Marginal value calculation

[hyunjimoon]

Goal:

• compare the marginal increase and decrease of death generated from 1% increase of variant_acuity_multiplier across 52 regions
• first to compare sensitivity of major costs [death + hospitalization + ] Q1. what other components of cost do we have?

• Equation:

• compare $\epsilon\alpha(O{1})$ each variable to argue \frac{\partial{}}{{} Hazhir explained variant_accuity_multiplier's elasticity as the above. Q2. what value should be used for G in marginal value of vaccine (from pic. above)? Q3. is it correct $\epsilon_{\alpha}(O1)$ is marginal value of acuity whereas $\epsilon{\alpha}(O1d) - \epsilon{\alpha}(O_1B)$ is marginal value of vaccine?

*Variant Impact on Immunity Loss Time[Omicron]
*Variant Accuity Multiplier[Omicron]
Weight on Aggregate Death Hazard[VS]
Immunity Loss Time[NVx]
Immunity Loss Time[Vx]
Multiplier Vx Acuity[NVx]
Variant Transmission Multiplier[Delta]
Variant Transmission Multiplier[Omicron]
Sensitivity to Weather
Variant Vaccine Effectiveness Reduction[Omicron]
TestCoverageTime
TestCoverageSensitivity
dalp
ialp
Sensitivity Post Mortem Testing to Pressures
InputAve[PriorEndoAve]
Variant Intro Start Time[Rgn]
alpR[Rgn]
Base Fatality Rate for Unit Acuity[Rgn]
Baseline Daily Fraction Susceptible Seeking Tests[Rgn]
Confirmation Impact on Contact[Rgn]
Covid Acuity Relative to Flu[Rgn]
DeathReportingDelay[Rgn]
Dread Factor in Risk Perception[Rgn]
Impact of Population Density on Hospital Availability[Rgn]
Impact of Treatment on Fatality Rate[Rgn]
Learning and Death Reduction Rate[Rgn]
Min Contact Fraction[Rgn]
Multiplier Recent Infections to Test[Rgn]
Multiplier Transmission Risk For Asymptomatic[Rgn]
Patient Zero Arrival Time[Rgn]
Reference COVID Hospitalization Fraction Confirmed[Rgn]
Reference Force of Infection[Rgn]
Sensitivity of Fatality Rate to Acuity[Rgn]
Sensitivity of Contact Reduction to Utility[Rgn]
Strength of Adherence Fatigue[Rgn]
Time to Downgrade Risk[Rgn]
Time to Upgrade Risk[Rgn]
Total Asymptomatic Fraction[Rgn]
Weight on Reported Probability of Infection[Rgn]
Variant Intro Start Time2[Rgn]
 
Output Gap Decay Time (dy)
Direct Infection Impact Scale (ds)
Infection Duration (ti)
Mitigation Learning Decay Time (dl)
Learning Time (tl)
Psychological Exponent (epsilon)
Psychological Scale (beta)
State CRN Proportion (alpha)

Do we expect $\epsilon_{\alpha}(O)$ to increase or decrease if every region's variant accuity multiplier is increased by 1%, what would have been the death increase or decrease? One step further, what

[hyunjimoon]

@Batman-q96 we ended up with the following, during sensitivity calculating. logging for Thursday init

1. TypeError: 'NoneType' object is not subscriptable
2. KeyError

   
   C:\Users\amoon\Miniconda3\envs\VaccineMisinf\python.exe C:/Users/amoon/Dropbox/WINcode/VaccineMisinf/V79/VST_Sensitivity.py 
   Initialising <VST.vst.vst.Script object at 0x000002B31314A2C0>
   Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
   Initialising Covidparam_Sensitivity!
   Return code is 3221225477
   C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
   full_output_df = full_output_df.append(
   Initialising <VST.vst.vst.Script object at 0x000002B31314A170>
   Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
   Initialising Covidparam_Sensitivity!
   Return code is 3221225477
   C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
   full_output_df = full_output_df.append(
                                              1000
   Time                                               
   a[Alabama,Naive]                         1000.00000
   a[Alabama,NVx]                              3.01973
   a[Alabama,Vx]                              15.69550
   a[Alaska,Naive]                           902.34700
   a[Alaska,NVx]                               3.98111
   ...                                             ...
   Real World GDP Data (Gt)[Virginia]              NaN
   Real World GDP Data (Gt)[Washington]            NaN
   Real World GDP Data (Gt)[West Virginia]         NaN
   Real World GDP Data (Gt)[Wisconsin]             NaN
   Real World GDP Data (Gt)[Wyoming]               NaN

