drop_na()
}
out.m.t = data.frame()
for (i in 1:4){
load(here('output','analysis', 'New folder', paste('out-sexM-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-sexM-',i,'.RDa', sep= "")))
out.m.t <- rbind(out.m.t, sex.M) %>% drop_na()
}
Expand All @@ -241,24 +240,98 @@ save(out.sex, file = here('output','analysis','out-sex.RDa'))
rm(out.f.t, out.m.t, out.sex.t, sex.F, sex.M)
```

```{r Output Race}
out.A.t = data.frame()
for (i in 1:4){
load(here('output','analysis','out',paste('out-raceA-',i,'.RDa', sep= "")))
out.A.t <- rbind(out.A.t, race.A) %>% drop_na()
}
out.B.t = data.frame()
for (i in 1:4){
load(here('output','analysis','out',paste('out-raceB-',i,'.RDa', sep= "")))
out.B.t <- rbind(out.B.t, race.B) %>% drop_na()
}
out.H.t = data.frame()
for (i in 1:4){
load(here('output','analysis','out',paste('out-raceH-',i,'.RDa', sep= "")))
out.H.t <- rbind(out.H.t, race.H) %>% drop_na()
}
out.W.t = data.frame()
for (i in 1:4){
load(here('output','analysis','out',paste('out-raceW-',i,'.RDa', sep= "")))
out.W.t <- rbind(out.W.t, race.W) %>% drop_na()
}
out.race.t <- out.A.t %>%
add_row(out.B.t) %>%
add_row(out.H.t) %>%
add_row(out.W.t)
out.race <- out.race.t %>%
merge(Outcome.to.Cause) %>%
mutate(Coef = as.numeric(as.character(O3_B)),
std = as.numeric(as.character(O3_SE)),
HR = round(exp(Coef * 10/1000),3),
HR.L = round(exp((Coef-1.96*std) * 10/1000),3),
HR.U = round(exp((Coef+1.96*std) * 10/1000),3),
Subgroup = "Race",
Value = race_Cat,
Value = factor(Value,
levels = c("White", "Hispanic", "Black", "Asian")),
Cause = factor(Cause, levels = cuz)) %>%
select(Cause, Subgroup, Value, HR, HR.L, HR.U, pValue)
save(out.race, file = here('output','analysis','out-race.RDa'))
rm(out.A.t, out.B.t, out.H.t, out.W.t, out.race.t,
race.A, race.B, race.H, race.W)
```

```{r}
out.asr <- out.age %>%
add_row(out.sex) %>%
add_row(out.race) %>%
mutate(tag = case_when(Value %in% c('White') ~ 'a',
Value %in% c('Male', '>75', 'Hispanic') ~ 'b',
Value %in% c('Female', '65-75', 'Black') ~ 'c',
T ~ 'd'))
out.miss <- out.race %>%
mutate(Subgroup = case_when(Value %in% c('Asian', 'Black') ~ 'Age',
T ~ 'Sex'),
tag = case_when(Value %in% c('Asian', 'Hispanic') ~ 'a',
T ~ 'd'))
out.miss[, 3:7] <- NA
out.asr <- out.asr %>%
add_row(out.miss) %>%
arrange(Cause, Subgroup, Value, tag) %>%
mutate(Subgroup = factor(Subgroup, levels = c("Age", "Sex", "Race")))
save(out.asr, file = here('output','analysis','out-asr.RDa'))
```

