add diagram representations of the set of equations #21

avallecam · 2023-09-18T23:38:31Z

Is it useful to complement equations with their diagram representations at this stage?

For the simulate_transmission episode, we need to assume that the learner already knows ODE's as in the prerequisites. So probably this is not needed for this episode. Could the new concept here be the contact matrix?

Examples of these are:

https://www.reconlearn.org/slides/basicvbd-modelling/basicvbd-modelling#9

In case appropriate, we can use the diagram[dot]net for concept maps with their formatting suggestions.

Fixes #21

avallecam · 2023-10-20T11:58:26Z

Nice addition with the DiagrammeR package. This is also related with #29 to use greek letters.

Fixes #21

* Created late task 1 episode file * Draft questions. objectives and section titles * Added notes on lesson content and provisional model equations * More lesson content to Model structures section * Outlines of remaining sections added * Edits to model structure section * Minor updates to model structures * Edits to introduction section * Add content to and reorder model parameters section * Added example plot to introduction * Minor edit to text * Add initial conditions section Added text and code to initial conditions section and updated initial plot to have same initial conditions * Reorder of sections * Updated text to introduction * Add generating trajectories section Added content to generating trajectories, which details specifying the initial conditions, demography vector and running the model * Added contact matrix section * Edits to tutorial content Content edits and reordering of some text * Changed naming of tutorial Updated name to simulating_transmission to better reflect tutorial content * Remove references from Rmd Citations have been changed to hyperlinks, so references no longer needed in Rmd header * Add file for `model_choices.Rmd` * Additions and edits to tutorial objectives * Update model_choices.Rmd Added tutorial content on all sections for Choosing a model * Update model_choices.Rmd Add 'Coming soon' to incomplete sections * Add uncertainty section Added section on how to account for uncertainty in R0 for influenza example * Fix typo * Add Comparing interventions tutorial * Remove default lesson * Update model_choices.Rmd Updated challenge outline to address #27 and to include Carpentries hint structure * Add glossary and add terms to `simulating_transmission` Glossary added in response to #24, additional transmission types added to `simulating_transmission` tutorial * Hide messages in output Fixes #26 for `simulating_transmission` and `compare_scenarios` * Update package and function notation Fixes #25 for current tutorials * Fix typo * Add function to view model names Fixes #23 * Add callout for exposed, infected, infectious Fixes #20 * Add instructor notes to tutorials Address #17 * Add concept dependencies to tutorials Addresses #19 * Add flow diagram of model equations Fixes #21 * Add definitions of outbreak and epidemic Added to `model_choices` tutorial and relevant definitions added to glossary * Add challenge to `model_choices` tutorial Fixes #14 * Remove reference to epidemic versus outbreak Keep tutorial content on the types of model used for epidemic versus outbreak analysis, but remove exact reference to epidemic and outbreak model types * Update intervention functions * Restructure tutorials Split `compare_interventions` into two tutorials : `modelling_interventions` and `compare_interventions` * Update outline of `compare_interventions` * Fix typo in ODE equations * Add section on mask wearing and vaccination Updates to school closure section as well as added sections on mask wearing and vaccination * typo and minor rephrase * Add updated ebola model definition * Update filenames Updating filenames to be consistent with the default naming of episodes from `create_episode` * Add to glossary terms Incubation period and latent period * Updates to parameter values used in Covid-19 example * Add greek letters to flow diagrams Fixes #29 * Remove reference to model library * Add flow diagrams to challenged answer * Add section on Vacamole model description * Add pak installation to setup chunks * Revert "Remove default lesson" This reverts commit 6eadba4. * Update config.yaml * Update renv.lock * Revert "Revert "Remove default lesson"" This reverts commit 8089e4c. * Revert "Update config.yaml" This reverts commit 4f2a8e1. * Update config.yaml * Fix typos * Fix typos * Style code * Improve figures * Remove {DiagrammeR} error message display * Move contact matrix definition * Colour nodes of vaccination classes * Fix typo * Rephrase documentation description * Update episodes/model-choices.Rmd Co-authored-by: Pratik Gupte <pratik.gupte@lshtm.ac.uk> * Change title * Fix typo * Update title `model_choices.Rmd` * Fix typo * Add section on outcomes of interest * Update uncertainty section Updated code to run multiple model simulations to be the same as vignette and replaced {data.table} functions with `stat_summary()` stay within Tidyverse * update axis labels size * Add baseline trajectories to intervention figures * Minor rephrasing * Add details to effect of mask wearing calculation * Add resource links to concept dependencies * Add further detail to glossary definitions --------- Co-authored-by: rozeggo <r.eggo@lshtm.ac.uk> Co-authored-by: Andree Valle Campos <avallecam@gmail.com> Co-authored-by: Pratik Gupte <pratik.gupte@lshtm.ac.uk>