[58936 rows x 1 columns] Initialising <VST.vst.vst.Script object at 0x000002B313442440> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Variant! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( 1000 Time
a[Alabama,Naive] 1000.00000 a[Alabama,NVx] 3.01973 a[Alabama,Vx] 15.69550 a[Alaska,Naive] 902.34700 a[Alaska,NVx] 3.98111 ... ... Real World GDP Data (Gt)[Virginia] NaN Real World GDP Data (Gt)[Washington] NaN Real World GDP Data (Gt)[West Virginia] NaN Real World GDP Data (Gt)[Wisconsin] NaN Real World GDP Data (Gt)[Wyoming] NaN

[58936 rows x 1 columns] Initialising <VST.vst.vst.Script object at 0x000002B313440970> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Variant! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( 0 0.208898 1 -1.075735 2 -0.595222 3 -0.039936 4 2.015113 ...
203 0.000000 204 0.000000 205 0.000000 206 0.000000 207 0.000000 Name: Variant Accuity Multiplier[Delta], Length: 208, dtype: float64 Initialising <VST.vst.vst.Script object at 0x000002B313441AE0> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Variant! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( Initialising <VST.vst.vst.Script object at 0x000002B313441F30> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Variant! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:103: RuntimeWarning: invalid value encountered in double_scalars new[0]=change[0]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:104: RuntimeWarning: invalid value encountered in double_scalars new[1]=change[1]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:105: RuntimeWarning: invalid value encountered in double_scalars new[2]=change[2]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:107: RuntimeWarning: invalid value encountered in double_scalars new[i-513]=change[i-513]/change[i] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:108: RuntimeWarning: invalid value encountered in double_scalars new[i-512]=change[i-512]/change[i] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:109: RuntimeWarning: invalid value encountered in double_scalars new[i-511]=change[i-511]/change[i] 0 NaN 1 NaN 2 NaN 3 -100.0 4 NaN ...
203 -100.0 204 -100.0 205 -100.0 206 -100.0 207 -100.0 Name: Variant Accuity Multiplier[Omicron], Length: 208, dtype: float64 Initialising <VST.vst.vst.Script object at 0x000002B313443550> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Variant! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( Initialising <VST.vst.vst.Script object at 0x000002B3134414E0> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Variant! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:103: RuntimeWarning: invalid value encountered in double_scalars new[0]=change[0]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:104: RuntimeWarning: invalid value encountered in double_scalars new[1]=change[1]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:105: RuntimeWarning: invalid value encountered in double_scalars new[2]=change[2]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:107: RuntimeWarning: invalid value encountered in double_scalars new[i-513]=change[i-513]/change[i] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:108: RuntimeWarning: invalid value encountered in double_scalars new[i-512]=change[i-512]/change[i] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:109: RuntimeWarning: invalid value encountered in double_scalars new[i-511]=change[i-511]/change[i] 0 NaN 1 NaN 2 NaN 3 -100.0 4 NaN ...
203 -100.0 204 -100.0 205 -100.0 206 -100.0 207 -100.0 Name: Variant Accuity Multiplier[BA5], Length: 208, dtype: float64 Initialising <VST.vst.vst.Script object at 0x000002B313443B80> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Immunity! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( Initialising <VST.vst.vst.Script object at 0x000002B3134430A0> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Immunity! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( 0 0.024125 1 0.371747 2 0.158730 3 0.000000 4 -0.000000 ...
203 0.000000 204 0.000000 205 0.000000 206 0.000000 207 0.000000 Name: Immunity Loss Time[Vx], Length: 208, dtype: float64 Initialising <VST.vst.vst.Script object at 0x000002B313442E00> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Immunity! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( Initialising <VST.vst.vst.Script object at 0x000002B313443BB0> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Immunity! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:103: RuntimeWarning: divide by zero encountered in double_scalars new[0]=change[0]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:104: RuntimeWarning: divide by zero encountered in double_scalars new[1]=change[1]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:105: RuntimeWarning: divide by zero encountered in double_scalars new[2]=change[2]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:107: RuntimeWarning: divide by zero encountered in double_scalars new[i-513]=change[i-513]/change[i] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:108: RuntimeWarning: divide by zero encountered in double_scalars new[i-512]=change[i-512]/change[i] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:109: RuntimeWarning: divide by zero encountered in double_scalars new[i-511]=change[i-511]/change[i] 0 inf 1 inf 2 inf 3 -100.0 4 inf ...
203 -100.0 204 -100.0 205 -100.0 206 -100.0 207 -100.0 Name: Immunity Loss Time[NVx], Length: 208, dtype: float64 1000 Time
a[Alabama,Naive] 1000.00000 a[Alabama,NVx] 3.01973 a[Alabama,Vx] 15.69550 a[Alaska,Naive] 902.34700 a[Alaska,NVx] 3.98111 ... ... Real World GDP Data (Gt)[Virginia] NaN Real World GDP Data (Gt)[Washington] NaN Real World GDP Data (Gt)[West Virginia] NaN Real World GDP Data (Gt)[Wisconsin] NaN Real World GDP Data (Gt)[Wyoming] NaN

