Merge branch 'main' of https://github.com/ABbiodiversity/MammalModels …

…into main
ABbiodiversity · Dec 20, 2023 · cb6675c · cb6675c
2 parents 7a88c68 + 4b3db64
commit cb6675c
Show file tree

Hide file tree

Showing 46 changed files with 9,610 additions and 329 deletions.
diff --git a/Mammals.Rproj b/Mammals.Rproj
@@ -14,3 +14,6 @@ LaTeX: pdfLaTeX
 
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
+
+BuildType: Website
+WebsitePath: C:/Users/mabec/Documents/R/MammalModels/bookdown
diff --git a/bookdown/01_Data-Collection.Rmd b/bookdown/01_Data-Collection.Rmd
@@ -10,11 +10,13 @@ As of `r Sys.Date()`, the ABMI has deployed X number of cameras across the provi
 
 The ABMI's remote camera deployment protocols can be accessed here: [Terrestrial ABMI Autonomous Recording Unit (ARU) and Remote Camera Trap Protocols](https://abmi.ca/home/publications/551-600/599).
 
-## List of camera projects
+## List of ABMI camera projects
 
 The following camera projects have been deployed by the ABMI:
 
-```{r, echo = FALSE, eval = TRUE}
+Note - would be nice to have a link to the WildTrax project for those projects that are published.
+
+```{r, echo = FALSE, eval = TRUE, message = FALSE, warning = FALSE}
 
 library(wildRtrax)
 library(keyring)
@@ -29,8 +31,10 @@ wt_auth()
 abmi_projects <- wt_get_download_summary(sensor_id = "CAM") |>
   filter(organization == "ABMI",
          !str_detect(project, "ACME|Pilot|Elk Island|Hare Coat|Sahtu|Ticks|Compression|wildRtrax|first|Lemming|Zoo")) |>
-  select(Project = project, Cameras = tasks, Status = status) |>
-  arrange(desc(Cameras))
+  mutate(Project = str_remove(project, "^ABMI ")) |>
+  select(Project, `No. Cameras` = tasks, Status = status)
+  # Would it be better to arrange by year?
+  # arrange(desc(Cameras))
 
 kable(abmi_projects)
 
@@ -39,17 +43,107 @@ kable(abmi_projects)
 
 ### Image Tagging
 
-Image tagging is done on the [WildTrax](https://wildtrax.ca/about/) platform. Raw data is also publicly from the ABMI via this platform.
+Image tagging is done on the [WildTrax](https://wildtrax.ca/about/) platform. Raw data is also publicly available from the ABMI via this platform.
+
+The image tagging protocols used by the ABMI can be accessed here: 
 
-The tagging protocols can be accessed here: 
+There is a companion R package, [*wildRtrax*](https://abbiodiversity.github.io/wildRtrax/), which is also publicly available and contains many useful functions for downloading and analyzing camera data hosted on the platform. Throughout this document, references will be made to functions within this package.
 
-There is a companion R package, *wildRtrax*, which is also publicly available and contains many useful functions for downloading and analyzing camera data on the platform. Throughout this document, references will be made to functions within this package.  
+Note: Would be nice to insert the wildRtrax package logo. 
 