Auto-generated via {sandpaper} Source : 969a11b Branch : main Author : Amanda Minter <amandalminter@gmail.com> Time : 2023-10-31 15:37:33 +0000 Message : Late task tutorials (#34) * Created late task 1 episode file * Draft questions. objectives and section titles * Added notes on lesson content and provisional model equations * More lesson content to Model structures section * Outlines of remaining sections added * Edits to model structure section * Minor updates to model structures * Edits to introduction section * Add content to and reorder model parameters section * Added example plot to introduction * Minor edit to text * Add initial conditions section Added text and code to initial conditions section and updated initial plot to have same initial conditions * Reorder of sections * Updated text to introduction * Add generating trajectories section Added content to generating trajectories, which details specifying the initial conditions, demography vector and running the model * Added contact matrix section * Edits to tutorial content Content edits and reordering of some text * Changed naming of tutorial Updated name to simulating_transmission to better reflect tutorial content * Remove references from Rmd Citations have been changed to hyperlinks, so references no longer needed in Rmd header * Add file for `model_choices.Rmd` * Additions and edits to tutorial objectives * Update model_choices.Rmd Added tutorial content on all sections for Choosing a model * Update model_choices.Rmd Add 'Coming soon' to incomplete sections * Add uncertainty section Added section on how to account for uncertainty in R0 for influenza example * Fix typo * Add Comparing interventions tutorial * Remove default lesson * Update model_choices.Rmd Updated challenge outline to address #27 and to include Carpentries hint structure * Add glossary and add terms to `simulating_transmission` Glossary added in response to #24, additional transmission types added to `simulating_transmission` tutorial * Hide messages in output Fixes #26 for `simulating_transmission` and `compare_scenarios` * Update package and function notation Fixes #25 for current tutorials * Fix typo * Add function to view model names Fixes #23 * Add callout for exposed, infected, infectious Fixes #20 * Add instructor notes to tutorials Address #17 * Add concept dependencies to tutorials Addresses #19 * Add flow diagram of model equations Fixes #21 * Add definitions of outbreak and epidemic Added to `model_choices` tutorial and relevant definitions added to glossary * Add challenge to `model_choices` tutorial Fixes #14 * Remove reference to epidemic versus outbreak Keep tutorial content on the types of model used for epidemic versus outbreak analysis, but remove exact reference to epidemic and outbreak model types * Update intervention functions * Restructure tutorials Split `compare_interventions` into two tutorials : `modelling_interventions` and `compare_interventions` * Update outline of `compare_interventions` * Fix typo in ODE equations * Add section on mask wearing and vaccination Updates to school closure section as well as added sections on mask wearing and vaccination * typo and minor rephrase * Add updated ebola model definition * Update filenames Updating filenames to be consistent with the default naming of episodes from `create_episode` * Add to glossary terms Incubation period and latent period * Updates to parameter values used in Covid-19 example * Add greek letters to flow diagrams Fixes #29 * Remove reference to model library * Add flow diagrams to challenged answer * Add section on Vacamole model description * Add pak installation to setup chunks * Revert "Remove default lesson" This reverts commit 6eadba4. * Update config.yaml * Update renv.lock * Revert "Revert "Remove default lesson"" This reverts commit 8089e4c. * Revert "Update config.yaml" This reverts commit 4f2a8e1. * Update config.yaml * Fix typos * Fix typos * Style code * Improve figures * Remove {DiagrammeR} error message display * Move contact matrix definition * Colour nodes of vaccination classes * Fix typo * Rephrase documentation description * Update episodes/model-choices.Rmd Co-authored-by: Pratik Gupte <pratik.gupte@lshtm.ac.uk> * Change title * Fix typo * Update title `model_choices.Rmd` * Fix typo * Add section on outcomes of interest * Update uncertainty section Updated code to run multiple model simulations to be the same as vignette and replaced {data.table} functions with `stat_summary()` stay within Tidyverse * update axis labels size * Add baseline trajectories to intervention figures * Minor rephrasing * Add details to effect of mask wearing calculation * Add resource links to concept dependencies * Add further detail to glossary definitions --------- Co-authored-by: rozeggo <r.eggo@lshtm.ac.uk> Co-authored-by: Andree Valle Campos <avallecam@gmail.com> Co-authored-by: Pratik Gupte <pratik.gupte@lshtm.ac.uk>

