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sedv8808 committed Aug 29, 2023
1 parent 56e68a7 commit 3d69cbd
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2,654 changes: 2,654 additions & 0 deletions inst/doc/images/neotomaUML_as.svg
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616 changes: 616 additions & 0 deletions inst/doc/images/site_collunit_dataset.svg
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536 changes: 536 additions & 0 deletions inst/doc/images/siteboundarydiagram.svg
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955 changes: 955 additions & 0 deletions inst/doc/images/understandingAgeRanges.svg
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604 changes: 604 additions & 0 deletions inst/doc/images/understanding_S4_structure.svg
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565 changes: 565 additions & 0 deletions inst/doc/images/understanding_S4_structure_get_datasets.svg
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423 changes: 423 additions & 0 deletions inst/doc/images/understanding_S4_structure_get_sites.svg
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272 changes: 272 additions & 0 deletions inst/doc/neotoma2-package_files/Proj4Leaflet-1.0.1/proj4leaflet.js
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(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;
}));
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