commit
4c2a41ae83
5 changed files with 212 additions and 0 deletions
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module git.wow.st/gmp/cget |
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go 1.14 |
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require ( |
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github.com/BurntSushi/toml v0.3.1 |
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github.com/domodwyer/mailyak v3.1.1+incompatible |
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github.com/mitchellh/go-homedir v1.1.0 |
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) |
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github.com/BurntSushi/toml v0.3.1 h1:WXkYYl6Yr3qBf1K79EBnL4mak0OimBfB0XUf9Vl28OQ= |
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github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU= |
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github.com/domodwyer/mailyak v1.2.0 h1:xCFvdXmHg3hwVey0OXQJrmKuDwcHfRZx7toiIaSi8hU= |
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github.com/domodwyer/mailyak v3.1.1+incompatible h1:oPtXn3+56LEFbdqH0bpuPRsqtijW9l2POpQe9sTUsSI= |
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github.com/domodwyer/mailyak v3.1.1+incompatible/go.mod h1:5NNYkn9hxcdNEOmmMx0yultN5VLorZQ+AWQo9iya+UY= |
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github.com/mitchellh/go-homedir v1.1.0 h1:lukF9ziXFxDFPkA1vsr5zpc1XuPDn/wFntq5mG+4E0Y= |
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github.com/mitchellh/go-homedir v1.1.0/go.mod h1:SfyaCUpYCn1Vlf4IUYiD9fPX4A5wJrkLzIz1N1q0pr0= |
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package main |
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import ( |
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"bufio" |
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"bytes" |
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"fmt" |
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"io" |
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"io/ioutil" |
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"log" |
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"net/http" |
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"net/smtp" |
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"os" |
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"os/exec" |
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"path" |
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"time" |
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"github.com/BurntSushi/toml" |
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homedir "github.com/mitchellh/go-homedir" |
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"github.com/domodwyer/mailyak" |
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) |
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type Config struct { |
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MailHost, Username, Password string |
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MailPort int |
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Len int64 |
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} |
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var conf Config |
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var confFile string |
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func getConf() Config { |
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confDir := path.Dir(confFile) |
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if _, err := os.Stat(confDir); os.IsNotExist(err) { |
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log.Printf("Creating config directory") |
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err = os.MkdirAll(confDir, 0777) |
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if err != nil { |
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log.Fatal("Cannot create config directory: ", err) |
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} |
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} |
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if _, err := os.Stat(confFile); os.IsNotExist(err) { |
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log.Printf("Creating config file") |
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f, err := os.Create(confFile) |
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if err != nil { |
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log.Fatal("Cannot create config file: ", err) |
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} |
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err = f.Close() |
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if err != nil { |
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log.Fatal("Error closing config file: ", err) |
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} |
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} |
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if _, err := toml.DecodeFile(confFile, &conf); err != nil { |
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log.Fatal("Error reading config file: ", err) |
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} |
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of, err := os.Create(path.Join(confDir, "c.R")) |
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if err != nil { |
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log.Fatal("Error creating R source file: ", err) |
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} |
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_, err = of.WriteString(rCode()) |
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if err != nil { |
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log.Fatal("Error writing R source code: ", err) |
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} |
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return conf |
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} |
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func save() { |
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of, err := os.Create(confFile) |
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if err != nil { |
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log.Fatal("Cannot open config file: ", err) |
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} |
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var buf bytes.Buffer |
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w := bufio.NewWriter(&buf) |
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enc := toml.NewEncoder(w) |
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enc.Encode(conf) |
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io.Copy(of, &buf) |
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err = of.Close() |
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if err != nil { |
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log.Fatal("Error closing config file: ", err) |
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} |
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} |
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func fetch() { |
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url := "https://health.data.ny.gov/api/views/xdss-u53e/rows.csv?accessType=DOWNLOAD" |
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resp, err := http.Get(url) |
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if err != nil { |
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log.Printf("HTTP error: ", err) |
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return |
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} |
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body, err := ioutil.ReadAll(resp.Body) |
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if err != nil { |
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log.Printf("Read error: ", err) |
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return |
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} |
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if int64(len(body)) == conf.Len { |
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log.Printf("Equal length, returning") |
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return |
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} |
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log.Printf("Length differs: body = %d", len(body)) |
