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README update

pull/4/head
hrbrmstr 6 years ago
parent
commit
ab9bc60d19
4 changed files with 106 additions and 6 deletions
  1. +53
    -2
      README.Rmd
  2. +53
    -4
      README.md
  3. BIN
      README_files/figure-markdown_github/unnamed-chunk-6-1.png
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      README_files/figure-markdown_github/unnamed-chunk-8-1.png

+ 53
- 2
README.Rmd View File

@ -45,6 +45,7 @@ suppressPackageStartupMessages(library(cdcfluview))
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(statebins))
suppressPackageStartupMessages(library(magrittr))
# current verison
packageVersion("cdcfluview")
@ -65,6 +66,56 @@ gg <- gg + theme_bw()
gg
```
```{r warning=FALSE, error=FALSE, message=FALSE}
dat <- get_flu_data(region="hhs",
sub_region=1:10,
data_source="ilinet",
years=2000:2014)
dat %<>%
mutate(REGION=factor(REGION,
levels=unique(REGION),
labels=c("Boston", "New York",
"Philadelphia", "Atlanta",
"Chicago", "Dallas",
"Kansas City", "Denver",
"San Francisco", "Seattle"),
ordered=TRUE)) %>%
mutate(season_week=ifelse(WEEK>=40, WEEK-40, WEEK),
season=ifelse(WEEK<40,
sprintf("%d-%d", YEAR-1, YEAR),
sprintf("%d-%d", YEAR, YEAR+1)))
prev_years <- dat %>% filter(season != "2014-2015")
curr_year <- dat %>% filter(season == "2014-2015")
curr_week <- tail(dat, 1)$season_week
gg <- ggplot()
gg <- gg + geom_point(data=prev_years,
aes(x=season_week, y=X..WEIGHTED.ILI, group=season),
color="#969696", size=1, alpa=0.25)
gg <- gg + geom_point(data=curr_year,
aes(x=season_week, y=X..WEIGHTED.ILI, group=season),
color="red", size=1.25, alpha=1)
gg <- gg + geom_line(data=curr_year,
aes(x=season_week, y=X..WEIGHTED.ILI, group=season),
size=1.25, color="#d7301f")
gg <- gg + geom_vline(xintercept=curr_week, color="#d7301f", size=0.5, linetype="dashed", alpha=0.5)
gg <- gg + facet_wrap(~REGION, ncol=3)
gg <- gg + labs(x=NULL, y="Weighted ILI Index",
title="ILINet - 1999-2015 year weighted flu index history by CDC region\nWeek Ending Jan 3, 2015 (Red == current season)\n")
gg <- gg + theme_bw()
gg <- gg + theme(panel.grid=element_blank())
gg <- gg + theme(strip.background=element_blank())
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}
gg_s <- state_flu %>%
filter(WEEKEND=="Jan-03-2015") %>%
@ -84,8 +135,8 @@ gg_s
### Test Results
```{r}
library(cdcfluview)
library(testthat)
suppressPackageStartupMessages(library(cdcfluview))
suppressPackageStartupMessages(library(testthat))
date()


+ 53
- 4
README.md View File

@ -30,6 +30,7 @@ suppressPackageStartupMessages(library(cdcfluview))
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(statebins))
suppressPackageStartupMessages(library(magrittr))
# current verison
packageVersion("cdcfluview")
@ -86,6 +87,54 @@ gg <- gg + theme_bw()
![](README_files/figure-markdown_github/unnamed-chunk-4-1.png)
``` r
dat <- get_flu_data(region="hhs",
sub_region=1:10,
data_source="ilinet",
years=2000:2014)
dat %<>%
mutate(REGION=factor(REGION,
levels=unique(REGION),
labels=c("Boston", "New York",
"Philadelphia", "Atlanta",
"Chicago", "Dallas",
"Kansas City", "Denver",
"San Francisco", "Seattle"),
ordered=TRUE)) %>%
mutate(season_week=ifelse(WEEK>=40, WEEK-40, WEEK),
season=ifelse(WEEK<40,
sprintf("%d-%d", YEAR-1, YEAR),
sprintf("%d-%d", YEAR, YEAR+1)))
prev_years <- dat %>% filter(season != "2014-2015")
curr_year <- dat %>% filter(season == "2014-2015")
curr_week <- tail(dat, 1)$season_week
gg <- ggplot()
gg <- gg + geom_point(data=prev_years,
aes(x=season_week, y=X..WEIGHTED.ILI, group=season),
color="#969696", size=1, alpa=0.25)
gg <- gg + geom_point(data=curr_year,
aes(x=season_week, y=X..WEIGHTED.ILI, group=season),
color="red", size=1.25, alpha=1)
gg <- gg + geom_line(data=curr_year,
aes(x=season_week, y=X..WEIGHTED.ILI, group=season),
size=1.25, color="#d7301f")
gg <- gg + geom_vline(xintercept=curr_week, color="#d7301f", size=0.5, linetype="dashed", alpha=0.5)
gg <- gg + facet_wrap(~REGION, ncol=3)
gg <- gg + labs(x=NULL, y="Weighted ILI Index",
title="ILINet - 1999-2015 year weighted flu index history by CDC region\nWeek Ending Jan 3, 2015 (Red == current season)\n")
gg <- gg + theme_bw()
gg <- gg + theme(panel.grid=element_blank())
gg <- gg + theme(strip.background=element_blank())
gg <- gg + theme(axis.ticks.x=element_blank())
gg <- gg + theme(axis.text.x=element_blank())
```
![](README_files/figure-markdown_github/unnamed-chunk-6-1.png)
``` r
gg_s <- state_flu %>%
filter(WEEKEND=="Jan-03-2015") %>%
select(state=STATENAME, value=ACTIVITY.LEVEL) %>%
@ -97,18 +146,18 @@ gg_s <- state_flu %>%
ggtitle("CDC State FluView (2015-01-03)")
```
![](README_files/figure-markdown_github/unnamed-chunk-6-1.png)
![](README_files/figure-markdown_github/unnamed-chunk-8-1.png)
### Test Results
``` r
library(cdcfluview)
library(testthat)
suppressPackageStartupMessages(library(cdcfluview))
suppressPackageStartupMessages(library(testthat))
date()
```
## [1] "Mon Jan 12 14:25:21 2015"
## [1] "Mon Jan 12 14:39:51 2015"
``` r
test_dir("tests/")


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