{
"cells": [
{
"cell_type": "markdown",
"id": "3ad67b01-3887-48b5-a669-222b3c5dcbe8",
"metadata": {},
"source": [
"## Analyzing data from Movebank"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "989214d5-edb0-48f8-8043-8cdc2eb4d61e",
"metadata": {},
"outputs": [],
"source": [
"import movekit as mkit"
]
},
{
"cell_type": "markdown",
"id": "b982e7c4-51c4-4f29-8b2e-4642adc9f223",
"metadata": {},
"source": [
"#### Read data input"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "24dd7e66-b325-4cf9-932e-14207f40c4d6",
"metadata": {},
"outputs": [
{
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"9637 Mangabey monkeys in Uganda (data from Waser 1975) \n",
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]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data = mkit.read_movebank('datasets/Mangabey_monkeys_in_Uganda.csv')\n",
"data.head()"
]
},
{
"cell_type": "markdown",
"id": "abf47dac-ca3a-4c46-8fbc-608cb21a9595",
"metadata": {},
"source": [
"#### Basic Data Analysis"
]
},
{
"cell_type": "markdown",
"id": "85dfd5d1-c188-4a5b-a893-aea4e6dbac06",
"metadata": {},
"source": [
"For further data analysis functions of `movekit` please refer to the other example notebooks or the documentation.\n",
"It is important to preprocess the data from Movebank, as the data often contains duplicates which can lead to problems in further analysis steps."
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "45507e0e-e847-4922-a3e9-db2d1cf4c518",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Total number of missing values = 14437\n",
"comments 9637\n",
"behavioural-classification 2400\n",
"study-specific-measurement 2400\n",
"time 0\n",
"animal_id 0\n",
"x 0\n",
"y 0\n",
"event-id 0\n",
"visible 0\n",
"location-long 0\n",
"location-lat 0\n",
"sensor-type 0\n",
"individual-taxon-canonical-name 0\n",
"tag-local-identifier 0\n",
"study-name 0\n",
"dtype: int64\n"
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"execution_count": 10,
"metadata": {},
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],
"source": [
"data = mkit.preprocess(data, interpolation = True, date_format = True) # important to indicate the date format of time by setting date_format=True when applying interpolation\n",
"data.head()"
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "347c7311-29eb-413c-ba18-edaa2a9df975",
"metadata": {},
"outputs": [
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"name": "stderr",
"output_type": "stream",
"text": [
"Extracting all absolute features: 100%|██████████| 100.0/100 [00:03<00:00, 32.24it/s]\n"
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},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
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"source": [
"data = mkit.extract_features(data)\n",
"data.head()"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "9b35da87-220d-4eca-89f3-bfa1fa5d087d",
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" 17 | \n",
" TK | \n",
" 49030.622798 | \n",
"
\n",
" \n",
"
\n",
"
"
],
"text/plain": [
" animal_id distance\n",
"0 BB 29292.196235\n",
"1 BC 32339.850273\n",
"2 BR 25428.128415\n",
"3 BT 56379.253280\n",
"4 CH 0.000000\n",
"5 FB 0.000000\n",
"6 HK 44779.676823\n",
"7 JA 0.000000\n",
"8 JE 42121.957235\n",
"9 KT 44881.459185\n",
"10 LN 36373.411270\n",
"11 M Group 69659.023543\n",
"12 O 48254.273757\n",
"13 PB 16140.353833\n",
"14 RF 55879.886570\n",
"15 S 17618.932566\n",
"16 SK 22967.788494\n",
"17 TK 49030.622798"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"#calculate for each animal the distance covered between 1972-5-1 and 1972-10-1 12:00:00\n",
"mkit.distance_by_time(data, '1972-5-1','1972-10-1 12:00:00')"
]
},
{
"cell_type": "markdown",
"id": "6cfa25be-26e4-427e-8f3a-f443aae92539",
"metadata": {
"tags": []
},
"source": [
"#### Create interactive maps with the geodata"
]
},
{
"cell_type": "markdown",
"id": "8f712754-3808-4e34-9441-0fd3541db8b9",
"metadata": {},
"source": [
"Using the geodata interactive maps can be created. By clicking on the marker points the animal_id and the time of each marker is displayed."
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "e9028dd9-9e9f-46d5-8683-b777221d9a57",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Plotting geo data for specified animals: 100%|██████████| 2/2 [00:00<00:00, 4.34it/s]\n"
]
},
{
"data": {
"text/html": [
"Make this Notebook Trusted to load map: File -> Trust Notebook
"
],
"text/plain": [
""
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# as the creation of the map is very time-confusing it is recommended to select a subsample of animals for which the map is created.\n",
"mkit.plot_geodata(data, animal_list=[\"BT\", \"KT\"])"
]
},
{
"cell_type": "markdown",
"id": "918acaa2-8fcc-4e19-b588-ce2ad11d488d",
"metadata": {},
"source": [
"Additionally the movement of individual animals can be retraced by including movement lines in between the different markers."
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "77e075fa-1755-40a5-b6f4-e42bb8b1b10b",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Plotting geo data for specified animals: 100%|██████████| 1/1 [00:00<00:00, 8.70it/s]\n"
]
},
{
"data": {
"text/html": [
"Make this Notebook Trusted to load map: File -> Trust Notebook
"
],
"text/plain": [
""
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# each movement line has a tooltip to follow the sequence of movement (here animal \"JA\" for example starts in south west)\n",
"movement_map = mkit.plot_geodata(data, animal_list=[\"JA\"], movement_lines=True)\n",
"movement_map"
]
},
{
"cell_type": "markdown",
"id": "7ffe43d6-2441-43e0-86e7-c5c7db202a16",
"metadata": {},
"source": [
"The created maps can also be saved locally."
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "e38af578-c500-4c10-98c5-e75b711a7bef",
"metadata": {},
"outputs": [],
"source": [
"#mkit.save_geodata_map(movement_map, \"mymap.html\")"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.7"
}
},
"nbformat": 4,
"nbformat_minor": 5
}