Updated 2023 Diatoms rendered quarto.

Added a readme, and rendered to html.

2023_Diatom_Waterchem/Aggregate_Dataset_R_Project_20Sep23.qmd

@@ -106,7 +106,7 @@ if (file.exists('data/waterchem_ds.RDS')) {
 
 This chunk of code creates a map of the distribution of diatom data. There are `r length(diatom_ds)` diatom sites, and there are `r length(waterchem_ds)` water chemistry sites. We want to plot them both. Here we're going to use the interactive `leaflet` package and colour code the plots using the Aggregate Dataset IDs.
 
-```{r mapdiatoms,echo=FALSE,fig.cap='Diatom aggregate surface sample calibration dataset distribution in North America. There are over 2000 sites ranging from Arctic Canada to the southern United States. Most aggregate datasets are limited to relatively small regions (e.g., states). Some datasets are large scale (e.g., EPA’s 2007 National Lake assessment). Observing the current site and aggregate dataset distributions aid in helping create new calibration datasets.'}
+```{r mapdiatoms,echo=FALSE,fig.cap='Diatom aggregate surface sample calibration dataset distribution in North America. There are over 2000 sites ranging from Arctic Canada to the southern United States. Most aggregate datasets are limited to relatively small regions (e.g., states). Some datasets are large scale (e.g., EPA 20R07 National Lake assessment). Observing the current site and aggregate dataset distributions aid in helping create new calibration datasets.'}
 
 diatom_siteloc <- as.data.frame(diatom_ds) %>%
     inner_join(drexel, by = 'siteid') %>%
@@ -120,7 +120,7 @@ leaflet::leaflet() %>%
   addTiles() %>%
   addCircleMarkers(lat = diatom_siteloc$lat,
                    lng = diatom_siteloc$long,
-                   color = pal(diatom_siteloc$aggregateid),
+                   # color = pal(diatom_siteloc$aggregateid),
                    group = "circles") %>%
   addLegend(pal = pal,
     values = diatom_siteloc$aggregatedatasetname,
@@ -188,15 +188,15 @@ There are `r nrow(wc_tx)` rows in the waterchem taxon table.
 
 ##### Water Chemistry Harmonization 
 
-```{r loadHarm, warning=FALSE, echo=FALSE}
+```{r waterHarm, warning=FALSE, echo=FALSE}
 waterchem_hm <- read.csv('data/waterchem_tx_harmonized.csv')
 waterchem_samples <- samples(waterchem_dl)
 
 waterchem_harmonized <- waterchem_samples %>% right_join(waterchem_hm)
 