 ## Species detections (2014-2021)
 
-Mammal species detections at ABMI sites sampled with cameras between 2014 and 2021.
+The map below displays mammal species detections at ABMI Ecosystem Health (core grid) sites sampled with cameras between 2014 and 2023. Each site is sampled with 4 individual cameras placed 600-m apart in a square shape.
+
+(Note: Need to add EH 2023)
+
+```{r, echo = FALSE, eval = TRUE, message = FALSE, warning = FALSE}
+
+library(sf)
+library(crosstalk) # Special branch of GH crosstalk repo required (filter-select-default)
+library(leaflet)
+library(leaflet.extras)
+ 
+g_drive <- "G:/Shared drives/ABMI Camera Mammals/"
+
+# Alberta provincial polygon
+sf_ab <- st_read(paste0(g_drive, "data/spatial/ab_prov.shp"),
+                 quiet = TRUE, stringsAsFactors = FALSE)
+
+# Site locations
+sites <- read_csv(paste0(g_drive, "data/lookup/climate/site-climate-summary_v2020.csv")) |>
+  select(site = SITE_ID,
+         latitude = PUBLIC_LATTITUDE,
+         longitude = PUBLIC_LONGITUDE)
+
+# Occurrence data
+occ <- read_csv(paste0(g_drive, "Results/Occurrence/ABMI/occurrence_eh_site_2023-01-23.csv")) |>
+  filter(!str_detect(site, "^W")) |>
+  mutate(site = as.numeric(site))
+
+# Species to display
+sp <- occ |>
+  group_by(common_name) |>
+  summarise(n = sum(present)) |>
+  filter(n >= 35,
+         !str_detect(common_name, "Ermine|Squirrel"),
+         !common_name == "Deer") |>
+  select(common_name) |>
+  pull()
+
+occ_subset <- occ |>
+  filter(common_name %in% sp) |>
+  mutate(year = str_sub(project, start = -4, end = -1)) |>
+  full_join(sites, by = "site") |>
+  mutate(present = ifelse(is.na(present), "Not Surveyed", present)) |>
+  mutate(present = factor(present, levels = c("Not Surveyed",
+                                                 "TRUE",
+                                                 "FALSE"))) |>
+  select(site, latitude, longitude, year, common_name, present) |>
+  arrange(site, year)
+
+# Create SharedData object for crosstalk interactivity
+shared_ss <- SharedData$new(occ_subset)
+
+# Palette
+pal <- colorFactor(palette = c("grey80",
+                               "gold",
+                               "darkred"),
+                   domain = occ_subset$present)
+
+# Create leaflet map
+map <- sf_ab |>
+  st_transform("+init=epsg:4326") %>%
+  leaflet() %>%
+  addTiles() %>%
+  addProviderTiles("CartoDB.Positron") %>%
+  addFullscreenControl() %>%
+  addResetMapButton() %>%
+  addScaleBar(position = "bottomright", 
+              options = scaleBarOptions(imperial = FALSE)) |>
+  
+  addPolylines(color = "#0a0909", weight = 2.5, smoothFactor = 0.2, opacity = 3, fill = FALSE) |>
+  
+  addCircleMarkers(data = shared_ss,
+                   color = ~pal(present), stroke = FALSE, fillOpacity = 1,
+                   radius = 6) |>
+  
+  addLegend(data = shared_ss, pal = pal, values = ~present,
+            position = "topright", opacity = 1, title = "Occurrence at Site:")
+
+```
+
+```{r, out.width="100%", fig.height=10, eval = TRUE, echo = FALSE, warning = FALSE, message = FALSE}
+
+# Create interactive filters
+bscols(widths = c(4, 3),
+       filter_select("common_name", "Species", shared_ss, ~common_name, multiple = FALSE, selected = "Moose"),
+       filter_select("year", "Sampling Year", shared_ss, ~year, multiple = TRUE))
 
-Shiny app.  
+# Display map
+map
+
+```
 
 ## Deployment duration lengths
 

diff --git a/bookdown/_book/404.html b/bookdown/_book/404.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Marcus Becker, Dr. David J. Huggard, Dr. David Roberts" />
 
 
-<meta name="date" content="2023-12-05" />
+<meta name="date" content="2023-12-19" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -58,8 +58,94 @@
 <link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
 <link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
 <script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
+<link href="libs/selectize-0.12.4/css/selectize.bootstrap3.css" rel="stylesheet" />
+<script src="libs/selectize-0.12.4/js/selectize.min.js"></script>
+<link href="libs/crosstalk-1.1.1.9000/css/crosstalk.min.css" rel="stylesheet" />
+<script src="libs/crosstalk-1.1.1.9000/js/crosstalk.min.js"></script>
+<meta name="viewport" content="width=device-width, initial-scale=1" />
+<link href="libs/bootstrap-grid-3.4.1/bootstrap-grid.min.css" rel="stylesheet" />
+<script src="libs/htmlwidgets-1.6.1/htmlwidgets.js"></script>
+<link href="libs/leaflet-1.3.1/leaflet.css" rel="stylesheet" />
+<script src="libs/leaflet-1.3.1/leaflet.js"></script>
+<link href="libs/leafletfix-1.0.0/leafletfix.css" rel="stylesheet" />
+<script src="libs/proj4-2.6.2/proj4.min.js"></script>
+<script src="libs/Proj4Leaflet-1.0.1/proj4leaflet.js"></script>
+<link href="libs/rstudio_leaflet-1.3.1/rstudio_leaflet.css" rel="stylesheet" />
+<script src="libs/leaflet-binding-2.1.1/leaflet.js"></script>
+<script src="libs/leaflet-providers-1.9.0/leaflet-providers_1.9.0.js"></script>
+<script src="libs/leaflet-providers-plugin-2.1.1/leaflet-providers-plugin.js"></script>
+<link href="libs/lfx-fullscreen-1.0.2/lfx-fullscreen-prod.css" rel="stylesheet" />
+<script src="libs/lfx-fullscreen-1.0.2/lfx-fullscreen-prod.js"></script>
+<link href="libs/leaflet-easybutton-1.3.1/easy-button.css" rel="stylesheet" />
+<script src="libs/leaflet-easybutton-1.3.1/easy-button.js"></script>
+<script src="libs/leaflet-easybutton-1.3.1/EasyButton-binding.js"></script>
+<link href="libs/ionicons-2.0.1/ionicons.min.css" rel="stylesheet" />
 
