diff --git a/README.Rmd b/README.Rmd index e79cfb0..60b8f03 100644 --- a/README.Rmd +++ b/README.Rmd @@ -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$group] + +gg <- gg + geom_text(data=top, aes(as.Date(x, origin="1970-01-01"), y, label=top_state), + hjust=1, family="Arial Narrow", size=3, nudge_x=-5, nudge_y=-0.001) +gg <- gg + scale_x_date(expand=c(0,0)) +gg <- gg + scale_y_continuous(label=scales::percent) +gg <- gg + labs(x=NULL, y=NULL, + title="Percent of In-State Deaths Due to Pneumonia and Pnfluenza (2010-Present)") +gg <- gg + theme_bw(base_family="Arial Narrow") +gg <- gg + theme(axis.text.x=element_text(margin=margin(0,0,0,0))) +gg <- gg + theme(axis.text.y=element_text(margin=margin(0,0,0,0))) +gg <- gg + theme(axis.ticks=element_blank()) +gg <- gg + theme(plot.title=element_text(face="bold", size=16)) gg ``` @@ -129,11 +162,7 @@ gg <- gg + theme(axis.ticks.x=element_blank()) gg <- gg + theme(axis.text.x=element_blank()) ``` -```{r echo=FALSE, fig.height=10, fig.width=6, warning=FALSE, error=FALSE, message=FALSE} -gg -``` - -```{r message=FALSE} +```{r message=FALSE, fig.height=5, fig.width=7} gg_s <- state_flu %>% filter(WEEKEND=="Jan-03-2015") %>% select(state=STATENAME, value=ACTIVITY.LEVEL) %>% @@ -143,9 +172,6 @@ gg_s <- state_flu %>% labels=c("Minimal", "Low", "Moderate", "High"), legend_position="bottom", legend_title="ILI Activity Level") + ggtitle("CDC State FluView (2015-01-03)") -``` - -```{r echo=FALSE, fig.height=5, fig.width=7} gg_s ``` diff --git a/README.md b/README.md index 3827596..e143e28 100644 --- a/README.md +++ b/README.md @@ -88,11 +88,48 @@ gg <- ggplot(flu, aes(x=WEEK, y=`% WEIGHTED ILI`, group=REGION)) gg <- gg + geom_line() gg <- gg + facet_wrap(~REGION, ncol=2) gg <- gg + theme_bw() +gg ``` - + - +``` r +msd <- get_mortality_surveillance_data() + +mutate(msd$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 +``` + + ``` 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 ``` - + ### 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 ======================================================================================================== diff --git a/README_files/README-unnamed-chunk-4-1.png b/README_files/README-unnamed-chunk-4-1.png new file mode 100644 index 0000000..8978423 Binary files /dev/null and b/README_files/README-unnamed-chunk-4-1.png differ diff --git a/README_files/README-unnamed-chunk-5-1.png b/README_files/README-unnamed-chunk-5-1.png index 0e692dd..e1ca890 100644 Binary files a/README_files/README-unnamed-chunk-5-1.png and b/README_files/README-unnamed-chunk-5-1.png differ diff --git a/README_files/README-unnamed-chunk-7-1.png b/README_files/README-unnamed-chunk-7-1.png index 0e692dd..f13718d 100644 Binary files a/README_files/README-unnamed-chunk-7-1.png and b/README_files/README-unnamed-chunk-7-1.png differ