 w_hz <- waterchem_harmonized %>% 
   group_by(age, units, replacement, depth, siteid, sitename, lat, long, elev) %>%
-  summarise(count = mean(value), n=n())
+  summarise(count = mean(value), n = n())
 ```
 
 ##### Water Chemistry Statistics

2023_Diatom_Waterchem/Aggregate_Dataset_R_Project_20Sep23_files/libs/Proj4Leaflet-1.0.1/proj4leaflet.js

@@ -0,0 +1,272 @@
+(function (factory) {
+	var L, proj4;
+	if (typeof define === 'function' && define.amd) {
+		// AMD
+		define(['leaflet', 'proj4'], factory);
+	} else if (typeof module === 'object' && typeof module.exports === "object") {
+		// Node/CommonJS
+		L = require('leaflet');
+		proj4 = require('proj4');
+		module.exports = factory(L, proj4);
+	} else {
+		// Browser globals
+		if (typeof window.L === 'undefined' || typeof window.proj4 === 'undefined')
+			throw 'Leaflet and proj4 must be loaded first';
+		factory(window.L, window.proj4);
+	}
+}(function (L, proj4) {
+	if (proj4.__esModule && proj4.default) {
+		// If proj4 was bundled as an ES6 module, unwrap it to get
+		// to the actual main proj4 object.
+		// See discussion in https://github.com/kartena/Proj4Leaflet/pull/147
+		proj4 = proj4.default;
+	}
+
+	L.Proj = {};
+
+	L.Proj._isProj4Obj = function(a) {
+		return (typeof a.inverse !== 'undefined' &&
+			typeof a.forward !== 'undefined');
+	};
+
+	L.Proj.Projection = L.Class.extend({
+		initialize: function(code, def, bounds) {
+			var isP4 = L.Proj._isProj4Obj(code);
+			this._proj = isP4 ? code : this._projFromCodeDef(code, def);
+			this.bounds = isP4 ? def : bounds;
+		},
+
+		project: function (latlng) {
+			var point = this._proj.forward([latlng.lng, latlng.lat]);
+			return new L.Point(point[0], point[1]);
+		},
+
+		unproject: function (point, unbounded) {
+			var point2 = this._proj.inverse([point.x, point.y]);
+			return new L.LatLng(point2[1], point2[0], unbounded);
+		},
+
+		_projFromCodeDef: function(code, def) {
+			if (def) {
+				proj4.defs(code, def);
+			} else if (proj4.defs[code] === undefined) {
+				var urn = code.split(':');
+				if (urn.length > 3) {
+					code = urn[urn.length - 3] + ':' + urn[urn.length - 1];
+				}
+				if (proj4.defs[code] === undefined) {
+					throw 'No projection definition for code ' + code;
+				}
+			}
+
+			return proj4(code);
+		}
+	});
+
+	L.Proj.CRS = L.Class.extend({
+		includes: L.CRS,
+
+		options: {
+			transformation: new L.Transformation(1, 0, -1, 0)
+		},
+
+		initialize: function(a, b, c) {
+			var code,
+			    proj,
+			    def,
+			    options;
+
+			if (L.Proj._isProj4Obj(a)) {
+				proj = a;
+				code = proj.srsCode;
+				options = b || {};
+
+				this.projection = new L.Proj.Projection(proj, options.bounds);
+			} else {
+				code = a;
+				def = b;
+				options = c || {};
+				this.projection = new L.Proj.Projection(code, def, options.bounds);
+			}
+
+			L.Util.setOptions(this, options);
+			this.code = code;
+			this.transformation = this.options.transformation;
+
+			if (this.options.origin) {
+				this.transformation =
+					new L.Transformation(1, -this.options.origin[0],
+						-1, this.options.origin[1]);
+			}
+
+			if (this.options.scales) {
+				this._scales = this.options.scales;
+			} else if (this.options.resolutions) {
+				this._scales = [];
+				for (var i = this.options.resolutions.length - 1; i >= 0; i--) {
+					if (this.options.resolutions[i]) {
+						this._scales[i] = 1 / this.options.resolutions[i];
+					}
+				}
+			}
+
+			this.infinite = !this.options.bounds;
+
+		},
+
+		scale: function(zoom) {
+			var iZoom = Math.floor(zoom),
+				baseScale,
+				nextScale,
+				scaleDiff,
+				zDiff;
+			if (zoom === iZoom) {
+				return this._scales[zoom];
+			} else {
+				// Non-integer zoom, interpolate
+				baseScale = this._scales[iZoom];
+				nextScale = this._scales[iZoom + 1];
+				scaleDiff = nextScale - baseScale;
+				zDiff = (zoom - iZoom);
+				return baseScale + scaleDiff * zDiff;
+			}
+		},
+
+		zoom: function(scale) {
+			// Find closest number in this._scales, down
+			var downScale = this._closestElement(this._scales, scale),