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conf.Len = int64(len(body)) |
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save() |
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of, err := os.Create(path.Join(path.Dir(confFile), "rows.csv")) |
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if err != nil { |
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log.Fatal("Cannot create rows.csv: ", err) |
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} |
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_, err = of.Write(body) |
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if err != nil { |
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log.Fatal("Error writing rows.csv: ", err) |
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} |
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confDir := path.Dir(confFile) |
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cmd := exec.Command("R", "--no-save", "-f", path.Join(confDir, "c.R")) |
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log.Printf("Running R") |
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err = cmd.Run() |
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if err != nil { |
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log.Fatal("Error running R: ", err) |
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} |
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log.Printf("R completed") |
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if conf.MailHost == "" { |
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log.Print("No mail host set, returning") |
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return |
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} |
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f, err := os.Open("Rplots.pdf") |
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if err != nil { |
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log.Fatal("Error opening Rplots.pdf: ", err) |
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} |
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defer f.Close() |
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email := mailyak.New(fmt.Sprintf("%s:%d", conf.MailHost, conf.MailPort), |
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smtp.PlainAuth("", conf.Username, conf.Password, conf.MailHost)) |
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email.To("gmp@wow.st") |
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email.From("covid@wow.st") |
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msg := "Covid dashboard update for " + time.Now().Format("Monday, January 2 2006") |
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email.Subject(msg) |
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email.Plain().Set(msg) |
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email.Attach("dashboard.pdf", f) |
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err = email.Send() |
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if err != nil { |
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log.Print("Error sending email: ", err) |
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} |
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} |
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func main() { |
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log.Printf("starting") |
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homeDir, err := homedir.Dir() |
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if err != nil { |
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log.Fatal("Cannot locate user's home directory") |
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} |
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confFile = path.Join(homeDir, ".config", "cget", "cget.conf") |
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os.Chdir(path.Dir(confFile)) |
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getConf() |
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for { |
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fetch() |
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time.Sleep(time.Minute * 30) |
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} |
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log.Printf("done") |
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} |
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package main |
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import ( |
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"path" |
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) |
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func rCode() string { |
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return ` |
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library(tidyverse) |
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library(ggplot2) |
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library(gridExtra) |
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library(lubridate) |
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options(scipen=100000) |
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d <- read_csv('`+ path.Dir(confFile) + `/rows.csv') |
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d <- pivot_longer(d, c('New Positives', 'Total Number of Tests Performed')) |
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d <- transmute(d, date=mdy(d$'Test Date'), county=County, name=name, value=value) |
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queens <- subset(d, county=='Queens') |
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qrate <- pivot_wider(queens, names_from='name') %>% transmute(date=date,county=county,name='Positive Rate', value=ifelse(`+"`"+`New Positives`+"`"+`==0,0,`+"`"+`New Positives`+"`"+`/`+"`"+`Total Number of Tests Performed`+"`"+`)) |
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totals <- group_by(d, date, county='New York', name) %>% summarize(value=sum(value)) %>% ungroup |
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trate <- pivot_wider(totals, names_from='name') %>% transmute(date=date,county=county,name='Positive Rate', value=ifelse(`+"`"+`New Positives`+"`"+`==0,0,`+"`"+`New Positives`+"`"+`/`+"`"+`Total Number of Tests Performed`+"`"+`)) |
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d2 <- rbind(queens, totals) |
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p1 <- ggplot(queens, aes(x=date, y=value, color=name))+geom_line()+scale_y_log10(n.breaks=6)+labs(y='',color='')+ggtitle('Queens')+theme(plot.title=element_text(hjust = 0.5))+theme(legend.position='bottom') |
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#p2 <- ggplot(d, aes(x=date, y=value, color=name))+geom_line(data=queens)+stat_smooth(geom='line', linetype='dotted', data=queens, method='gam', se=FALSE)+geom_line(alpha=1/3, data=totals)+stat_smooth(geom='line', linetype='dotted', data=totals, method='gam', se=FALSE)+scale_y_log10(n.breaks=6)+labs(y='')+labs(color='')+ggtitle('New York')+theme(plot.title=element_text(hjust = 0.5))+theme(legend.position='bottom') |
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p2 <- ggplot(totals, aes(x=date, y=value, color=name))+geom_line()+stat_smooth(geom='line', linetype='dotted', method='gam', se=FALSE)+scale_y_log10(n.breaks=6)+labs(y='')+labs(color='')+ggtitle('New York')+theme(plot.title=element_text(hjust = 0.5))+theme(legend.position='bottom') |
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pr1 <- ggplot(qrate, aes(x=date, y=value)) + geom_line()+geom_smooth(method='gam',formula=y~s(x, bs="cs"),se=FALSE)+scale_y_continuous(labels = scales::percent,)+labs(y='Positive Rate')+coord_cartesian(ylim=c(0,0.04))+ggtitle('Queens')+theme(plot.title=element_text(hjust = 0.5)) |
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pr2 <- ggplot(trate, aes(x=date, y=value)) + geom_line()+geom_smooth(method='gam',formula=y~s(x, bs="cs"),se=FALSE)+scale_y_continuous(labels = scales::percent)+labs(y='Positive Rate')+coord_cartesian(ylim=c(0,0.04))+ggtitle('New York')+theme(plot.title=element_text(hjust = 0.5)) |
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p <- grid.arrange(p1,p2,pr1,pr2,ncol=2) |
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` |
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} |
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