[58936 rows x 1 columns] Traceback (most recent call last): File "C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py", line 130, in find_marginal_vax_eff param_base = vst_text.get_value("V79-OptimTest.out", param_name) File "C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\VST\vst\vst_text.py", line 57, in get_value value = float((regex.search(varregex, filetext))[0]) # Convert to numeric TypeError: 'NoneType' object is not subscriptable

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py", line 153, in results = find_marginal_vax_eff(param, 1.01) File "C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py", line 135, in find_marginal_vax_eff param_base = df.loc[param_name][0] File "C:\Users\amoon\Miniconda3\envs\VaccineMisinf\lib\site-packages\pandas\core\indexing.py", line 967, in getitem return self._getitem_axis(maybe_callable, axis=axis) File "C:\Users\amoon\Miniconda3\envs\VaccineMisinf\lib\site-packages\pandas\core\indexing.py", line 1194, in _getitem_axis return self._getitem_iterable(key, axis=axis) File "C:\Users\amoon\Miniconda3\envs\VaccineMisinf\lib\site-packages\pandas\core\indexing.py", line 1132, in _getitem_iterable keyarr, indexer = self._get_listlike_indexer(key, axis) File "C:\Users\amoon\Miniconda3\envs\VaccineMisinf\lib\site-packages\pandas\core\indexing.py", line 1330, in _get_listlike_indexer keyarr, indexer = ax._get_indexer_strict(key, axis_name) File "C:\Users\amoon\Miniconda3\envs\VaccineMisinf\lib\site-packages\pandas\core\indexes\base.py", line 5796, in _get_indexer_strict self._raise_if_missing(keyarr, indexer, axis_name) File "C:\Users\amoon\Miniconda3\envs\VaccineMisinf\lib\site-packages\pandas\core\indexes\base.py", line 5859, in _raise_if_missing raise KeyError(f"{not_found} not in index") KeyError: "['Weight on Reported Probability of Infection[Northern Mariana Islands]', 'Weight on Reported Probability of Infection[U.S. Virgin Islands]', 'Weight on Reported Probability of Infection[Guam]', 'Weight on Reported Probability of Infection[American Samoa]', 'Weight on Reported Probability of Infection[United States Minor Outlying Islands]', 'Weight on Reported Probability of Infection[Puerto Rico]'] not in index"

Process finished with exit code 1

[Batman-q96]

Looks like we mistyped a parameter value. Not sure which

On Sun, Dec 11, 2022, 8:10 PM Angie.H Moon @.***> wrote:

@Batman-q96 https://github.com/Batman-q96 we ended up with the following, during sensitivity calculating.

