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Tested and fixed.
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@jonathanhhb
jonathanhhb committed Aug 2, 2024
1 parent 9faff5e commit 82fa252
Showing 1 changed file with 52 additions and 53 deletions.
105 changes: 52 additions & 53 deletions nnmm/measles.ipynb
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"cells": [
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{
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{
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},
{
"cell_type": "code",
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},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 4,
"metadata": {},
"outputs": [
{
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{
"cell_type": "code",
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"execution_count": 5,
"metadata": {},
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"source": [
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},
{
"cell_type": "code",
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"execution_count": 6,
"metadata": {},
"outputs": [
{
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},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 8,
"metadata": {},
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"source": [
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},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": 9,
"metadata": {},
"outputs": [
{
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"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 21/21 [00:04<00:00, 4.26it/s]\n"
"100%|██████████| 21/21 [00:05<00:00, 4.15it/s]\n"
]
}
],
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},
{
"cell_type": "code",
"execution_count": 17,
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Elapsed time for drawing dates of death: 0:00:00.654421\n",
"Elapsed time for drawing dates of death: 0:00:00.667460\n",
"First 32 DoBs (should all be negative - these agents were born before today):\n",
"[ -8451 -7876 -14985 -808 -7663 -20228 -5030 -5101 -10742 -19333\n",
" -1238 -19324 -13411 -20192 -16865 -277 -24848 -1730 -20736 -3790\n",
" -16112 -11334 -32463 -20992 -4079 -5179 -5480 -7983 -13712 -24750\n",
" -11784 -3217]\n",
"[-30359 -24387 -31137 -16381 -13762 -19198 -18734 -27217 -19568 -24373\n",
" -34586 -4386 -2811 -13038 -13684 -25348 -5824 -2658 -26425 -1189\n",
" -5712 -14872 -17131 -1841 -10854 -16200 -14029 -19870 -18354 -12493\n",
" -22093 -22632]\n",
"First 32 DoDs (should all be positive - these agents will all pass in the future):\n",
"[24396 16944 15843 30502 19803 6234 21686 30864 9730 12929 30017 4118\n",
" 16185 13362 3638 26696 4617 34803 8495 25534 12775 20127 2043 10337\n",
" 28937 10406 19620 19484 20093 8944 11622 26847]\n"
"[ 3491 5543 3855 15565 13584 15589 13739 1412 6874 4753 1722 26142\n",
" 27996 19020 7129 7207 29605 14269 3725 24623 25630 20375 17988 18177\n",
" 13919 1107 14869 10227 14392 21691 2035 8619]\n"
]
}
],
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},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 11174483/11174483 [00:15<00:00, 741058.92it/s]"
"100%|██████████| 11170971/11170971 [00:15<00:00, 736245.68it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Elapsed time for pushing dates of death: 0:00:15.215003\n",
"Non-disease mortality: tracked 11,174,483, untracked 84,996,635\n"
"Elapsed time for pushing dates of death: 0:00:15.313127\n",
"Non-disease mortality: tracked 11,170,971, untracked 85,000,147\n"
]
},
{
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},
{
"cell_type": "code",
"execution_count": 19,
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 20,
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 21,
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 16,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 17,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 22,
"execution_count": 28,
"metadata": {},
"outputs": [],
"source": [
"@nb.njit((nb.uint32, nb.uint16[:], nb.uint8[:], nb.int32[:], nb.int64 ), parallel=True)\n",
"@nb.njit((nb.uint32, nb.uint8[:], nb.uint8[:], nb.int32[:], nb.int64), parallel=True)\n",
"def _update_susceptibility_based_on_ri_timer(count, ri_timer, susceptibility, dob, tick):\n",
" for i in nb.prange(count):\n",
" if ri_timer[i] > 0:\n",
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},
{
"cell_type": "code",
"execution_count": 29,
"execution_count": 19,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 23,
"execution_count": 20,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"initial_infections.sum()=2,402,987\n",