Auto-generated via {sandpaper} Source : 237d7bb Branch : md-outputs Author : GitHub Actions <actions@github.com> Time : 2023-10-31 16:15:02 +0000 Message : markdown source builds Auto-generated via {sandpaper} Source : 969a11b Branch : main Author : Amanda Minter <amandalminter@gmail.com> Time : 2023-10-31 15:37:33 +0000 Message : Late task tutorials (#34) * Created late task 1 episode file * Draft questions. objectives and section titles * Added notes on lesson content and provisional model equations * More lesson content to Model structures section * Outlines of remaining sections added * Edits to model structure section * Minor updates to model structures * Edits to introduction section * Add content to and reorder model parameters section * Added example plot to introduction * Minor edit to text * Add initial conditions section Added text and code to initial conditions section and updated initial plot to have same initial conditions * Reorder of sections * Updated text to introduction * Add generating trajectories section Added content to generating trajectories, which details specifying the initial conditions, demography vector and running the model * Added contact matrix section * Edits to tutorial content Content edits and reordering of some text * Changed naming of tutorial Updated name to simulating_transmission to better reflect tutorial content * Remove references from Rmd Citations have been changed to hyperlinks, so references no longer needed in Rmd header * Add file for `model_choices.Rmd` * Additions and edits to tutorial objectives * Update model_choices.Rmd Added tutorial content on all sections for Choosing a model * Update model_choices.Rmd Add 'Coming soon' to incomplete sections * Add uncertainty section Added section on how to account for uncertainty in R0 for influenza example * Fix typo * Add Comparing interventions tutorial * Remove default lesson * Update model_choices.Rmd Updated challenge outline to address #27 and to include Carpentries hint structure * Add glossary and add terms to `simulating_transmission` Glossary added in response to #24, additional transmission types added to `simulating_transmission` tutorial * Hide messages in output Fixes #26 for `simulating_transmission` and `compare_scenarios` * Update package and function notation Fixes #25 for current tutorials * Fix typo * Add function to view model names Fixes #23 * Add callout for exposed, infected, infectious Fixes #20 * Add instructor notes to tutorials Address #17 * Add concept dependencies to tutorials Addresses #19 * Add flow diagram of model equations Fixes #21 * Add definitions of outbreak and epidemic Added to `model_choices` tutorial and relevant definitions added to glossary * Add challenge to `model_choices` tutorial Fixes #14 * Remove reference to epidemic versus outbreak Keep tutorial content on the types of model used for epidemic versus outbreak analysis, but remove exact reference to epidemic and outbreak model types * Update intervention functions * Restructure tutorials Split `compare_interventions` into two tutorials : `modelling_interventions` and `compare_interventions` * Update outline of `compare_interventions` * Fix typo in ODE equations * Add section on mask wearing and vaccination Updates to school closure section as well as added sections on mask wearing and vaccination * typo and minor rephrase * Add updated ebola model definition * Update filenames Updating filenames to be consistent with the default naming of episodes from `create_episode` * Add to glossary terms Incubation period and latent period * Updates to parameter values used in Covid-19 example * Add greek letters to flow diagrams Fixes #29 * Remove reference to model library * Add flow diagrams to challenged answer * Add section on Vacamole model description * Add pak installation to setup chunks * Revert "Remove default lesson" This reverts commit 6eadba4. * Update config.yaml * Update renv.lock * Revert "Revert "Remove default lesson"" This reverts commit 8089e4c. * Revert "Update config.yaml" This reverts commit 4f2a8e1. * Update config.yaml * Fix typos * Fix typos * Style code * Improve figures * Remove {DiagrammeR} error message display * Move contact matrix definition * Colour nodes of vaccination classes * Fix typo * Rephrase documentation description * Update episodes/model-choices.Rmd Co-authored-by: Pratik Gupte <pratik.gupte@lshtm.ac.uk> * Change title * Fix typo * Update title `model_choices.Rmd` * Fix typo * Add section on outcomes of interest * Update uncertainty section Updated code to run multiple model simulations to be the same as vignette and replaced {data.table} functions with `stat_summary()` stay within Tidyverse * update axis labels size * Add baseline trajectories to intervention figures * Minor rephrasing * Add details to effect of mask wearing calculation * Add resource links to concept dependencies * Add further detail to glossary definitions --------- Co-authored-by: rozeggo <r.eggo@lshtm.ac.uk> Co-authored-by: Andree Valle Campos <avallecam@gmail.com> Co-authored-by: Pratik Gupte <pratik.gupte@lshtm.ac.uk>

