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Aug 9, 2023
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Dev #1

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51bf95b
PKG: updated requirements.txt
TomMonks Jun 20, 2023
ecb742b
PKG: __version__==0.2.0
TomMonks Jun 20, 2023
99aad6c
SIMPY: updated Scenario constructor to accept params
TomMonks Jun 28, 2023
9337e46
PKG: updated package scenario code
TomMonks Jun 28, 2023
9ecad89
PKG: version tag 1.0.0
TomMonks Jun 28, 2023
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159 changes: 122 additions & 37 deletions content/02_model_code/04_model.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -492,22 +492,110 @@
" \n",
" Passed to a model and its process classes\n",
" '''\n",
" def __init__(self, random_number_set=DEFAULT_RNG_SET):\n",
" def __init__(self, random_number_set=DEFAULT_RNG_SET,\n",
" n_triage=DEFAULT_N_TRIAGE,\n",
" n_reg=DEFAULT_N_REG,\n",
" n_exam=DEFAULT_N_EXAM,\n",
" n_trauma=DEFAULT_N_TRAUMA,\n",
" n_cubicles_1=DEFAULT_N_CUBICLES_1,\n",
" n_cubicles_2=DEFAULT_N_CUBICLES_2,\n",
" triage_mean=DEFAULT_TRIAGE_MEAN,\n",
" reg_mean=DEFAULT_REG_MEAN,\n",
" reg_var=DEFAULT_REG_VAR,\n",
" exam_mean=DEFAULT_EXAM_MEAN,\n",
" exam_var=DEFAULT_EXAM_VAR,\n",
" trauma_mean=DEFAULT_TRAUMA_MEAN,\n",
" trauma_treat_mean=DEFAULT_TRAUMA_TREAT_MEAN,\n",
" trauma_treat_var=DEFAULT_TRAUMA_TREAT_VAR,\n",
" non_trauma_treat_mean=DEFAULT_NON_TRAUMA_TREAT_MEAN,\n",
" non_trauma_treat_var=DEFAULT_NON_TRAUMA_TREAT_VAR,\n",
" non_trauma_treat_p=DEFAULT_NON_TRAUMA_TREAT_P,\n",
" prob_trauma=DEFAULT_PROB_TRAUMA):\n",
" '''\n",
" The init method sets up our defaults.\n",
" Create a scenario to parameterise the simulation model\n",
" \n",
" Parameters:\n",
" -----------\n",
" random_number_set: int, optional (default=DEFAULT_RNG_SET)\n",
" Set to control the initial seeds of each stream of pseudo\n",
" random numbers used in the model.\n",
" \n",
" n_triage: int\n",
" The number of triage cubicles\n",
" \n",
" n_reg: int\n",
" The number of registration clerks\n",
" \n",
" n_exam: int\n",
" The number of examination rooms\n",
" \n",
" n_trauma: int\n",
" The number of trauma bays for stablisation\n",
" \n",
" n_cubicles_1: int\n",
" The number of non-trauma treatment cubicles\n",
" \n",
" n_cubicles_2: int\n",
" The number of trauma treatment cubicles\n",
" \n",
" triage_mean: float\n",
" Mean duration of the triage distribution (Exponential)\n",
" \n",
" reg_mean: float\n",
" Mean duration of the registration distribution (Lognormal)\n",
" \n",
" reg_var: float\n",
" Variance of the registration distribution (Lognormal)\n",
" \n",
" exam_mean: float\n",
" Mean of the examination distribution (Normal)\n",
" \n",
" exam_var: float\n",
" Variance of the examination distribution (Normal)\n",
" \n",
" trauma_mean: float\n",
" Mean of the trauma stabilisation distribution (Exponential)\n",
" \n",
" trauma_treat_mean: float\n",
" Mean of the trauma cubicle treatment distribution (Lognormal)\n",
" \n",
" trauma_treat_var: float\n",
" Variance of the trauma cubicle treatment distribution (Lognormal)\n",
" \n",
" non_trauma_treat_mean: float\n",
" Mean of the non trauma treatment distribution\n",