 
+<style type="text/css">
+pre > code.sourceCode { white-space: pre; position: relative; }
+pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span:empty { height: 1.2em; }
+.sourceCode { overflow: visible; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+pre.sourceCode { margin: 0; }
+@media screen {
+div.sourceCode { overflow: auto; }
+}
+@media print {
+pre > code.sourceCode { white-space: pre-wrap; }
+pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+}
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
+    position: relative; left: -1em; text-align: right; vertical-align: baseline;
+    border: none; display: inline-block;
+    -webkit-touch-callout: none; -webkit-user-select: none;
+    -khtml-user-select: none; -moz-user-select: none;
+    -ms-user-select: none; user-select: none;
+    padding: 0 4px; width: 4em;
+    color: #aaaaaa;
+  }
+pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
+div.sourceCode
+  {   }
+@media screen {
+pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
+}
+code span.al { color: #ff0000; font-weight: bold; } /* Alert */
+code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
+code span.at { color: #7d9029; } /* Attribute */
+code span.bn { color: #40a070; } /* BaseN */
+code span.bu { color: #008000; } /* BuiltIn */
+code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
+code span.ch { color: #4070a0; } /* Char */
+code span.cn { color: #880000; } /* Constant */
+code span.co { color: #60a0b0; font-style: italic; } /* Comment */
+code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
+code span.do { color: #ba2121; font-style: italic; } /* Documentation */
+code span.dt { color: #902000; } /* DataType */
+code span.dv { color: #40a070; } /* DecVal */
+code span.er { color: #ff0000; font-weight: bold; } /* Error */
+code span.ex { } /* Extension */
+code span.fl { color: #40a070; } /* Float */
+code span.fu { color: #06287e; } /* Function */
+code span.im { color: #008000; font-weight: bold; } /* Import */
+code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
+code span.kw { color: #007020; font-weight: bold; } /* Keyword */
+code span.op { color: #666666; } /* Operator */
+code span.ot { color: #007020; } /* Other */
+code span.pp { color: #bc7a00; } /* Preprocessor */
+code span.sc { color: #4070a0; } /* SpecialChar */
+code span.ss { color: #bb6688; } /* SpecialString */
+code span.st { color: #4070a0; } /* String */
+code span.va { color: #19177c; } /* Variable */
+code span.vs { color: #4070a0; } /* VerbatimString */
+code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
+</style>
 
 <style type="text/css">
 
@@ -114,7 +200,7 @@
 <ul>
 <li class="chapter" data-level="2.1" data-path="data-collection.html"><a href="data-collection.html#abmi-use-of-remote-cameras"><i class="fa fa-check"></i><b>2.1</b> ABMI use of remote cameras</a></li>
 <li class="chapter" data-level="2.2" data-path="data-collection.html"><a href="data-collection.html#camera-deployment-protocols"><i class="fa fa-check"></i><b>2.2</b> Camera deployment protocols</a></li>
-<li class="chapter" data-level="2.3" data-path="data-collection.html"><a href="data-collection.html#list-of-camera-projects"><i class="fa fa-check"></i><b>2.3</b> List of camera projects</a>
+<li class="chapter" data-level="2.3" data-path="data-collection.html"><a href="data-collection.html#list-of-abmi-camera-projects"><i class="fa fa-check"></i><b>2.3</b> List of ABMI camera projects</a>
 <ul>
 <li class="chapter" data-level="2.3.1" data-path="data-collection.html"><a href="data-collection.html#image-tagging"><i class="fa fa-check"></i><b>2.3.1</b> Image Tagging</a></li>
 </ul></li>