4 add files for lct paper #7

lenaploetzke · 2025-01-24T13:54:35Z

Changes and Information

Please briefly list the changes (main added features, changed items, or corrected bugs) made:

Added simulation scripts, shell scripts (to get all the data with one command), and plot scripts used to create the figures of the LCT paper.
I validated that the figures in the paper look the same as the outputs using these files.

If need be, add additional information and what the reviewer should look out for in particular:

I tried to document what is happening really detailed, such that my work can be easily continued. If I missed out anything, please comment.

Functionality is taken from SciCompMod/memilio#1164 with adapted paths.

Closes #4

annawendler

This is very good! :) I just made a few comments regarding documentation.

annawendler · 2025-01-28T16:26:23Z

2024_Ploetzke_et_al_Revisiting_Linear_Chain_Trick/README.md

+## Overview
+Below is an overview of the files and the paper sections they belong to.
+
+- Section 4.2: The file [lct_impact_distribution_assumption](lct_impact_distribution_assumption.cpp) provides the functionality to run simulations to assess the impact of the distribution assumption or different numbers of subcompartments. The dynamics at change points and epidemic peaks can be examined using this script. The population is not divided into age groups for these experiments. All simulation results are created and saved in `.h5` files when the shell script [get_data_numerical_experiments](get_data_numerical_experiments.sh) is executed. The visualizations of these simulation results in the paper were created using the python script [plot_numerical_experiments](plot_numerical_experiments.py).


Suggested change

- Section 4.2: The file [lct_impact_distribution_assumption](lct_impact_distribution_assumption.cpp) provides the functionality to run simulations to assess the impact of the distribution assumption or different numbers of subcompartments. The dynamics at change points and epidemic peaks can be examined using this script. The population is not divided into age groups for these experiments. All simulation results are created and saved in `.h5` files when the shell script [get_data_numerical_experiments](get_data_numerical_experiments.sh) is executed. The visualizations of these simulation results in the paper were created using the python script [plot_numerical_experiments](plot_numerical_experiments.py).

- Section 4.2: The file [lct_impact_distribution_assumption](lct_impact_distribution_assumption.cpp) provides the functionality to run simulations to assess the impact of the distribution assumption by choosing different numbers of subcompartments. The dynamics at change points and epidemic peaks can be examined using this script. The population is not divided into age groups for these experiments. All simulation results are created and saved in `.h5` files when the shell script [get_data_numerical_experiments](get_data_numerical_experiments.sh) is executed. The visualizations of these simulation results in the paper were created using the python script [plot_numerical_experiments](plot_numerical_experiments.py).

annawendler · 2025-01-28T16:26:33Z

2024_Ploetzke_et_al_Revisiting_Linear_Chain_Trick/README.md

+
+- Section 4.2: The file [lct_impact_distribution_assumption](lct_impact_distribution_assumption.cpp) provides the functionality to run simulations to assess the impact of the distribution assumption or different numbers of subcompartments. The dynamics at change points and epidemic peaks can be examined using this script. The population is not divided into age groups for these experiments. All simulation results are created and saved in `.h5` files when the shell script [get_data_numerical_experiments](get_data_numerical_experiments.sh) is executed. The visualizations of these simulation results in the paper were created using the python script [plot_numerical_experiments](plot_numerical_experiments.py).
+
+- Section 4.3: With the file [lct_impact_age_resolution](lct_impact_age_resolution.cpp), one can run simulations to assess the impact of including an age resolution. The simulation results are created and saved together with the results for section 4.2 with the shellscript [get_data_numerical_experiments](get_data_numerical_experiments.sh). The visualizations are also created with [plot_numerical_experiments](plot_numerical_experiments.py).


Suggested change

- Section 4.3: With the file [lct_impact_age_resolution](lct_impact_age_resolution.cpp), one can run simulations to assess the impact of including an age resolution. The simulation results are created and saved together with the results for section 4.2 with the shellscript [get_data_numerical_experiments](get_data_numerical_experiments.sh). The visualizations are also created with [plot_numerical_experiments](plot_numerical_experiments.py).

