added PSM functions

[W-Mohammed]

Hi Khader,

Please review the branch and let me know if you are happy.
I have created new functions, including the run PSM model. The model now considers the intervention's costs according to the published treatment schedule.

Please let me know if you have any questions.

[W-Mohammed]

Salam all!

I have added functions to:

• estimate the adverse events for the treatments and
• calculate PPS treatment costs.

I have tested the functions and updated the documentation to make things more transparent.

I have PSA and one-way sensitivity analysis (OWSA) functions, which should be the end of my programming tasks.

I am still waiting for at least one of you to review the code and approve the pull request to consolidate it with the main branch on GitHub, which will allow the website to update. @Khader-Habash, I was expecting you to finish it by now.

[abeero126]

Thank you Wael for your email We all were extremly busy with some urgent issues during the last 2 weeks and we could not review the codes. This week we are planning to do the reviosn. As models in R are still new for us we may require more time than expected Regards, Abeer

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On Sat, 25 May 2024 at 08:42, Wael Mohammed ***@***.***> wrote: Salam all! I have added functions to: - estimate the adverse events for the treatments and - calculate PPS treatment costs. I have tested the functions and updated the documentation to make things more transparent. I have PSA and one-way sensitivity analysis (OWSA) functions, which should be the end of my programming tasks. I am still waiting for at least one of you to review the code and approve the pull request to consolidate it with the main branch on GitHub, which will allow the website to update. @Khader-Habash <https://github.com/Khader-Habash>, I was expecting you to finish it by now. — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BG7Q6SZUGAPBUKIOHHBA6UDZEAQDXAVCNFSM6AAAAABHYPULZ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZQHAYDMNBZGI> . You are receiving this because your review was requested.Message ID: ***@***.***>

[W-Mohammed]

Salam all,

I am sorry to add to your work. I have just made significant changes to the model and its auxiliary functions.

I have just finished adding the PSA and One Way Sensitivity Analysis functions, including a tornado plotting function.

I have also added default data objects. These are lists of data that contain model parameters, PSA parameters and DSA parameters. They are all documented and start with the prefixes l_psm_, l_psa_ and l_dsa_, respectively. These data are from the Chinese data.

Moreover, I changed the inputs of the adverse events function from a list of lists to a list of scalars. If you have reviewed that function, you should spend a few minutes reviewing the updated function. This change makes the model more adaptable and accessible for handling the PSA and DSA functions. Another similar change was the output of the run_psm function, which is now a vector rather than a list for PSA and DSA reasons.

[Khader-Habash]

Hi Wael, Thanks for the update. I will start reviewing the code thoroughly this week. I've quickly ran through the repository and wanted to verify if the updates applied to the PSM file match those in the separate functions. This is my first time reviewing code. I've cloned the repository to my local device to start the review. Is this the right approach? Do you have any technical tips that could help with the review process? Best Regards.

…

On Mon, May 27, 2024 at 11:22 PM Wael Mohammed ***@***.***> wrote: Salam all, I am sorry to add to your work. I have just made significant changes to the model and its auxiliary functions. I have just finished adding the PSA and One Way Sensitivity Analysis functions, including a tornado plotting function. I have also added default data objects. These are lists of data that contain model parameters, PSA parameters and DSA parameters. They are all documented and start with the prefixes l_psm_, l_psa_ and l_dsa_, respectively. These data are from the Chinese data. Moreover, I changed the inputs of the adverse events function from a list of lists to a list of scalars. If you have reviewed that function, you should spend a few minutes reviewing the updated function. This change makes the model more adaptable and accessible for handling the PSA and DSA functions. Another similar change was the output of the run_psm function, which is now a vector rather than a list for PSA and DSA reasons. — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BFN23MU3J56DVXQ4PWVS6DDZEOIZ7AVCNFSM6AAAAABHYPULZ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZUGAYTGNZRGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[W-Mohammed]

Khader, You have started things the right way. I can add a few pointers: - use the "Git" tab in your RStudio to: 1. Switch to the right branch, and 2. Pull or get the latest changes in the respective branch. You can find YouTube demos for how to switch branches and pull changes. Remember to pull changes every time you open your RStudio for the latest version of the code. Regarding the code in the vignettes, this code is now obsolete and needs to be updated.

…

On Thu, 30 May 2024, 12:11 khader Habash, ***@***.***> wrote: Hi Wael, Thanks for the update. I will start reviewing the code thoroughly this week. I've quickly ran through the repository and wanted to verify if the updates applied to the PSM file match those in the separate functions. This is my first time reviewing code. I've cloned the repository to my local device to start the review. Is this the right approach? Do you have any technical tips that could help with the review process? Best Regards. On Mon, May 27, 2024 at 11:22 PM Wael Mohammed ***@***.***> wrote: > Salam all, > > I am sorry to add to your work. I have just made significant changes to > the model and its auxiliary functions. > > I have just finished adding the PSA and One Way Sensitivity Analysis > functions, including a tornado plotting function. > > I have also added default data objects. These are lists of data that > contain model parameters, PSA parameters and DSA parameters. They are all > documented and start with the prefixes l_psm_, l_psa_ and l_dsa_, > respectively. These data are from the Chinese data. > > Moreover, I changed the inputs of the adverse events function from a list > of lists to a list of scalars. If you have reviewed that function, you > should spend a few minutes reviewing the updated function. This change > makes the model more adaptable and accessible for handling the PSA and DSA > functions. Another similar change was the output of the run_psm function, > which is now a vector rather than a list for PSA and DSA reasons. > > — > Reply to this email directly, view it on GitHub > < #1 (comment)>, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/BFN23MU3J56DVXQ4PWVS6DDZEOIZ7AVCNFSM6AAAAABHYPULZ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZUGAYTGNZRGI> > . > You are receiving this because you were mentioned.Message ID: > ***@***.***> > — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AN4PTYXBMEWVBHOFASY4JFTZE4CNNAVCNFSM6AAAAABHYPULZ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZZGMZDENZYGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>