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Added README example for mortality data. Sucks to be in Hawaii

tags/v0.5.2
boB Rudis 4 years ago
parent
commit
159835e688
5 changed files with 78 additions and 14 deletions
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      README.Rmd
  2. +42
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      README.md
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+ 36
- 10
README.Rmd View File

@ -58,7 +58,7 @@ options(width=120)
### Usage
```{r message=FALSE}
```{r message=FALSE, warning=FALSE, fig.height=10, fig.width=6}
library(cdcfluview)
library(ggplot2)
library(dplyr)
@ -77,9 +77,42 @@ gg <- ggplot(flu, aes(x=WEEK, y=`% WEIGHTED ILI`, group=REGION))
gg <- gg + geom_line()
gg <- gg + facet_wrap(~REGION, ncol=2)
gg <- gg + theme_bw()
gg
```
```{r echo=FALSE, fig.height=10, fig.width=6}
```{r message=FALSE, warning=FALSE, fig.height=6, fig.width=10}
msd <- get_mortality_surveillance_data()
mutate(msd$by_state, ym=as.Date(sprintf("%04d-%02d-1", Year, Week), "%Y-%U-%u")) %>%
select(state, wk=ym, death_pct=`Percent of Deaths Due to Pneumonia and Influenza`) %>%
mutate(death_pct=death_pct/100) -> df
gg <- ggplot() + geom_smooth(data=df, aes(wk, death_pct, group=state),
se=FALSE, color="#2b2b2b", size=0.25)
gb <- ggplot_build(gg)
gb$data[[1]] %>%
arrange(desc(x)) %>%
group_by(group) %>%
slice(1) %>%
ungroup() %>%
arrange(desc(y)) %>%
head(1) -> top
top_state <- sort(unique(msd$by_state$state))[top$group]
gg <- gg + geom_text(data=top, aes(as.Date(x, origin="1970-01-01"), y, label=top_state),
hjust=1, family="Arial Narrow", size=3, nudge_x=-5, nudge_y=-0.001)
gg <- gg + scale_x_date(expand=c(0,0))
gg <- gg + scale_y_continuous(label=scales::percent)
gg <- gg + labs(x=NULL, y=NULL,
title="Percent of In-State Deaths Due to Pneumonia and Pnfluenza (2010-Present)")
gg <- gg + theme_bw(base_family="Arial Narrow")
gg <- gg + theme(axis.text.x=element_text(margin=margin(0,0,0,0)))
gg <- gg + theme(axis.text.y=element_text(margin=margin(0,0,0,0)))
gg <- gg + theme(axis.ticks=element_blank())
gg <- gg + theme(plot.title=element_text(face="bold", size=16))
gg
```
@ -129,11 +162,7 @@ gg <- gg + theme(axis.ticks.x=element_blank())
gg <- gg + theme(axis.text.x=element_blank())
```
```{r echo=FALSE, fig.height=10, fig.width=6, warning=FALSE, error=FALSE, message=FALSE}
gg
```
```{r message=FALSE}
```{r message=FALSE, fig.height=5, fig.width=7}
gg_s <- state_flu %>%
filter(WEEKEND=="Jan-03-2015") %>%
select(state=STATENAME, value=ACTIVITY.LEVEL) %>%
@ -143,9 +172,6 @@ gg_s <- state_flu %>%
labels=c("Minimal", "Low", "Moderate", "High"),
legend_position="bottom", legend_title="ILI Activity Level") +
ggtitle("CDC State FluView (2015-01-03)")
```
```{r echo=FALSE, fig.height=5, fig.width=7}
gg_s
```


+ 42
- 4
README.md View File

@ -88,11 +88,48 @@ gg <- ggplot(flu, aes(x=WEEK, y=`% WEIGHTED ILI`, group=REGION))
gg <- gg + geom_line()
gg <- gg + facet_wrap(~REGION, ncol=2)
gg <- gg + theme_bw()
gg
```
<img src="README_files/README-unnamed-chunk-5-1.png" width="576" />
<img src="README_files/README-unnamed-chunk-4-1.png" width="576" />
<img src="README_files/README-unnamed-chunk-7-1.png" width="576" />
``` r
msd <- get_mortality_surveillance_data()
mutate(msd$by_state, ym=as.Date(sprintf("%04d-%02d-1", Year, Week), "%Y-%U-%u")) %>%
select(state, wk=ym, death_pct=`Percent of Deaths Due to Pneumonia and Influenza`) %>%
mutate(death_pct=death_pct/100) -> df
gg <- ggplot() + geom_smooth(data=df, aes(wk, death_pct, group=state),
se=FALSE, color="#2b2b2b", size=0.25)
gb <- ggplot_build(gg)
gb$data[[1]] %>%
arrange(desc(x)) %>%
group_by(group) %>%
slice(1) %>%
ungroup() %>%
arrange(desc(y)) %>%
head(1) -> top
top_state <- sort(unique(msd$by_state$state))[top$group]
gg <- gg + geom_text(data=top, aes(as.Date(x, origin="1970-01-01"), y, label=top_state),
hjust=1, family="Arial Narrow", size=3, nudge_x=-5, nudge_y=-0.001)
gg <- gg + scale_x_date(expand=c(0,0))
gg <- gg + scale_y_continuous(label=scales::percent)
gg <- gg + labs(x=NULL, y=NULL,
title="Percent of In-State Deaths Due to Pneumonia and Pnfluenza (2010-Present)")
gg <- gg + theme_bw(base_family="Arial Narrow")
gg <- gg + theme(axis.text.x=element_text(margin=margin(0,0,0,0)))
gg <- gg + theme(axis.text.y=element_text(margin=margin(0,0,0,0)))
gg <- gg + theme(axis.ticks=element_blank())
gg <- gg + theme(plot.title=element_text(face="bold", size=16))
gg
```
<img src="README_files/README-unnamed-chunk-5-1.png" width="960" />
``` r
gg_s <- state_flu %>%
@ -104,9 +141,10 @@ gg_s <- state_flu %>%
labels=c("Minimal", "Low", "Moderate", "High"),
legend_position="bottom", legend_title="ILI Activity Level") +
ggtitle("CDC State FluView (2015-01-03)")
gg_s
```
<img src="README_files/README-unnamed-chunk-9-1.png" width="672" />
<img src="README_files/README-unnamed-chunk-7-1.png" width="672" />
### Test Results
@ -115,7 +153,7 @@ library(cdcfluview)
library(testthat)
date()
#> [1] "Mon Sep 26 01:39:06 2016"
#> [1] "Mon Sep 26 11:16:43 2016"
test_dir("tests/")
#> testthat results ========================================================================================================


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