- Section 4.3: With the file [lct_impact_age_resolution](lct_impact_age_resolution.cpp), one can run simulations to assess the impact of including an age resolution into the model. The simulation results are created and saved together with the results for section 4.2 with the shellscript [get_data_numerical_experiments](get_data_numerical_experiments.sh). The visualizations are also created with [plot_numerical_experiments](plot_numerical_experiments.py).

annawendler · 2025-01-28T16:26:41Z

2024_Ploetzke_et_al_Revisiting_Linear_Chain_Trick/README.md

+
+- Section 4.3: With the file [lct_impact_age_resolution](lct_impact_age_resolution.cpp), one can run simulations to assess the impact of including an age resolution. The simulation results are created and saved together with the results for section 4.2 with the shellscript [get_data_numerical_experiments](get_data_numerical_experiments.sh). The visualizations are also created with [plot_numerical_experiments](plot_numerical_experiments.py).
+
+- Section 4.4: Run time measurements are possible with the file [lct_runtime](lct_runtime.cpp). `OpenMP` is used to measure the run times. The target `lct_runtime` is only built if the option `MEMILIO_ENABLE_OPENMP` is enabled. The Slurm script [get_runtimes_lct](get_runtimes_lct.sh) can be used to define a job to measure the run time for different numbers of subcompartments. This script can be easily adapted to use an adaptive solver. To use the optimization flag `-O0`, uncomment the suitable line in the [CMakeLists file](CMakeLists.txt). Visualizations of the run times in the paper were created using the python script [plot_runtimes_lct](plot_runtimes_lct.py).


Suggested change

- Section 4.4: Run time measurements are possible with the file [lct_runtime](lct_runtime.cpp). `OpenMP` is used to measure the run times. The target `lct_runtime` is only built if the option `MEMILIO_ENABLE_OPENMP` is enabled. The Slurm script [get_runtimes_lct](get_runtimes_lct.sh) can be used to define a job to measure the run time for different numbers of subcompartments. This script can be easily adapted to use an adaptive solver. To use the optimization flag `-O0`, uncomment the suitable line in the [CMakeLists file](CMakeLists.txt). Visualizations of the run times in the paper were created using the python script [plot_runtimes_lct](plot_runtimes_lct.py).

- Section 4.4: Run time measurements are possible with the file [lct_runtime](lct_runtime.cpp). `OpenMP` is used to measure the run times. The target `lct_runtime` is only built if the option `MEMILIO_ENABLE_OPENMP` is enabled. The Slurm script [get_runtimes_lct](get_runtimes_lct.sh) can be used to define a job to measure the run time for different numbers of subcompartments. This script can be easily adapted for the use of an adaptive solver. To use the optimization flag `-O0`, uncomment the suitable line in the [CMakeLists file](CMakeLists.txt). Visualizations of the run times in the paper were created using the python script [plot_runtimes_lct](plot_runtimes_lct.py).

annawendler · 2025-01-28T16:29:40Z

2024_Ploetzke_et_al_Revisiting_Linear_Chain_Trick/download_data.py

+    if not os.path.isdir(data_folder):
+        os.makedirs(data_folder)
+
+    # Download data in format required.


Can you add a comment why you download the case data twice, once with and once without moving average or what the different data sets are used for?

annawendler · 2025-01-28T16:29:48Z

2024_Ploetzke_et_al_Revisiting_Linear_Chain_Trick/get_data_numerical_experiments.sh

+
+# Fifth case: Increase the effective reproduction number at simulation day 2 to different values and 
+# simulate for 200 days to compare epidemic peaks.
+# Also perform simulations with TimeExposed scaled by 0.5 or 2.


Suggested change

# Also perform simulations with TimeExposed scaled by 0.5 or 2.

# Also perform simulations with TimeExposed scaled with 0.5 or 2.

annawendler · 2025-01-28T16:56:10Z

2024_Ploetzke_et_al_Revisiting_Linear_Chain_Trick/plot_numerical_experiments.py

+    return max
+
+
+def plot_day_peak_daily_new_transmissions(func_get_file_name, Reffs, subcompartments, file_name=""):


Suggested change

def plot_day_peak_daily_new_transmissions(func_get_file_name, Reffs, subcompartments, file_name=""):

def plot_epidemic_peak_timing(func_get_file_name, Reffs, subcompartments, file_name=""):

Easier to read for me than twice the word day in function name. Maybe plot_epidemic_peak_size for the other function as well.

