uhs.Rmd

---
title: "UHS Testing Results"
date: "`r format(Sys.time(), '%d %B %Y')`"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE,
                      fig.height = 3, fig.width = 7)
```

```{r}
library(tidyverse)
#library(googledrive)
library(googlesheets4)
library(RcppRoll)
```

```{r eval=FALSE}
# do this once to authorize within google drive
drive_auth("byandell@wisc.edu")
gs4_auth(token = drive_token())
```

```{r eval=FALSE}
# do this once to authorize within google sheets
gs4_auth(email = "byandell@wisc.edu",
         scopes = "https://www.googleapis.com/auth/spreadsheets.readonly")
```

```{r}
roll7 <- function(x) {
  x <- roll_mean(x, 7)
  c(rep(x[1], 6), x)
}
uhs <- scan("data/uhs.txt", "char")
uhs <- read_sheet(uhs,
                  sheet = "COVID-data")
uhs <- uhs %>%
  select(Date_of_results:Facstaff_positives) %>%
  rename(
    Date = "Date_of_results",
    student_total = "Student_total_tests",
    student_positive = "Student_positives",
    facstaff_total = "Facstaff_total_tests",
    facstaff_positive = "Facstaff_positives") %>%
  filter(!is.na(student_total)) %>%
  mutate(Date = as.POSIXct(Date)) %>%
  pivot_longer(student_total:facstaff_positive, names_to = "group", values_to = "value") %>%
  mutate(count_type = str_remove(group, ".*_"),
         group = str_remove(group, "_.*")) %>%
  pivot_wider(names_from = "count_type", values_from = "value") %>%
  group_by(group) %>%
  mutate(cum_pos = cumsum(positive),
         cum_total = cumsum(total),
         roll_pos = roll7(positive),
         roll_total = roll7(total),
         cum_pct = 100 * cum_pos / cum_total,
         roll_pct = 100 * roll_pos / roll_total) %>%
  ungroup()
```

```{r}
ggplot(uhs) +
  aes(Date, positive, col = group) + 
  geom_point() +
  geom_path(linetype = "dashed") +
  geom_path(aes(y=roll_pos), size = 2) +
  ylab("Number Positive")
```

```{r}
ggplot(uhs) +
  aes(Date, roll_pct, col = group) + 
  geom_path(size = 2) +
  ylab("Percent Positive (7-day rolling mean)")
```

```{r}
ggplot(uhs) +
  aes(Date, cum_pos, col = group) + 
  geom_path(size = 2) +
  ylab("Cumulative Number Positive")
```