"(model.population.itimer > 0).sum()=2,402,987\n"
"initial_infections.sum()=2,405,278\n",
"(model.population.itimer > 0).sum()=2,405,278\n"
]
}
],
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},
{
"cell_type": "code",
"execution_count": 24,
"execution_count": 21,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 419/419 [00:01<00:00, 299.12it/s]"
"100%|██████████| 419/419 [00:01<00:00, 311.27it/s]"
]
},
{
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},
{
"cell_type": "code",
"execution_count": 25,
"execution_count": 22,
"metadata": {},
"outputs": [],
"source": [
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{
"cell_type": "code",
"execution_count": 26,
"execution_count": 23,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 27,
"execution_count": 24,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 28,
"execution_count": 27,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
" 0%| | 11/3650 [00:02<13:29, 4.50it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Running SIA campaign=(10, [1, 3, 5], 0.8) at tick 10\n"
" 0%| | 0/3650 [00:00<?, ?it/s]\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 3650/3650 [05:11<00:00, 11.71it/s]\n"
"ename": "TypeError",
"evalue": "No matching definition for argument type(s) int64, array(uint8, 1d, C), array(uint8, 1d, C), array(int32, 1d, C), int64",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[27], line 10\u001b[0m\n\u001b[1;32m 8\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m phase \u001b[38;5;129;01min\u001b[39;00m model\u001b[38;5;241m.\u001b[39mphases:\n\u001b[1;32m 9\u001b[0m tstart \u001b[38;5;241m=\u001b[39m datetime\u001b[38;5;241m.\u001b[39mnow(tz\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;66;03m# noqa: DTZ005\u001b[39;00m\n\u001b[0;32m---> 10\u001b[0m \u001b[43mphase\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodel\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtick\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 11\u001b[0m tfinish \u001b[38;5;241m=\u001b[39m datetime\u001b[38;5;241m.\u001b[39mnow(tz\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;66;03m# noqa: DTZ005\u001b[39;00m\n\u001b[1;32m 12\u001b[0m delta \u001b[38;5;241m=\u001b[39m tfinish \u001b[38;5;241m-\u001b[39m tstart\n",
"Cell \u001b[0;32mIn[26], line 12\u001b[0m, in \u001b[0;36mdo_ri\u001b[0;34m(model, tick)\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdo_ri\u001b[39m(model, tick):\n\u001b[0;32m---> 12\u001b[0m \u001b[43m_update_susceptibility_based_on_ri_timer\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpopulation\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcount\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmodel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpopulation\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mri_timer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmodel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpopulation\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msusceptibility\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmodel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpopulation\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdob\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtick\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 13\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m\n",
"File \u001b[0;32m~/.local/lib/python3.10/site-packages/numba-0.60.0-py3.10-linux-x86_64.egg/numba/core/dispatcher.py:658\u001b[0m, in \u001b[0;36m_DispatcherBase._explain_matching_error\u001b[0;34m(self, *args, **kws)\u001b[0m\n\u001b[1;32m 655\u001b[0m args \u001b[38;5;241m=\u001b[39m [\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtypeof_pyval(a) \u001b[38;5;28;01mfor\u001b[39;00m a \u001b[38;5;129;01min\u001b[39;00m args]\n\u001b[1;32m 656\u001b[0m msg \u001b[38;5;241m=\u001b[39m (\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNo matching definition for argument type(s) \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 657\u001b[0m \u001b[38;5;241m%\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m, \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mjoin(\u001b[38;5;28mmap\u001b[39m(\u001b[38;5;28mstr\u001b[39m, args)))\n\u001b[0;32m--> 658\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(msg)\n",
"\u001b[0;31mTypeError\u001b[0m: No matching definition for argument type(s) int64, array(uint8, 1d, C), array(uint8, 1d, C), array(int32, 1d, C), int64"
]
}
],
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