annawendler · 2025-01-28T16:56:53Z

2024_Ploetzke_et_al_Revisiting_Linear_Chain_Trick/plot_numerical_experiments.py

+    (timing of the epidemic peak) for different effective reproduction numbers and different assumptions 
+    regarding the number of subcompartments.
+
+    @param[in] func_get_file_name: Function that returns the paths to a file with suitable simulation results


Suggested change

@param[in] func_get_file_name: Function that returns the paths to a file with suitable simulation results

@param[in] func_get_file_name: Function that returns the path to the files with suitable simulation results

annawendler · 2025-01-28T16:57:00Z

2024_Ploetzke_et_al_Revisiting_Linear_Chain_Trick/plot_numerical_experiments.py

+def get_file_name(result_dir, Reff, num_subcompartments, boolsubcomp=False):
+    """ Gives a paths to a file with the simulation results for an LCT model with num_subcompartments subcompartments, 
+    where the effective reproduction number is set to Reff at simulation time 2.
+    This uses standard defined naming convention of the lct simulations.


Suggested change

This uses standard defined naming convention of the lct simulations.

This uses standard defined naming convention of the LCT simulations.

annawendler · 2025-01-28T16:57:04Z

2024_Ploetzke_et_al_Revisiting_Linear_Chain_Trick/plot_numerical_experiments.py

+    result_dir = os.path.join(os.path.dirname(
+        __file__), "simulation_results", "simulation_lct_numerical_experiments")
+
+    # Define which figures of the paper should be created. Figure 12 is created with another pyton script.


Suggested change

# Define which figures of the paper should be created. Figure 12 is created with another pyton script.

# Define which figures of the paper should be created. Figure 12 is created with another python script.

annawendler · 2025-01-28T16:57:12Z

2024_Ploetzke_et_al_Revisiting_Linear_Chain_Trick/plot_runtimes_lct.py

+
+
+def plot_runtime_and_steps(json_file, file_name=''):
+    """ Creates a plot with two y-axis: One for the run time measurements and one for the required number of time steps


Suggested change

""" Creates a plot with two y-axis: One for the run time measurements and one for the required number of time steps

""" Creates a plot with two y-axes: One for the run time measurements and one for the required number of time steps

annawendler · 2025-02-03T14:41:08Z

2024_Ploetzke_et_al_Revisiting_Linear_Chain_Trick/README.md

+- Section 4.4: Run time measurements are possible with the file [lct_runtime](lct_runtime.cpp). `OpenMP` is used to measure the run times. The target `lct_runtime` is only built if the option `MEMILIO_ENABLE_OPENMP` is enabled. The Slurm script [get_runtimes_lct](get_runtimes_lct.sh) can be used to define a job to measure the run time for different numbers of subcompartments. This script can be easily adapted to use an adaptive solver. To use the optimization flag `-O0`, uncomment the suitable line in the [CMakeLists file](CMakeLists.txt). Visualizations of the run times in the paper were created using the python script [plot_runtimes_lct](plot_runtimes_lct.py).
+
+- Section 4.5: A COVID-19 inspired scenario in Germany in 2020 is defined in the file [lct_covid19_inspired_scenario](lct_covid19_inspired_scenario.cpp). The simulation results are created and saved with the shell script [get_data_covid19_inspired](get_data_covid19_inspired.sh). 
+The simulation is initialized using real data, which has to be downloaded beforehand. Please execute the file [download_infection_data](download_infection_data.py) for this purpose.


Suggested change

The simulation is initialized using real data, which has to be downloaded beforehand. Please execute the file [download_infection_data](download_infection_data.py) for this purpose.

The simulation is initialized using reported data, which has to be downloaded beforehand. Please execute the file [download_infection_data](download_data.py) for this purpose.

