{"metadata":{"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"pygments_lexer":"ipython3","nbconvert_exporter":"python","version":"3.6.4","file_extension":".py","codemirror_mode":{"name":"ipython","version":3},"name":"python","mimetype":"text/x-python"}},"nbformat_minor":4,"nbformat":4,"cells":[{"cell_type":"markdown","source":"# Overview\nThere have been questions about the test site locations on the discussion forum, so I thought I'd put together a brief virtual tour of the four test sites with a little added commentary. (This is also an excuse for me to play with maps in Python in a very rudimentary way.)\n","metadata":{}},{"cell_type":"code","source":"import numpy as np # linear algebra\nimport pandas as pd # data processing, CSV file I/O (e.g. pd.read_csv)\nimport os\nimport folium\nfrom IPython.display import Image\nfrom IPython.core.interactiveshell import InteractiveShell\nInteractiveShell.ast_node_interactivity = \"all\"\n","metadata":{"_uuid":"8f2839f25d086af736a60e9eeb907d3b93b6e0e5","_cell_guid":"b1076dfc-b9ad-4769-8c92-a6c4dae69d19","_kg_hide-input":true,"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"# Overview map\n\nThe four sites are:\n\n* SSW: Sapsucker Woods (eastern North America)\n* SNE: Sierra Nevada (western North America)\n* COR: Costa Rica (Central America)\n* COL: Colombia (South America)\n\n## Geographic precision\nWe have latitude and longitude to two decimal places; 0.01 degree of latitude represents 1.1 km. The given coordinates may serve as an approximate centerpoint for somewhat larger zones (of unknown size). Clues from listening to the training  soundscapes suggest to me that recordings are being made from multiple different points within the general area. \n","metadata":{}},{"cell_type":"code","source":"\nm_1 = folium.Map(location=[30, -93], tiles='Stamen terrain', zoom_start=3)\nfolium.Marker(\n    location=[5.57, -75.85], \n    popup='Coordinates given for COL', # pop-up label for the marker\n    icon=folium.Icon()\n).add_to(m_1)\nfolium.Marker(\n    location=[42.47, -76.45], \n    popup='Coordinates given for SSW', # pop-up label for the marker\n    icon=folium.Icon()\n).add_to(m_1)\nfolium.Marker(\n    location=[38.49, -119.95], \n    popup='Coordinates given for SNE', # pop-up label for the marker\n    icon=folium.Icon()\n).add_to(m_1)\nfolium.Marker(\n    location=[10.12, -84.51], \n    popup='Coordinates given for COR', # pop-up label for the marker\n    icon=folium.Icon()\n).add_to(m_1)\n\nm_1","metadata":{"_kg_hide-input":true,"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"# SSW, Sapsucker Woods, Ithaca, New York, USA\n\nThe marker shows the location of the given test site coordinates. This is the one case in which we know a bit more about the zone the coordinates represent, for the convenient reason that Sapsucker Woods is explicitly mapped and well defined. \n\n","metadata":{}},{"cell_type":"code","source":"\nm_1 = folium.Map(location=[42.47, -76.45], tiles='openstreetmap', zoom_start=13)\nfolium.Marker(\n    location=[42.47, -76.45], \n    popup='Coordinates given for SSW', # pop-up label for the marker\n    icon=folium.Icon()\n).add_to(m_1)\nm_1\n\n","metadata":{"_kg_hide-input":true,"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"**Notes about Sapsucker Woods**:\n* This is the home of the **Cornell Lab of Ornithology**, which appears on the map near the north end of Sapsucker Woods after zooming in a bit. \n* **Noise pollution**:\n    * **Airport**: The regional airport just north of Sapsucker Woods explains the occasional loud planes that can  be heard in the training soundscapes. \n    * **Highways**: Various roads, but especially the multi-lane Highway 13, drone in the background of some of the soundscape recordings.\n\nAs a birder, I made a \"pilgrimage\" to Sapsucker Woods, so I'll share a few photos from my visit:","metadata":{}},{"cell_type":"code","source":"Image(filename = \"../input/misc-images/DSC00714.JPG\")\n","metadata":{"_kg_hide-input":true,"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"At the time of my visit, these signs were posted at entry points to Sapsucker Woods. I think we can reasonalby assume the the recordings are from the Sapsucker Woods proper, and not in the broader Ithaca area. Due to privacy concerns, putting up microphonese that might pick up conversations is something that isn't likely to be done just anywhere, at least in the United States. ","metadata":{}},{"cell_type":"code","source":"Image(filename = \"../input/misc-images/DSC00713.JPG\", width=300)\nImage(filename = \"../input/misc-images/DSC00721.JPG\", height=300)\n","metadata":{"_kg_hide-input":true,"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"* **Habitats**:\nA mix of **forest** and shallow **wetland** habitats dominate at Sapsucker Woods. The landscape was formerly farmed, but abandoned due to wetness (ref: https://www.allaboutbirds.org/news/view-from-sapsucker-woods-100-years-later/), so forests are second growth. Suburban and open field habitats border the woods proper, so the soundscapes could cover substantial habitat diversity.\n    \n* **Season for the recording**:\nMy photos are from an autumn visit, but the soundscape recordings were collected from **February through August** of 2017. This is the broadest time frame of any of the four sites. The collection of birds varies over the course of this time period, including at various times:\n\n    * Overwintering species: birds that winter at Sapsucker Woods but go north for breeding season.\n    * Year-round residents. \n    * Pass-through migrants: ones that stop for a bit on their way farther north; these are often plenty vocal.