Auto-generated via {sandpaper} Source : 969a11b Branch : main Author : Amanda Minter <amandalminter@gmail.com> Time : 2023-10-31 15:37:33 +0000 Message : Late task tutorials (#34) * Created late task 1 episode file * Draft questions. objectives and section titles * Added notes on lesson content and provisional model equations * More lesson content to Model structures section * Outlines of remaining sections added * Edits to model structure section * Minor updates to model structures * Edits to introduction section * Add content to and reorder model parameters section * Added example plot to introduction * Minor edit to text * Add initial conditions section Added text and code to initial conditions section and updated initial plot to have same initial conditions * Reorder of sections * Updated text to introduction * Add generating trajectories section Added content to generating trajectories, which details specifying the initial conditions, demography vector and running the model * Added contact matrix section * Edits to tutorial content Content edits and reordering of some text * Changed naming of tutorial Updated name to simulating_transmission to better reflect tutorial content * Remove references from Rmd Citations have been changed to hyperlinks, so references no longer needed in Rmd header * Add file for `model_choices.Rmd` * Additions and edits to tutorial objectives * Update model_choices.Rmd Added tutorial content on all sections for Choosing a model * Update model_choices.Rmd Add 'Coming soon' to incomplete sections * Add uncertainty section Added section on how to account for uncertainty in R0 for influenza example * Fix typo * Add Comparing interventions tutorial * Remove default lesson * Update model_choices.Rmd Updated challenge outline to address #27 and to include Carpentries hint structure * Add glossary and add terms to `simulating_transmission` Glossary added in response to #24, additional transmission types added to `simulating_transmission` tutorial * Hide messages in output Fixes #26 for `simulating_transmission` and `compare_scenarios` * Update package and function notation Fixes #25 for current tutorials * Fix typo * Add function to view model names Fixes #23 * Add callout for exposed, infected, infectious Fixes #20 * Add instructor notes to tutorials Address #17 * Add concept dependencies to tutorials Addresses #19 * Add flow diagram of model equations Fixes #21 * Add definitions of outbreak and epidemic Added to `model_choices` tutorial and relevant definitions added to glossary * Add challenge to `model_choices` tutorial Fixes #14 * Remove reference to epidemic versus outbreak Keep tutorial content on the types of model used for epidemic versus outbreak analysis, but remove exact reference to epidemic and outbreak model types * Update intervention functions * Restructure tutorials Split `compare_interventions` into two tutorials : `modelling_interventions` and `compare_interventions` * Update outline of `compare_interventions` * Fix typo in ODE equations * Add section on mask wearing and vaccination Updates to school closure section as well as added sections on mask wearing and vaccination * typo and minor rephrase * Add updated ebola model definition * Update filenames Updating filenames to be consistent with the default naming of episodes from `create_episode` * Add to glossary terms Incubation period and latent period * Updates to parameter values used in Covid-19 example * Add greek letters to flow diagrams Fixes #29 * Remove reference to model library * Add flow diagrams to challenged answer * Add section on Vacamole model description * Add pak installation to setup chunks * Revert "Remove default lesson" This reverts commit 6eadba4. * Update config.yaml * Update renv.lock * Revert "Revert "Remove default lesson"" This reverts commit 8089e4c. * Revert "Update config.yaml" This reverts commit 4f2a8e1. * Update config.yaml * Fix typos * Fix typos * Style code * Improve figures * Remove {DiagrammeR} error message display * Move contact matrix definition * Colour nodes of vaccination classes * Fix typo * Rephrase documentation description * Update episodes/model-choices.Rmd Co-authored-by: Pratik Gupte <pratik.gupte@lshtm.ac.uk> * Change title * Fix typo * Update title `model_choices.Rmd` * Fix typo * Add section on outcomes of interest * Update uncertainty section Updated code to run multiple model simulations to be the same as vignette and replaced {data.table} functions with `stat_summary()` stay within Tidyverse * update axis labels size * Add baseline trajectories to intervention figures * Minor rephrasing * Add details to effect of mask wearing calculation * Add resource links to concept dependencies * Add further detail to glossary definitions --------- Co-authored-by: rozeggo <r.eggo@lshtm.ac.uk> Co-authored-by: Andree Valle Campos <avallecam@gmail.com> Co-authored-by: Pratik Gupte <pratik.gupte@lshtm.ac.uk>

