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about.Rmd
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about.Rmd
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---
title: 'About the CUBE Project'
output:
html_document:
theme:
version: 4
css: styles.css
---
<head>
<!-- Google tag (gtag.js) -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-8F9R0B5L51"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-8F9R0B5L51');
</script>
</head>
```{r setup, include=F}
set.seed(124)
knitr::opts_chunk$set(
message = FALSE,
warning = FALSE,
echo = FALSE,
comment = "#>",
collapse = TRUE
)
```
```{r}
library(dplyr)
library(leaflet)
googlesheets4::gs4_deauth()
data_url <- 'https://docs.google.com/spreadsheets/d/1zSHLGGOSBIOgN3BXXGl2jPtJLBF6OExAznjqmRnzrTY/edit?usp=sharing'
# read site geo data and set marker colors based on type of site
sites <-
googlesheets4::read_sheet(
data_url, sheet = 'locations'
) |>
dplyr::mutate(
color = dplyr::case_when(
type == 'LTC' ~ 'darkblue',
type == 'LTC (Active)' ~ 'blue',
type == 'University' ~ 'purple',
type == 'Daycare' ~ 'green',
type == 'School' ~ 'orange',
type == 'Library' ~ 'cadetblue',
type == 'Hospital' ~ 'darkred',
type == 'Hospital (Active)' ~ 'red',
TRUE ~ 'gray'
))
# Possible values are "red", "darkred", "lightred", "orange", "beige", "green", "darkgreen", "lightgreen", "blue", "darkblue", "lightblue", "purple", "darkpurple", "pink", "cadetblue", "white", "gray", "lightgray", "black"
# values to output in map description text
n_site <- sites |> nrow()
n_ltc <- sites |>
dplyr::filter(type == "LTC") |>
nrow()
n_dc <- sites |>
dplyr::filter(type %in% c('School','Daycare')) |>
nrow()
n_uni <- sites |>
dplyr::filter(type == 'University') |>
nrow()
n_lib <- sites |>
dplyr::filter(type == 'Library') |>
nrow()
# define Marker style: white cube logo on coloured background
icons <- leaflet::awesomeIcons(
icon = 'cube',
library = 'ion',
iconColor = 'white',
spin = F,
markerColor = sites$color
)
city_coords <- tribble(
~city, ~lat, ~lng,
'Ottawa', 44.9, -75.7,
'Toronto', 43.2, -79.3,
'Sault Ste. Marie', 46.0, -84.3
)
# set zoom level for locking map
zmlvl <- 5
ontario_map <-
leaflet::leaflet(
width = '90%',
height = 325,
padding = '2rem',
options = leafletOptions(zoomControl = TRUE)
) |>
# set the zoom to ~province level
setView(lng = -80, lat = 45, zoom = zmlvl) |>
# add the grey-shaded map tiles from cartoDB
addProviderTiles(
provider = providers$CartoDB.PositronNoLabels,
# disable the zoom controls
options = providerTileOptions(
zoomControl = TRUE,
maxZoom = zmlvl + 1,
minZoom = zmlvl - 2)
) |>
leaflet::addLabelOnlyMarkers(
data = city_coords,
lat = ~lat,
lng = ~lng,
label = ~city,
labelOptions = leaflet::labelOptions(
textsize = '2px',
noHide = T,
direction = "bottom",
style = list(
"color" = "#0a0a0a",
"size" = "10px",
"font-family" = "sans-serif",
"font-style" = "bold",
"box-shadow" = "1px 1px rgba(0,0,0,0.25)",
"font-size" = "12px",
"border-color" = "none",
"background-color" = "none"
)
)
) |>
# add the custom cube markers we defined above
addAwesomeMarkers(
data = sites,
lng = ~ lon,
lat = ~ lat,
icon = icons,
label = ~type,
popup = NULL,
clusterOptions = markerClusterOptions(
freezeAtZoom = zmlvl,
zoomToBoundsOnClick = F
)
)
# ignore Oauth
googlesheets4::gs4_deauth()
data_url <- 'https://docs.google.com/spreadsheets/d/1zSHLGGOSBIOgN3BXXGl2jPtJLBF6OExAznjqmRnzrTY/edit?usp=sharing'
faq_section <- googlesheets4::read_sheet(data_url, sheet = 'FAQ') |>
bs4cards::cards(
title = question,
text = answer,
breakpoint = 5,
border_width = 1,
border_radius = 3,
border_colour = '#bbbbbb',
# label_colour = '#51616f',
)
```
::: {##about-page}
-------------------------------------------------------
## Overview
{#infographic .img-responsive .img-fluid .rounded width="1050"}
- The Coronavirus in the Urban Built Environment (CUBE) project seeks to develop environmental sampling as a spatially-resolved method for monitoring COVID-19 in congregate settings such as long-term care homes (LTC), universities, public schools, and day-cares.\
- We collect samples by swabbing floors; then, the swabs are tested for COVID-19 using an [RT-qPCR](https://en.wikipedia.org/wiki/Reverse_transcription_polymerase_chain_reaction) assay developed by [DNA Genotek](https://www.dnagenotek.com/) and/or a novel CRISPR-based device.\
- Currently, we are focused on facilities located in Toronto, Ottawa, and Sault Ste. Marie.
--------------------------------------------------------
## Long-Term Care Homes Study
[DOI: 10.1056/EVIDoa2200203](https://evidence.nejm.org/doi/full/10.1056/EVIDoa2200203)
<center style="padding: 1rem;">
{#infographic .img-responsive .img-fluid .rounded width="400"}
</center>
--------------------------------------------------------
## Study Locations
Our research team has conducted environmental surface surveillance studies at `r n_site` buildings to date across Toronto, Ottawa, and Sault Ste. Marie, including `r n_ltc` long-term care homes, `r n_dc` schools and day-cares, `r n_uni` university buildings, and `r n_lib` public libraries.
::: {style="margin: auto; display: flex; align-content: center; align-items: center; align: center; text-align: center;"}
```{r show map, message=F, warning=F, echo=F, fig.height=3, fig.width=3, fig.align='center'}
# display the map
ontario_map
```
:::
------------------------------------------------------------------------
<!-- FAQs card -->
## Frequently Asked Questions
```{r faqs, results='asis'}
faq_section
```
<br>
:::