1. TypeError: 'NoneType' object is not subscriptable
2. KeyError

C:\Users\amoon\Miniconda3\envs\VaccineMisinf\python.exe C:/Users/amoon/Dropbox/WINcode/VaccineMisinf/V79/VST_Sensitivity.py Initialising <VST.vst.vst.Script object at 0x000002B31314A2C0> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Sensitivity! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( Initialising <VST.vst.vst.Script object at 0x000002B31314A170> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Sensitivity! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( 1000 Time a[Alabama,Naive] 1000.00000 a[Alabama,NVx] 3.01973 a[Alabama,Vx] 15.69550 a[Alaska,Naive] 902.34700 a[Alaska,NVx] 3.98111 ... ... Real World GDP Data (Gt)[Virginia] NaN Real World GDP Data (Gt)[Washington] NaN Real World GDP Data (Gt)[West Virginia] NaN Real World GDP Data (Gt)[Wisconsin] NaN Real World GDP Data (Gt)[Wyoming] NaN

[58936 rows x 1 columns] Initialising <VST.vst.vst.Script object at 0x000002B313442440> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Variant! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( 1000 Time a[Alabama,Naive] 1000.00000 a[Alabama,NVx] 3.01973 a[Alabama,Vx] 15.69550 a[Alaska,Naive] 902.34700 a[Alaska,NVx] 3.98111 ... ... Real World GDP Data (Gt)[Virginia] NaN Real World GDP Data (Gt)[Washington] NaN Real World GDP Data (Gt)[West Virginia] NaN Real World GDP Data (Gt)[Wisconsin] NaN Real World GDP Data (Gt)[Wyoming] NaN

[58936 rows x 1 columns] Initialising <VST.vst.vst.Script object at 0x000002B313440970> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Variant! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( 0 0.208898 1 -1.075735 2 -0.595222 3 -0.039936 4 2.015113 ... 203 0.000000 204 0.000000 205 0.000000 206 0.000000 207 0.000000 Name: Variant Accuity Multiplier[Delta], Length: 208, dtype: float64 Initialising <VST.vst.vst.Script object at 0x000002B313441AE0> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Variant! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( Initialising <VST.vst.vst.Script object at 0x000002B313441F30> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Variant! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:103: RuntimeWarning: invalid value encountered in double_scalars new[0]=change[0]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:104: RuntimeWarning: invalid value encountered in double_scalars new[1]=change[1]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:105: RuntimeWarning: invalid value encountered in double_scalars new[2]=change[2]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:107: RuntimeWarning: invalid value encountered in double_scalars new[i-513]=change[i-513]/change[i] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:108: RuntimeWarning: invalid value encountered in double_scalars new[i-512]=change[i-512]/change[i] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:109: RuntimeWarning: invalid value encountered in double_scalars new[i-511]=change[i-511]/change[i] 0 NaN 1 NaN 2 NaN 3 -100.0 4 NaN ... 203 -100.0 204 -100.0 205 -100.0 206 -100.0 207 -100.0 Name: Variant Accuity Multiplier[Omicron], Length: 208, dtype: float64 Initialising <VST.vst.vst.Script object at 0x000002B313443550> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Variant! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( Initialising <VST.vst.vst.Script object at 0x000002B3134414E0> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Variant! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:103: RuntimeWarning: invalid value encountered in double_scalars new[0]=change[0]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:104: RuntimeWarning: invalid value encountered in double_scalars new[1]=change[1]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:105: RuntimeWarning: invalid value encountered in double_scalars new[2]=change[2]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:107: RuntimeWarning: invalid value encountered in double_scalars new[i-513]=change[i-513]/change[i] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:108: RuntimeWarning: invalid value encountered in double_scalars new[i-512]=change[i-512]/change[i] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:109: RuntimeWarning: invalid value encountered in double_scalars new[i-511]=change[i-511]/change[i] 0 NaN 1 NaN 2 NaN 3 -100.0 4 NaN ... 203 -100.0 204 -100.0 205 -100.0 206 -100.0 207 -100.0 Name: Variant Accuity Multiplier[BA5], Length: 208, dtype: float64 Initialising <VST.vst.vst.Script object at 0x000002B313443B80> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Immunity! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( Initialising <VST.vst.vst.Script object at 0x000002B3134430A0> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Immunity! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( 0 0.024125 1 0.371747 2 0.158730 3 0.000000 4 -0.000000 ... 203 0.000000 204 0.000000 205 0.000000 206 0.000000 207 0.000000 Name: Immunity Loss Time[Vx], Length: 208, dtype: float64 Initialising <VST.vst.vst.Script object at 0x000002B313442E00> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Immunity! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( Initialising <VST.vst.vst.Script object at 0x000002B313443BB0> Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||! Initialising Covidparam_Immunity! Return code is 3221225477 C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:142: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. full_output_df = full_output_df.append( C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:103: RuntimeWarning: divide by zero encountered in double_scalars new[0]=change[0]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:104: RuntimeWarning: divide by zero encountered in double_scalars new[1]=change[1]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:105: RuntimeWarning: divide by zero encountered in double_scalars new[2]=change[2]/change[3] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:107: RuntimeWarning: divide by zero encountered in double_scalars new[i-513]=change[i-513]/change[i] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:108: RuntimeWarning: divide by zero encountered in double_scalars new[i-512]=change[i-512]/change[i] C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:109: RuntimeWarning: divide by zero encountered in double_scalars new[i-511]=change[i-511]/change[i] 0 inf 1 inf 2 inf 3 -100.0 4 inf ... 203 -100.0 204 -100.0 205 -100.0 206 -100.0 207 -100.0 Name: Immunity Loss Time[NVx], Length: 208, dtype: float64 1000 Time a[Alabama,Naive] 1000.00000 a[Alabama,NVx] 3.01973 a[Alabama,Vx] 15.69550 a[Alaska,Naive] 902.34700 a[Alaska,NVx] 3.98111 ... ... Real World GDP Data (Gt)[Virginia] NaN Real World GDP Data (Gt)[Washington] NaN Real World GDP Data (Gt)[West Virginia] NaN Real World GDP Data (Gt)[Wisconsin] NaN Real World GDP Data (Gt)[Wyoming] NaN