" \n",
" non_trauma_treat_var: float\n",
" Variance of the non trauma treatment distribution\n",
" \n",
" non_trauma_treat_p: float\n",
" Probability non trauma patient requires treatment\n",
" \n",
" prob_trauma: float\n",
" probability that a new arrival is a trauma patient.\n",
" '''\n",
" # sampling\n",
" self.random_number_set = random_number_set\n",
" \n",
" # store parameters for sampling\n",
" self.triage_mean = triage_mean\n",
" self.reg_mean = reg_mean\n",
" self.reg_var = reg_var\n",
" self.exam_mean= exam_mean\n",
" self.exam_var = exam_var\n",
" self.trauma_mean = trauma_mean\n",
" self.trauma_treat_mean = trauma_treat_mean\n",
" self.trauma_treat_var = trauma_treat_var\n",
" self.non_trauma_treat_mean = non_trauma_treat_mean\n",
" self.non_trauma_treat_var = non_trauma_treat_var\n",
" self.non_trauma_treat_p = non_trauma_treat_p\n",
" self.prob_trauma = prob_trauma\n",
" \n",
" self.init_sampling()\n",
" \n",
" # count of each type of resource\n",
" self.init_resourse_counts()\n",
" self.init_resourse_counts(n_triage, n_reg, n_exam, n_trauma,\n",
" n_cubicles_1, n_cubicles_2)\n",
" \n",
" def set_random_no_set(self, random_number_set):\n",
" '''\n",
Expand All @@ -521,18 +609,19 @@
" self.random_number_set = random_number_set\n",
" self.init_sampling()\n",
"\n",
" def init_resourse_counts(self):\n",
" def init_resourse_counts(self, n_triage, n_reg, n_exam, n_trauma,\n",
" n_cubicles_1, n_cubicles_2):\n",
" '''\n",
" Init the counts of resources to default values...\n",
" '''\n",
" self.n_triage = DEFAULT_N_TRIAGE\n",
" self.n_reg = DEFAULT_N_REG\n",
" self.n_exam = DEFAULT_N_EXAM\n",
" self.n_trauma = DEFAULT_N_TRAUMA\n",
" self.n_triage = n_triage\n",
" self.n_reg = n_reg\n",
" self.n_exam = n_exam\n",
" self.n_trauma = n_trauma\n",
" \n",
" # non-trauma (1), trauma (2) treatment cubicles\n",
" self.n_cubicles_1 = DEFAULT_N_CUBICLES_1\n",
" self.n_cubicles_2 = DEFAULT_N_CUBICLES_2\n",
" self.n_cubicles_1 = n_cubicles_1\n",
" self.n_cubicles_2 = n_cubicles_2\n",
"\n",
" def init_sampling(self):\n",
" '''\n",
Expand All @@ -546,40 +635,40 @@
" # create distributions\n",
" \n",
" # Triage duration\n",
" self.triage_dist = Exponential(DEFAULT_TRIAGE_MEAN, \n",
" self.triage_dist = Exponential(self.triage_mean, \n",
" random_seed=self.seeds[0])\n",
" \n",
" # Registration duration (non-trauma only)\n",
" self.reg_dist = Lognormal(DEFAULT_REG_MEAN, \n",
" np.sqrt(DEFAULT_REG_VAR),\n",
" self.reg_dist = Lognormal(self.reg_mean, \n",
" np.sqrt(self.reg_var),\n",
" random_seed=self.seeds[1])\n",
" \n",
" # Evaluation (non-trauma only)\n",
" self.exam_dist = Normal(DEFAULT_EXAM_MEAN,\n",
" np.sqrt(DEFAULT_EXAM_VAR),\n",
" self.exam_dist = Normal(self.exam_mean,\n",
" np.sqrt(self.exam_var),\n",
" random_seed=self.seeds[2])\n",
" \n",
" # Trauma/stablisation duration (trauma only)\n",
" self.trauma_dist = Exponential(DEFAULT_TRAUMA_MEAN, \n",
" self.trauma_dist = Exponential(self.trauma_mean, \n",
" random_seed=self.seeds[3])\n",
" \n",
" # Non-trauma treatment\n",
" self.nt_treat_dist = Lognormal(DEFAULT_NON_TRAUMA_TREAT_MEAN, \n",
" np.sqrt(DEFAULT_NON_TRAUMA_TREAT_VAR),\n",
" self.nt_treat_dist = Lognormal(self.non_trauma_treat_mean, \n",