Auto-generated via {sandpaper} Source : dd92d5c Branch : md-outputs Author : GitHub Actions <actions@github.com> Time : 2023-11-07 00:36:38 +0000 Message : markdown source builds Auto-generated via {sandpaper} Source : 969a11b Branch : main Author : Amanda Minter <amandalminter@gmail.com> Time : 2023-10-31 15:37:33 +0000 Message : Late task tutorials (#34) * Created late task 1 episode file * Draft questions. objectives and section titles * Added notes on lesson content and provisional model equations * More lesson content to Model structures section * Outlines of remaining sections added * Edits to model structure section * Minor updates to model structures * Edits to introduction section * Add content to and reorder model parameters section * Added example plot to introduction * Minor edit to text * Add initial conditions section Added text and code to initial conditions section and updated initial plot to have same initial conditions * Reorder of sections * Updated text to introduction * Add generating trajectories section Added content to generating trajectories, which details specifying the initial conditions, demography vector and running the model * Added contact matrix section * Edits to tutorial content Content edits and reordering of some text * Changed naming of tutorial Updated name to simulating_transmission to better reflect tutorial content * Remove references from Rmd Citations have been changed to hyperlinks, so references no longer needed in Rmd header * Add file for `model_choices.Rmd` * Additions and edits to tutorial objectives * Update model_choices.Rmd Added tutorial content on all sections for Choosing a model * Update model_choices.Rmd Add 'Coming soon' to incomplete sections * Add uncertainty section Added section on how to account for uncertainty in R0 for influenza example * Fix typo * Add Comparing interventions tutorial * Remove default lesson * Update model_choices.Rmd Updated challenge outline to address #27 and to include Carpentries hint structure * Add glossary and add terms to `simulating_transmission` Glossary added in response to #24, additional transmission types added to `simulating_transmission` tutorial * Hide messages in output Fixes #26 for `simulating_transmission` and `compare_scenarios` * Update package and function notation Fixes #25 for current tutorials * Fix typo * Add function to view model names Fixes #23 * Add callout for exposed, infected, infectious Fixes #20 * Add instructor notes to tutorials Address #17 * Add concept dependencies to tutorials Addresses #19 * Add flow diagram of model equations Fixes #21 * Add definitions of outbreak and epidemic Added to `model_choices` tutorial and relevant definitions added to glossary * Add challenge to `model_choices` tutorial Fixes #14 * Remove reference to epidemic versus outbreak Keep tutorial content on the types of model used for epidemic versus outbreak analysis, but remove exact reference to epidemic and outbreak model types * Update intervention functions * Restructure tutorials Split `compare_interventions` into