[58936 rows x 1 columns] Traceback (most recent call last): File "C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py", line 130, in find_marginal_vax_eff param_base = vst_text.get_value("V79-OptimTest.out", param_name) File "C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\VST\vst\vst_text.py", line 57, in get_value value = float((regex.search(varregex, filetext))[0]) # Convert to numeric TypeError: 'NoneType' object is not subscriptable

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py", line 153, in results = find_marginal_vax_eff(param, 1.01) File "C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py", line 135, in find_marginal_vax_eff param_base = df.loc[param_name][0] File "C:\Users\amoon\Miniconda3\envs\VaccineMisinf\lib\site-packages\pandas\core\indexing.py", line 967, in getitem return self._getitem_axis(maybe_callable, axis=axis) File "C:\Users\amoon\Miniconda3\envs\VaccineMisinf\lib\site-packages\pandas\core\indexing.py", line 1194, in _getitem_axis return self._getitem_iterable(key, axis=axis) File "C:\Users\amoon\Miniconda3\envs\VaccineMisinf\lib\site-packages\pandas\core\indexing.py", line 1132, in _getitem_iterable keyarr, indexer = self._get_listlike_indexer(key, axis) File "C:\Users\amoon\Miniconda3\envs\VaccineMisinf\lib\site-packages\pandas\core\indexing.py", line 1330, in _get_listlike_indexer keyarr, indexer = ax._get_indexer_strict(key, axis_name) File "C:\Users\amoon\Miniconda3\envs\VaccineMisinf\lib\site-packages\pandas\core\indexes\base.py", line 5796, in _get_indexer_strict self._raise_if_missing(keyarr, indexer, axis_name) File "C:\Users\amoon\Miniconda3\envs\VaccineMisinf\lib\site-packages\pandas\core\indexes\base.py", line 5859, in _raise_if_missing raise KeyError(f"{not_found} not in index") KeyError: "['Weight on Reported Probability of Infection[Northern Mariana Islands]', 'Weight on Reported Probability of Infection[U.S. Virgin Islands]', 'Weight on Reported Probability of Infection[Guam]', 'Weight on Reported Probability of Infection[American Samoa]', 'Weight on Reported Probability of Infection[United States Minor Outlying Islands]', 'Weight on Reported Probability of Infection[Puerto Rico]'] not in index"