" np.sqrt(self.non_trauma_treat_var),\n",
" random_seed=self.seeds[4])\n",
" \n",
" # treatment of trauma patients\n",
" self.treat_dist = Lognormal(DEFAULT_TRAUMA_TREAT_MEAN, \n",
" np.sqrt(DEFAULT_TRAUMA_TREAT_VAR),\n",
" self.treat_dist = Lognormal(self.trauma_treat_mean, \n",
" np.sqrt(self.non_trauma_treat_var),\n",
" random_seed=self.seeds[5])\n",
" \n",
" # probability of non-trauma patient requiring treatment\n",
" self.nt_p_treat_dist = Bernoulli(DEFAULT_NON_TRAUMA_TREAT_P, \n",
" self.nt_p_treat_dist = Bernoulli(self.non_trauma_treat_p, \n",
" random_seed=self.seeds[6])\n",
" \n",
" \n",
" # probability of non-trauma versus trauma patient\n",
" self.p_trauma_dist = Bernoulli(DEFAULT_PROB_TRAUMA, \n",
" self.p_trauma_dist = Bernoulli(self.prob_trauma, \n",
" random_seed=self.seeds[7])\n",
" \n",
" # init sampling for non-stationary poisson process\n",
Expand Down Expand Up @@ -752,7 +841,7 @@
"metadata": {},
"outputs": [],
"source": [
"class NonTraumaPathway(object):\n",
"class NonTraumaPathway:\n",
" '''\n",
" Encapsulates the process a patient with minor injuries and illness.\n",
" \n",
Expand Down Expand Up @@ -1536,8 +1625,8 @@
"text": [
"Running multiple replications => done.\n",
"\n",
"CPU times: user 2.52 s, sys: 42.7 ms, total: 2.56 s\n",
"Wall time: 3.88 s\n"
"CPU times: user 2.09 s, sys: 12.9 ms, total: 2.11 s\n",
"Wall time: 3.46 s\n"
]
},
{
Expand Down Expand Up @@ -1821,20 +1910,16 @@
" scenarios['base'] = Scenario()\n",
" \n",
" # extra triage capacity\n",
" scenarios['triage+1'] = Scenario()\n",
" scenarios['triage+1'].n_triage += 1\n",
" scenarios['triage+1'] = Scenario(n_triage=DEFAULT_N_TRIAGE+1)\n",
" \n",
" # extra examination capacity\n",
" scenarios['exam+1'] = Scenario()\n",
" scenarios['exam+1'].n_exam += 1\n",
" scenarios['exam+1'] = Scenario(n_exam=DEFAULT_N_EXAM+1)\n",
" \n",
" # extra non-trauma treatment capacity\n",
" scenarios['treat+1'] = Scenario()\n",
" scenarios['treat+1'].n_cubicles_1 += 1\n",
" scenarios['treat+1'] = Scenario(n_cubicles_1=DEFAULT_N_CUBICLES_1+1)\n",
" \n",
" scenarios['triage+exam'] = Scenario()\n",
" scenarios['triage+exam'].n_triage += 1\n",
" scenarios['triage+exam'].n_exam += 1\n",
" scenarios['triage+exam'] = Scenario(n_triage=DEFAULT_N_TRIAGE+1,\n",
" n_exam=DEFAULT_N_EXAM+1)\n",
" \n",
" return scenarios"
]
Expand Down Expand Up @@ -2170,7 +2255,7 @@
},
{
"cell_type": "code",
"execution_count": 91,
"execution_count": 26,
"id": "4d2d0e59",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -2272,7 +2357,7 @@
"5 Trauma treatment 168.27 209.12 195.16 150.37 193.69"
]
},
"execution_count": 91,
"execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -2298,7 +2383,7 @@
},
{
"cell_type": "code",
"execution_count": 123,
"execution_count": 27,
"id": "e6453c53",
"metadata": {},
"outputs": [
Expand Down
10 changes: 5 additions & 5 deletions src/requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
matplotlib==3.3.4
numpy==1.19.2
pandas==1.2.3
scipy==1.6.1
simpy==4.0.1
matplotlib>=3.3.4
numpy>=1.19.2
pandas>=1.2.3
scipy>=1.6.1
simpy>=4.0.1
Empty file removed src/test_pacakge.ipynb
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