two tutorials : `modelling_interventions` and `compare_interventions` * Update outline of `compare_interventions` * Fix typo in ODE equations * Add section on mask wearing and vaccination Updates to school closure section as well as added sections on mask wearing and vaccination * typo and minor rephrase * Add updated ebola model definition * Update filenames Updating filenames to be consistent with the default naming of episodes from `create_episode` * Add to glossary terms Incubation period and latent period * Updates to parameter values used in Covid-19 example * Add greek letters to flow diagrams Fixes #29 * Remove reference to model library * Add flow diagrams to challenged answer * Add section on Vacamole model description * Add pak installation to setup chunks * Revert "Remove default lesson" This reverts commit 6eadba4. * Update config.yaml * Update renv.lock * Revert "Revert "Remove default lesson"" This reverts commit 8089e4c. * Revert "Update config.yaml" This reverts commit 4f2a8e1. * Update config.yaml * Fix typos * Fix typos * Style code * Improve figures * Remove {DiagrammeR} error message display * Move contact matrix definition * Colour nodes of vaccination classes * Fix typo * Rephrase documentation description * Update episodes/model-choices.Rmd Co-authored-by: Pratik Gupte <pratik.gupte@lshtm.ac.uk> * Change title * Fix typo * Update title `model_choices.Rmd` * Fix typo * Add section on outcomes of interest * Update uncertainty section Updated code to run multiple model simulations to be the same as vignette and replaced {data.table} functions with `stat_summary()` stay within Tidyverse * update axis labels size * Add baseline trajectories to intervention figures * Minor rephrasing * Add details to effect of mask wearing calculation * Add resource links to concept dependencies * Add further detail to glossary definitions --------- Co-authored-by: rozeggo <r.eggo@lshtm.ac.uk> Co-authored-by: Andree Valle Campos <avallecam@gmail.com> Co-authored-by: Pratik Gupte <pratik.gupte@lshtm.ac.uk>

avallecam added the question Further information is requested label Sep 18, 2023

amanda-minter added a commit that referenced this issue Sep 25, 2023

Add flow diagram of model equations

f8a4795

Fixes #21

avallecam closed this as completed Oct 20, 2023

amanda-minter added a commit that referenced this issue Oct 23, 2023

Add flow diagram of model equations

616daa3

Fixes #21

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add diagram representations of the set of equations #21

add diagram representations of the set of equations #21

avallecam commented Sep 18, 2023

avallecam commented Oct 20, 2023 •

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add diagram representations of the set of equations #21

add diagram representations of the set of equations #21

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avallecam commented Sep 18, 2023

avallecam commented Oct 20, 2023 • edited Loading

avallecam commented Oct 20, 2023 •

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