+				downZoom = this._scales.indexOf(downScale),
+				nextScale,
+				nextZoom,
+				scaleDiff;
+			// Check if scale is downScale => return array index
+			if (scale === downScale) {
+				return downZoom;
+			}
+			if (downScale === undefined) {
+				return -Infinity;
+			}
+			// Interpolate
+			nextZoom = downZoom + 1;
+			nextScale = this._scales[nextZoom];
+			if (nextScale === undefined) {
+				return Infinity;
+			}
+			scaleDiff = nextScale - downScale;
+			return (scale - downScale) / scaleDiff + downZoom;
+		},
+
+		distance: L.CRS.Earth.distance,
+
+		R: L.CRS.Earth.R,
+
+		/* Get the closest lowest element in an array */
+		_closestElement: function(array, element) {
+			var low;
+			for (var i = array.length; i--;) {
+				if (array[i] <= element && (low === undefined || low < array[i])) {
+					low = array[i];
+				}
+			}
+			return low;
+		}
+	});
+
+	L.Proj.GeoJSON = L.GeoJSON.extend({
+		initialize: function(geojson, options) {
+			this._callLevel = 0;
+			L.GeoJSON.prototype.initialize.call(this, geojson, options);
+		},
+
+		addData: function(geojson) {
+			var crs;
+
+			if (geojson) {
+				if (geojson.crs && geojson.crs.type === 'name') {
+					crs = new L.Proj.CRS(geojson.crs.properties.name);
+				} else if (geojson.crs && geojson.crs.type) {
+					crs = new L.Proj.CRS(geojson.crs.type + ':' + geojson.crs.properties.code);
+				}
+
+				if (crs !== undefined) {
+					this.options.coordsToLatLng = function(coords) {
+						var point = L.point(coords[0], coords[1]);
+						return crs.projection.unproject(point);
+					};
+				}
+			}
+
+			// Base class' addData might call us recursively, but
+			// CRS shouldn't be cleared in that case, since CRS applies
+			// to the whole GeoJSON, inluding sub-features.
+			this._callLevel++;
+			try {
+				L.GeoJSON.prototype.addData.call(this, geojson);
+			} finally {
+				this._callLevel--;
+				if (this._callLevel === 0) {
+					delete this.options.coordsToLatLng;
+				}
+			}
+		}
+	});
+
+	L.Proj.geoJson = function(geojson, options) {
+		return new L.Proj.GeoJSON(geojson, options);
+	};
+
+	L.Proj.ImageOverlay = L.ImageOverlay.extend({
+		initialize: function (url, bounds, options) {
+			L.ImageOverlay.prototype.initialize.call(this, url, null, options);
+			this._projectedBounds = bounds;
+		},
+
+		// Danger ahead: Overriding internal methods in Leaflet.
+		// Decided to do this rather than making a copy of L.ImageOverlay
+		// and doing very tiny modifications to it.
+		// Future will tell if this was wise or not.
+		_animateZoom: function (event) {
+			var scale = this._map.getZoomScale(event.zoom);
+			var northWest = L.point(this._projectedBounds.min.x, this._projectedBounds.max.y);
+			var offset = this._projectedToNewLayerPoint(northWest, event.zoom, event.center);
+
+			L.DomUtil.setTransform(this._image, offset, scale);
+		},
+
+		_reset: function () {
+			var zoom = this._map.getZoom();
+			var pixelOrigin = this._map.getPixelOrigin();
+			var bounds = L.bounds(
+				this._transform(this._projectedBounds.min, zoom)._subtract(pixelOrigin),
+				this._transform(this._projectedBounds.max, zoom)._subtract(pixelOrigin)
+			);
+			var size = bounds.getSize();
+
+			L.DomUtil.setPosition(this._image, bounds.min);
+			this._image.style.width = size.x + 'px';
+			this._image.style.height = size.y + 'px';
+		},
+
+		_projectedToNewLayerPoint: function (point, zoom, center) {
+			var viewHalf = this._map.getSize()._divideBy(2);
+			var newTopLeft = this._map.project(center, zoom)._subtract(viewHalf)._round();
+			var topLeft = newTopLeft.add(this._map._getMapPanePos());
+
+			return this._transform(point, zoom)._subtract(topLeft);
+		},
+
+		_transform: function (point, zoom) {
+			var crs = this._map.options.crs;
+			var transformation = crs.transformation;
+			var scale = crs.scale(zoom);
+
+			return transformation.transform(point, scale);
+		}
+	});
+
+	L.Proj.imageOverlay = function (url, bounds, options) {
+		return new L.Proj.ImageOverlay(url, bounds, options);
+	};
+
+	return L.Proj;
+}));