\n    * Breeding migrants: ones that arrive from the south in spring and stay at Sapsucker Woods for breeding season. \n    \nThe February through August time period emphasizes spring migration and the breeding season, which is when birds tend to be the most vocal; southward fall migration largely picks up later in the year. \n\n* **eBird coverage**: \nSapsucker Woods is **exceptionally well documented on eBird**, something that should come as no surprise given that the Cornell Lab of Ornithology is the home of eBird. The multiple eBird hotspots in Sapsucker Woods collectively have **over 20,000 checklists**! \n","metadata":{}},{"cell_type":"markdown","source":"# SNE, Sierra Nevada, Alpine County, California, USA\n\nHere's a terrain view of the next site, as it is in the high Sierras. Most of the land in the area is part of a National Forest. \n\nFor all of the remaining site maps, the starting zoom is the same as for the Sapsucker Woods site; in that case, all recording locations fit well within the map view. However, we haven't been given any information about how geographically dispersed the specific microphone locations were at the other sites.","metadata":{}},{"cell_type":"code","source":"m_1 = folium.Map(location=[38.49, -119.95], tiles='Stamen Terrain', zoom_start=13)\n#folium.LayerControl().add_to(m_1)\n#folium.Map(location=[38.49, -119.95], tiles='Stamen Terrain', zoom_start=13).add_to(m_1)\nfolium.Marker(\n    location=[38.49, -119.95], \n    popup='Coordinates given for SNE', # pop-up label for the marker\n    icon=folium.Icon()\n).add_to(m_1)\n\n\nm_1\n","metadata":{"_kg_hide-input":true,"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"* **Habitats**: This is a mountainous area. Taking a look at Google Street View reveals a **coniferous forest** transitioning to higher elevation peaks with low-growing **alpine vegetation**. Several **deep lakes** (suitable for diving ducks) dot the region. \n\n* **Season for the recording**: All recordings for this site are from May. \n\n* **eBird coverage**: Of the hotspots in the vicinity, the number of checklists per hotspot ranges from less than a dozen to a maximum of 176 at the time I looked. Winter checklists are nearly non-existent, likely because the mountains are snowed in at that time of year, so at least the checklists that do exist are more concentrated in the time of year that matters. \n\n* **Species in the training set**: This site almost certainly has the lowest count of possible species among the four sites. Given that species diversity tends to decline with latitude and altitude, this is perhaps not surprising for a high altitude site that is also one of the more northerly.\n","metadata":{}},{"cell_type":"markdown","source":"# Alajuela, San Ramón, Costa Rica\nI'm using the regular Open Street Map basemap here. I'd prefer to show an air photo/satellite view from a free map server, or give options to toggle between base maps. However, my attempts to find a way to do so failed (and if anyone can point me to a solution, I'd appreciate it). Meanwhile, it is easy enough to manually punch the coordinates into something like Google maps for those more informative map views. ","metadata":{}},{"cell_type":"markdown","source":"","metadata":{}},{"cell_type":"code","source":"m_1 = folium.Map(location=[10.12, -84.51], tiles='openstreetmap', zoom_start=13)\nfolium.Marker(\n    location=[10.12, -84.51], \n    popup='Coordinates given for COR', # pop-up label for the marker\n    icon=folium.Icon()\n).add_to(m_1)\n\nm_1\n\n","metadata":{"_kg_hide-input":true,"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"* **Habitats**: The broader region contains a patchwork of **farmland**, **forest**, and an **urban** area. At least one of the training soundscapes inculdes sounds of barking dogs and (likely) roosters, implying the presence of small farms or rural residences and that the recordings aren't restricted to just a forest reserve (though that could also be represented). Different cohorts of species are likely to be found in deep forest settings compared to settings with second-growth, edges, and tangled vegetation. Farmed plots tend to be in the lower elevations, with forested areas generallly correlating with extra topography. The site is inland from the coast; natural water is in the form of streams and rivers, though some small farm ponds may be present. \n\n* **Season for the recording**: All recordings for this site are from September and October. In addition to the diverse population of resident species, an assortment of species that migrate north for the breeding season would be returning to lower latitudes at this time of year. However, some of the returning migrant songbirds may vocalize less in autumn on their non-breeding zones compared to spring at their breeding territories. \n\n* **Weather**: September and October are part of the wet season, according to https://weatherspark.com/y/15509/Average-Weather-in-San-Ramón-Costa-Rica-Year-Round.  \n\n* **eBird coverage**: A number of the hotspots in the vicinity have hundreds of checklists. This is helpful, but at both of the low latitude sites, the biodiversity is extremely high. Therefore, lots of checklists by skilled birders are necessary to provide reliable information about species frequency. \n\n","metadata":{}},{"cell_type":"markdown","source":"# Jardín, Departamento de Antioquia, Colombia\n\n","metadata":{}},{"cell_type":"code","source":"m_1 = folium.Map(location=[5.57, -75.85], tiles='openstreetmap', zoom_start=13)\nfolium.Marker(\n    location=[5.57, -75.85], \n    popup='Coordinates given for COL', # pop-up label for the marker\n    icon=folium.Icon()\n).add_to(m_1)\n\nm_1","metadata":{"_kg_hide-input":true,"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"* **Habitats**: As with the COR site, the broader region contains a patchwork of farmland, forest, and an urban area. Considerable topography provides an extra element of habitat diversity. \n\n* **Season for the recording**: September, October, and November. Similar to COR, migrants would be returning from northerly areas during this period, adding to the already diverse resident species.\n\n* **Weather**: Those months are part of the rainy season, based on info from this location in the vicinity: https://weatherspark.com/y/22472/Average-Weather-in-Pueblorrico-Colombia-Year-Round\n\n* **eBird coverage**: See comments for COR.","metadata":{}},{"cell_type":"markdown","source":"\nLicense\n\nCopyright 2021 J.M. Reuter\n\nLicensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at\n\nhttp://www.apache.org/licenses/LICENSE-2.0\n\nUnless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.\n","metadata":{}}]}