Process finished with exit code 1

— Reply to this email directly, view it on GitHub https://github.com/hyunjimoon/VaccineMisinf/issues/1#issuecomment-1345730028, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKCD4KEZCDA62DV63AADVI3WMZ3RVANCNFSM6AAAAAAREGEBLA . You are receiving this because you were mentioned.Message ID: @.***>

[hyunjimoon]

We added in avg cost calculations in addition to marginal, and generated values for both sets of data. These values were not based on calibrated result of epidemic or econ model so the values are non-interpretable. Especially for economic optimization, after reducing the degree of freedom descibed in #4 the fit to data became poor.

Data results

0      0.208898
1     -1.075735
2     -0.595222
3     -0.039936
4      2.015113
         ...   
203    0.000000
204    0.000000
205    0.000000
206    0.000000
207    0.000000
Length: 208, dtype: float64
0      0.028180
1      0.000505
2     -0.000249
3      0.000003
4      0.028621
         ...   
203    0.000003
204    0.000002
205    0.000004
206    0.000002
207    0.000002
Length: 208, dtype: float64
Initialising <VST.vst.vst.Script object at 0x000002B2ABDCF700>
Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
Initialising Covidparam_Variant!
Return code is 3221225477
C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:138: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  full_output_df = full_output_df.append(
Initialising <VST.vst.vst.Script object at 0x000002B2ABDCE740>
Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
Initialising Covidparam_Variant!
Return code is 3221225477
C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:138: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  full_output_df = full_output_df.append(
Initialising <VST.vst.vst.Script object at 0x000002B2ABDCEB30>
Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
Initialising Covidparam_Variant!
Return code is 3221225477
C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:138: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  full_output_df = full_output_df.append(
0      1.133896
1     -0.371747
2     -0.317460
3      0.000000
4      0.755668
         ...   
203    0.000000
204    0.000000
205    0.000000
206    0.000000
207    0.000000
Length: 208, dtype: float64
0      6.298320e-03
1     -1.523313e-03
2     -9.856388e-04
3      6.257271e-07
4      5.469001e-03
           ...     
203    7.652563e-07
204    4.796463e-07
205    1.617640e-06
206    2.845656e-07
207    4.135425e-07
Length: 208, dtype: float64
Initialising <VST.vst.vst.Script object at 0x000002B2ABDCD210>
Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
Initialising Covidparam_Variant!
Return code is 3221225477
C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:138: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  full_output_df = full_output_df.append(
Initialising <VST.vst.vst.Script object at 0x000002B2ABDCF040>
Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
Initialising Covidparam_Variant!
Return code is 3221225477
C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:138: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  full_output_df = full_output_df.append(
Initialising <VST.vst.vst.Script object at 0x000002B2ABDCEFE0>
Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
Initialising Covidparam_Variant!
Return code is 3221225477
C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:138: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  full_output_df = full_output_df.append(
0      5.548854e-01
1      7.177044e-12
2     -1.587302e-01
3      0.000000e+00
4     -0.000000e+00
           ...     
203    0.000000e+00
204    0.000000e+00
205    0.000000e+00
206    0.000000e+00
207    0.000000e+00
Length: 208, dtype: float64
0      2.425487e-03
1      4.057763e-04
2      2.108006e-04
3      2.737556e-07
4      1.458310e-03
           ...     
203    3.222132e-07
204    2.717996e-07
205    5.108335e-07
206    1.659966e-07
207    2.363100e-07
Length: 208, dtype: float64
Initialising <VST.vst.vst.Script object at 0x000002B2ABDCF010>
Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
Initialising Covidparam_Immunity!
Return code is 3221225477
C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:138: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  full_output_df = full_output_df.append(
Initialising <VST.vst.vst.Script object at 0x000002B2ABDCD720>
Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
Initialising Covidparam_Immunity!
Return code is 3221225477
C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:138: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  full_output_df = full_output_df.append(
Initialising <VST.vst.vst.Script object at 0x000002B2ABDCDA20>
Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
Initialising Covidparam_Immunity!
Return code is 3221225477
C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:138: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  full_output_df = full_output_df.append(
0      0.024125
1      0.371747
2      0.158730
3      0.000000
4     -0.000000
         ...   
203    0.000000
204    0.000000
205    0.000000
206    0.000000
207    0.000000
Length: 208, dtype: float64
0      0.000370
1      0.003147
2      0.003342
3      0.000000
4      0.000690
         ...   
203    0.000000
204    0.000000
205    0.000000
206    0.000000
207    0.000000
Length: 208, dtype: float64
Initialising <VST.vst.vst.Script object at 0x000002B2ABDCE800>
Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
Initialising Covidparam_Immunity!
Return code is 3221225477
C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:138: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  full_output_df = full_output_df.append(
Initialising <VST.vst.vst.Script object at 0x000002B2ABDCF1F0>
Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
Initialising Covidparam_Immunity!
Return code is 3221225477
C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:138: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  full_output_df = full_output_df.append(
Initialising <VST.vst.vst.Script object at 0x000002B2ABDCF4F0>
Overwriting default savecmd with VDF2CSV|!|!|../SAVEFILE.txt|||!
Initialising Covidparam_Immunity!
Return code is 3221225477
C:\Users\amoon\Dropbox\WINcode\VaccineMisinf\V79\VST_Sensitivity.py:138: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  full_output_df = full_output_df.append(
0     -0.844391
1     -0.371747
2     -1.269841
3      0.000000
4     -2.015113
         ...   
203    0.000000
204    0.000000
205    0.000000
206    0.000000
207    0.000000
Length: 208, dtype: float64
0     -5.568353e-03
1     -1.928192e-03
2     -4.854166e-03
3     -5.475112e-07
4     -4.674576e-03
           ...     
203   -5.907242e-07
204   -2.877878e-07
205   -8.513892e-07
206   -2.134242e-07
207   -3.840038e-07
Length: 208, dtype: float64