```{r Output Urbanicity}
out.urban.t = data.frame()
for (i in 1:4){
load(here('output','analysis', 'New folder', paste('out-urban-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-urban-',i,'.RDa', sep= "")))
out.urban.t <- rbind(out.urban.t, loc.urban) %>%
filter(!is.na(Outcome))
}
out.suburban.t = data.frame()
for (i in 1:4){
load(here('output','analysis', 'New folder', paste('out-suburban-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-suburban-',i,'.RDa', sep= "")))
out.suburban.t <- rbind(out.suburban.t, loc.suburban) %>%
filter(!is.na(Outcome))
}
out.rural.t = data.frame()
for (i in 1:4){
load(here('output','analysis', 'New folder', paste('out-rural-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-rural-',i,'.RDa', sep= "")))
out.rural.t <- rbind(out.rural.t, loc.rural) %>%
filter(!is.na(Outcome))
}
Expand Down Expand Up @@ -289,21 +362,21 @@ rm(out.urban.t, out.suburban.t, out.rural.t, out.urbanicity.t,
```{r Output SES Urban}
out.sesL.t = data.frame()
for (i in 1:4){
load(here('output','analysis', 'New folder', paste('out-sesL-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-sesL-',i,'.RDa', sep= "")))
out.sesL.t <- rbind(out.sesL.t, ses.Low) %>%
filter(!is.na(Outcome))
}
out.sesM.t = data.frame()
for (i in 1:4){
load(here('output','analysis', 'New folder', paste('out-sesM-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-sesM-',i,'.RDa', sep= "")))
out.sesM.t <- rbind(out.sesM.t, ses.Mid) %>%
filter(!is.na(Outcome))
}
out.sesH.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder',paste('out-sesH-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-sesH-',i,'.RDa', sep= "")))
out.sesH.t <- rbind(out.sesH.t, ses.High) %>%
filter(!is.na(Outcome))
}
Expand Down Expand Up @@ -335,7 +408,7 @@ rm(out.sesL.t, out.sesM.t, out.sesH.t, out.sesUrban.t,
```{r Output Region}
out.W.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder',paste('out-west-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-west-',i,'.RDa', sep= "")))
out.W.t <- rbind(out.W.t, region.W) %>%
filter(!is.na(Outcome))
}
Expand All @@ -349,14 +422,14 @@ for (i in 1:4){
out.S.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder',paste('out-south-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-south-',i,'.RDa', sep= "")))
out.S.t <- rbind(out.S.t, region.S) %>%
filter(!is.na(Outcome))
}
out.NE.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder', paste('out-northeast-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-northeast-',i,'.RDa', sep= "")))
out.NE.t <- rbind(out.NE.t, region.NE) %>%
filter(!is.na(Outcome))
}
Expand Down Expand Up @@ -387,23 +460,23 @@ rm(out.W.t, out.MW.t, out.S.t, out.NE.t, out.region.t,
```{r Output Bufferzone}
out.bz6.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder',paste('out-pm-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-pm-',i,'.RDa', sep= "")))
out.bz6.t <- rbind(out.bz6.t, out.pm) %>% drop_na()
}
out.bz6.t <- out.bz6.t %>%
mutate(Value = "6-mile")
out.bz12.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder',paste('out-pm-bz12-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-pm-bz12-',i,'.RDa', sep= "")))
out.bz12.t <- rbind(out.bz12.t, out.pm.bz12) %>% drop_na()
}
out.bz12.t <- out.bz12.t %>%
mutate(Value = "12-mile")
out.bz24.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder',paste('out-pm-bz24-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-pm-bz24-',i,'.RDa', sep= "")))
out.bz24.t <- rbind(out.bz24.t, out.pm.bz24) %>% drop_na()
}
out.bz24.t <- out.bz24.t %>%
Expand Down Expand Up @@ -434,23 +507,23 @@ rm(out.bz6.t, out.bz12.t, out.bz24.t, out.buffer.t,
```{r Output Exposure Measure}
out.ses.maxh.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder',paste('out-ses-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-ses-',i,'.RDa', sep= "")))
out.ses.maxh.t <- rbind(out.ses.maxh.t, out.ses) %>% drop_na()
}
out.ses.maxh.t <- out.ses.maxh.t %>%
mutate(Value = "1-hr Max")
out.ses.8hmax.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder',paste('out-ses-8hmax-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-ses-8hmax-',i,'.RDa', sep= "")))
out.ses.8hmax.t <- rbind(out.ses.8hmax.t, out.ses.8h) %>% drop_na()
}
out.ses.8hmax.t <- out.ses.8hmax.t %>%
mutate(Value = "8-hr Max")
out.ses.avgh.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder',paste('out-ses-avgh-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-ses-avgh-',i,'.RDa', sep= "")))
out.ses.avgh.t <- rbind(out.ses.avgh.t, out.ses.h) %>% drop_na()
}
out.ses.avgh.t <- out.ses.avgh.t %>%
Expand Down Expand Up @@ -480,23 +553,23 @@ rm(out.ses.maxh.t, out.ses.8hmax.t, out.ses.avgh.t, out.ses.exp.t,
```{r Output Exposure Measure}
out.pm.maxh.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder',paste('out-pm-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-pm-',i,'.RDa', sep= "")))
out.pm.maxh.t <- rbind(out.pm.maxh.t, out.pm) %>% drop_na()
}
out.pm.maxh.t <- out.pm.maxh.t %>%
mutate(Value = "1-hr Max")
out.pm.8hmax.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder',paste('out-pm-8hmax-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-pm-8hmax-',i,'.RDa', sep= "")))
out.pm.8hmax.t <- rbind(out.pm.8hmax.t, out.pm.8h) %>% drop_na()
}
out.pm.8hmax.t <- out.pm.8hmax.t %>%
mutate(Value = "8-hr Max")
out.pm.avgh.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder',paste('out-pm-avgh-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-pm-avgh-',i,'.RDa', sep= "")))
out.pm.avgh.t <- rbind(out.pm.avgh.t, out.pm.h) %>% drop_na()
}
out.pm.avgh.t <- out.pm.avgh.t %>%
Expand Down Expand Up @@ -537,7 +610,7 @@ save(out.exposure, file = here('output','analysis','out-exposure.RDa'))
```{r Output BRFSS}
out.brfss0.t = data.frame()
for (i in 1:4){
load(here('output','analysis','New folder',paste('out-pm-brfss0-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-pm-brfss0-',i,'.RDa', sep= "")))
out.brfss0.t <- rbind(out.brfss0.t, out.pm.brfss0) %>% drop_na()
}
Expand All @@ -546,7 +619,7 @@ out.brfss0.t <- out.brfss0.t %>%
out.brfss.t = data.frame()
for (i in 1:7){
load(here('output','analysis','New folder',paste('out-pm-brfss-',i,'.RDa', sep= "")))
load(here('output','analysis','out',paste('out-pm-brfss-',i,'.RDa', sep= "")))
out.brfss.t <- rbind(out.brfss.t, out.pm.brfss) %>% drop_na()
}
Expand Down
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