Or rename the script.

add files

22c206f

lenaploetzke self-assigned this Jan 24, 2025

lenaploetzke linked an issue Jan 24, 2025 that may be closed by this pull request

Add files for LCT paper #4

Open

adapt runtime plot script

490bd4c

lenaploetzke requested a review from annawendler January 24, 2025 14:15

Forgot to add one comment

14b4078

annawendler requested changes Jan 28, 2025

View reviewed changes

annawendler reviewed Feb 3, 2025

View reviewed changes

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

4 add files for lct paper #7

4 add files for lct paper #7

lenaploetzke commented Jan 24, 2025 •

edited

Loading

annawendler left a comment

annawendler Jan 28, 2025

annawendler Jan 28, 2025

annawendler Jan 28, 2025

annawendler Jan 28, 2025 •

edited

Loading

annawendler Jan 28, 2025

annawendler Jan 28, 2025

annawendler Jan 28, 2025

annawendler Jan 28, 2025

annawendler Jan 28, 2025

annawendler Jan 28, 2025

annawendler Feb 3, 2025


		- Section 4.2: The file [lct_impact_distribution_assumption](lct_impact_distribution_assumption.cpp) provides the functionality to run simulations to assess the impact of the distribution assumption or different numbers of subcompartments. The dynamics at change points and epidemic peaks can be examined using this script. The population is not divided into age groups for these experiments. All simulation results are created and saved in `.h5` files when the shell script [get_data_numerical_experiments](get_data_numerical_experiments.sh) is executed. The visualizations of these simulation results in the paper were created using the python script [plot_numerical_experiments](plot_numerical_experiments.py).

		- Section 4.3: With the file [lct_impact_age_resolution](lct_impact_age_resolution.cpp), one can run simulations to assess the impact of including an age resolution. The simulation results are created and saved together with the results for section 4.2 with the shellscript [get_data_numerical_experiments](get_data_numerical_experiments.sh). The visualizations are also created with [plot_numerical_experiments](plot_numerical_experiments.py).


		- Section 4.3: With the file [lct_impact_age_resolution](lct_impact_age_resolution.cpp), one can run simulations to assess the impact of including an age resolution. The simulation results are created and saved together with the results for section 4.2 with the shellscript [get_data_numerical_experiments](get_data_numerical_experiments.sh). The visualizations are also created with [plot_numerical_experiments](plot_numerical_experiments.py).

		- Section 4.4: Run time measurements are possible with the file [lct_runtime](lct_runtime.cpp). `OpenMP` is used to measure the run times. The target `lct_runtime` is only built if the option `MEMILIO_ENABLE_OPENMP` is enabled. The Slurm script [get_runtimes_lct](get_runtimes_lct.sh) can be used to define a job to measure the run time for different numbers of subcompartments. This script can be easily adapted to use an adaptive solver. To use the optimization flag `-O0`, uncomment the suitable line in the [CMakeLists file](CMakeLists.txt). Visualizations of the run times in the paper were created using the python script [plot_runtimes_lct](plot_runtimes_lct.py).

	# Also perform simulations with TimeExposed scaled by 0.5 or 2.
	# Also perform simulations with TimeExposed scaled with 0.5 or 2.

		return max


		def plot_day_peak_daily_new_transmissions(func_get_file_name, Reffs, subcompartments, file_name=""):

	def plot_day_peak_daily_new_transmissions(func_get_file_name, Reffs, subcompartments, file_name=""):
	def plot_epidemic_peak_timing(func_get_file_name, Reffs, subcompartments, file_name=""):

	@param[in] func_get_file_name: Function that returns the paths to a file with suitable simulation results
	@param[in] func_get_file_name: Function that returns the path to the files with suitable simulation results

	This uses standard defined naming convention of the lct simulations.
	This uses standard defined naming convention of the LCT simulations.

	# Define which figures of the paper should be created. Figure 12 is created with another pyton script.
	# Define which figures of the paper should be created. Figure 12 is created with another python script.



		def plot_runtime_and_steps(json_file, file_name=''):
		""" Creates a plot with two y-axis: One for the run time measurements and one for the required number of time steps

	""" Creates a plot with two y-axis: One for the run time measurements and one for the required number of time steps
	""" Creates a plot with two y-axes: One for the run time measurements and one for the required number of time steps

	The simulation is initialized using real data, which has to be downloaded beforehand. Please execute the file [download_infection_data](download_infection_data.py) for this purpose.
	The simulation is initialized using reported data, which has to be downloaded beforehand. Please execute the file [download_infection_data](download_data.py) for this purpose.

4 add files for lct paper #7

Are you sure you want to change the base?

4 add files for lct paper #7

Conversation

lenaploetzke commented Jan 24, 2025 • edited Loading

Changes and Information

annawendler left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

annawendler Jan 28, 2025 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

lenaploetzke commented Jan 24, 2025 •

edited

Loading

annawendler Jan 28, 2025 •

edited

Loading