Skip to content

Commit

Permalink
occurrence maps
Browse files Browse the repository at this point in the history
  • Loading branch information
@mabecker89
mabecker89 committed Dec 21, 2023
1 parent cb6675c commit db58c7c
Show file tree
Hide file tree
Showing 17 changed files with 3,872 additions and 444 deletions.
13 changes: 8 additions & 5 deletions bookdown/01_Data-Collection.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,8 @@ The ABMI's remote camera deployment protocols can be accessed here: [Terrestrial

The following camera projects have been deployed by the ABMI:

Organize by year? Use gt package?

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}
Expand Down Expand Up @@ -108,7 +110,7 @@ shared_ss <- SharedData$new(occ_subset)
# Palette
pal <- colorFactor(palette = c("grey80",
"gold",
"darkred"),
"black"),
domain = occ_subset$present)
# Create leaflet map
Expand Down Expand Up @@ -136,18 +138,19 @@ map <- sf_ab |>
```{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))
bscols(widths = c(3, 3),
filter_checkbox("year", "Sampling Year:", shared_ss, ~year, columns = 2),
filter_select("common_name", "Species:", shared_ss, ~common_name, multiple = FALSE, selected = "Badger"))
# Display map
map
```


## Deployment duration lengths

Here we can include all those figures. Yay.
Here we can include all those figures. Yay. Do we really want that?



Expand Down
14 changes: 1 addition & 13 deletions bookdown/README.md
View file
Original file line number Diff line number Diff line change
@@ -1,13 +1 @@
Welcome!

This is a minimal example of a book based on R Markdown and **bookdown** (https://github.com/rstudio/bookdown).

This template provides a skeleton file structure that you can edit to create your book.

The contents inside the .Rmd files provide some pointers to help you get started, but feel free to also delete the content in each file and start fresh.

Additional resources:

The **bookdown** book: https://bookdown.org/yihui/bookdown/

The **bookdown** package reference site: https://pkgs.rstudio.com/bookdown
Using remote camera trap images to estimate densities and develop habitat models for mammals in Alberta, Canada
108 changes: 12 additions & 96 deletions bookdown/_book/404.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,31 +5,25 @@
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>Page not found | Using remote camera trap images to estimate densities and develop habitat models for mammals in Alberta, Canada</title>
<meta name="description" content="<p>This is a minimal example of using the bookdown package to write a book.
set in the _output.yml file.
The HTML output format for this example is bookdown::gitbook,</p>" />
<meta name="description" content="ABMI Camera Methods and Mammal Modeling" />
<meta name="generator" content="bookdown 0.37 and GitBook 2.6.7" />

<meta property="og:title" content="Page not found | Using remote camera trap images to estimate densities and develop habitat models for mammals in Alberta, Canada" />
<meta property="og:type" content="book" />

<meta property="og:description" content="<p>This is a minimal example of using the bookdown package to write a book.
set in the _output.yml file.
The HTML output format for this example is bookdown::gitbook,</p>" />
<meta name="github-repo" content="rstudio/bookdown-demo" />
<meta property="og:description" content="ABMI Camera Methods and Mammal Modeling" />
<meta name="github-repo" content="ABbiodiversity/MammalModels" />

<meta name="twitter:card" content="summary" />
<meta name="twitter:title" content="Page not found | Using remote camera trap images to estimate densities and develop habitat models for mammals in Alberta, Canada" />

<meta name="twitter:description" content="<p>This is a minimal example of using the bookdown package to write a book.
set in the _output.yml file.
The HTML output format for this example is bookdown::gitbook,</p>" />
<meta name="twitter:description" content="ABMI Camera Methods and Mammal Modeling" />


<meta name="author" content="Marcus Becker, Dr. David J. Huggard, Dr. David Roberts" />


<meta name="date" content="2023-12-19" />
<meta name="date" content="2023-12-20" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
Expand Down Expand Up @@ -58,22 +52,22 @@
<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>
<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>
<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>
<script src="libs/htmlwidgets-1.6.2/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-binding-2.1.2/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>
<script src="libs/leaflet-providers-plugin-2.1.2/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" />
Expand All @@ -82,70 +76,6 @@
<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">

Expand Down Expand Up @@ -187,7 +117,7 @@
<nav role="navigation">

<ul class="summary">
<li><a href="./">A Minimal Book Example</a></li>
<li><a href="./">ABMI Mammal Models</a></li>

<li class="divider"></li>
<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Introduction</a>
Expand Down Expand Up @@ -296,7 +226,7 @@ <h1>Page not found</h1>
"size": 2
},
"edit": {
"link": "https://github.com/USERNAME/REPO/edit/BRANCH/%s",
"link": "https://github.com/ABbiodiversity/MammalModels/tree/main/bookdown%s",
"text": "Edit"
},
"history": {
Expand All @@ -319,20 +249,6 @@ <h1>Page not found</h1>
});
</script>

<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
var src = "true";
if (src === "" || src === "true") src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.9/latest.js?config=TeX-MML-AM_CHTML";
if (location.protocol !== "file:")
if (/^https?:/.test(src))
src = src.replace(/^https?:/, '');
script.src = src;
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>

</html>
22 changes: 8 additions & 14 deletions bookdown/_book/blocks.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,31 +5,25 @@
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>Chapter 5 Blocks | Using remote camera trap images to estimate densities and develop habitat models for mammals in Alberta, Canada</title>
<meta name="description" content="<p>This is a minimal example of using the bookdown package to write a book.
set in the _output.yml file.
The HTML output format for this example is bookdown::gitbook,</p>" />
<meta name="description" content="ABMI Camera Methods and Mammal Modeling" />
<meta name="generator" content="bookdown 0.37 and GitBook 2.6.7" />

<meta property="og:title" content="Chapter 5 Blocks | Using remote camera trap images to estimate densities and develop habitat models for mammals in Alberta, Canada" />
<meta property="og:type" content="book" />

<meta property="og:description" content="<p>This is a minimal example of using the bookdown package to write a book.
set in the _output.yml file.
The HTML output format for this example is bookdown::gitbook,</p>" />
<meta name="github-repo" content="rstudio/bookdown-demo" />
<meta property="og:description" content="ABMI Camera Methods and Mammal Modeling" />
<meta name="github-repo" content="ABbiodiversity/MammalModels" />

<meta name="twitter:card" content="summary" />
<meta name="twitter:title" content="Chapter 5 Blocks | Using remote camera trap images to estimate densities and develop habitat models for mammals in Alberta, Canada" />

<meta name="twitter:description" content="<p>This is a minimal example of using the bookdown package to write a book.
set in the _output.yml file.
The HTML output format for this example is bookdown::gitbook,</p>" />
<meta name="twitter:description" content="ABMI Camera Methods and Mammal Modeling" />


<meta name="author" content="Marcus Becker, Dr. David J. Huggard, Dr. David Roberts" />


<meta name="date" content="2023-12-19" />
<meta name="date" content="2023-12-20" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
Expand Down Expand Up @@ -64,16 +58,16 @@
<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>
<script src="libs/htmlwidgets-1.6.2/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-binding-2.1.2/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>
<script src="libs/leaflet-providers-plugin-2.1.2/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" />
Expand Down
Loading

0 comments on commit db58c7c

Please sign in to comment.