[hyunjimoon]

I compared where we are heading with Hazhir's paper design and listed some questions (noted as Q).

our state

Q1. what do you think about the rows? compared to paper design, I don't know whether "Responsiveness to risk (consider excluding it all together) , Vaccine costs per person, Vaccine efficacy against death and transmission" are included in 22 parameters

Q2. how are bold boxes in the column, as our final output? Separating each cost component for sensitivity might be informative, but for vaccination value elasticity, I think separating costs might confuse the readers, considering its complexity.

Q3. (to Babak and Hazhir) for plots, we are aiming for tornado plots which sorts by sensitivity; what parameters do you expect/experienced/literature say to be important for both sensitivity and vaccination value elasticity? Having this feel would help us greatly for sanity check. We thought immunity loss time of vaccinated and naive would be important.

Q4. (to Hazhir) why do we have vaccine immunity loss time for non-vaccinated?

Hazhir's paper design summary

hypothesis: ignoring behavioral response will change the outcomes and reduces fit significantly

data:

1. Marginal and Average value of vaccination (per person) broken down into lives, hospitalizations, GDP loss; consider future projections in value of vaccination vs. only historical outcomes.

2. Sensitivity of these outcomes to key model parameters/assumptions:

   • Duration of immunity (after natural and vaccine immunity)
   • Baseline transmission rates (3a)
   • Responsiveness to risk (consider excluding it all together)
   • Vaccine costs per person
   • Vaccine efficacy against death and transmission

automated summary statistics

• results of the vensim run (below csv generated from VST attached for costs from the final epidemic + econ combined model run which reflect econ calibration, but not epidemic calibration) has zero hospitalization and death cost for all time points. Covidparam_Sensitivity.csv