wastewaterMMSD.Rmd

---
title: "Wastewater MMSD"
author: "`r paste('Brian Yandell,', format(Sys.time(), '%d %B %Y'))`"
output:
  word_document: default
  html_document: default
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE,
                      fig.width = 7, fig.height = 4)
```

This is just the MMSD Interceptor sites from the 12/08/2020 data sheet, with the last measurement being 12/1/2020. This document summarizes quarantine information. The R code file can be found in the [pandemic github repository](https://github.com/UW-Madison-DataScience/pandemic/blob/master/wastewaterMMSD.Rmd).

```{r}
library(tidyverse)
library(readxl)
library(broom)
library(RcppRoll)
kprint <- function(...) {
  if(interactive()) {
    print(...)
  } else {
    knitr::kable(...)
  }
}
```

```{r}
filename <- "data/wastewater/UW and MMSD Report for SARS-Cov-2 Influent Samples 010821vF.xlsx"
#"data/wastewater/UW and MMSD Report for SARS-Cov-2 Influent Samples 12.08.20vFinal.xlsx"
```

```{r warning = FALSE, message = FALSE}
missing_codes <- c("","NA","0","Undetected","Not Detected",
                   "Field Parameters to be filled in", 
                   "Inhibited-to be re-ran", "#DIV/0!")
water_MMSD <- read_excel(filename,
                    na = missing_codes, skip = 12,
                    col_types = c(rep("text", 4), rep("numeric", 4)),
                    sheet = 4) %>%
  select(-c(3,6,8)) %>%
  rename(Date = "Collection Date",
         Site = "Sample Description",
         Qual = "Yes/No",
         AVG = "Gene Copies / 1L...5",
         PMMoV = "Gene Copies / 1L...7") %>%
  mutate(Date = str_replace_all(Date, "\\.", "/")) %>%
  filter(str_detect(Date, "\\/2020")) %>%
  mutate(Date = as.Date(Date, format = "%m/%d/%Y"),
         Site = str_remove(str_remove(Site, "MMSD Interceptor "), ". Sample.*"),
         Site = ifelse(Site == "P11.", "P11", Site)) %>%
  pivot_longer(AVG:PMMoV, names_to = "assay", values_to = "value")
```

```{r}
ggplot(water_MMSD) +
  aes(Date,value, col = Site) +
  facet_wrap(~ assay, scales = "free_y") +
  geom_point() +
  scale_y_log10() +
  geom_smooth(method = "loess", se = FALSE, formula = "y ~ x") +
  ggtitle("MMSD Sites with Smooth Curves")
```

```{r}
ggplot(water_MMSD) +
  aes(Date,value, col = Site) +
  facet_wrap(~ assay, scales = "free_y") +
  geom_point() +
  scale_y_log10() +
  geom_smooth(aes(x = Date, y = value), method = "lm", se = FALSE, size = 1,
              col = "black",
              data = water_MMSD %>%
                filter(Date >= max(Date) - 10)) +
  ggtitle("MMSD Sites with Trend for Last 10 Days")
```

![Sewer Main Map](data/wastewater/SewerMainMap.pdf)