Add greek letters to model figure #29

rozeggo · 2023-10-05T10:55:18Z

https://github.com/epiverse-trace/tutorials/blob/late_task_1/episodes/simulating_transmission.Rmd
In Simulating Transmission figure, could the greek letters for parameters that are referenced right after align with the model figure? i.e. have them added?

May be easier to wait for the harmonisation of figure construction/style coming from data.org to prevent duplication of effort.

amanda-minter · 2023-10-09T08:29:49Z

The R package used to create the figure (DiagrammeR) doesn't currently support adding latex but there are some workarounds.

Agree it is worth waiting for input from data.org in case there are suggestions for version controlled flow diagrams.

rozeggo · 2023-10-16T12:26:08Z

@Bisaloo Hi Hugo, Do you know of a package or have a suggestion for a package or figure-making way that we can include greek letters?

Bisaloo · 2023-10-16T13:33:12Z

Didn't get the chance to try it but you should be able to add greek letters as HTML character rather than LaTeX equations. See rich-iannone/DiagrammeR#71 (comment)

amanda-minter · 2023-10-16T14:00:34Z

Thanks for this Hugo, adding as HTML character works great

Fixes #29

avallecam · 2023-10-20T12:03:16Z

I added and linked this to the writing guidelines for the tutorials as a feature reminder for upcoming ones.

Fixes #29

* 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>

rozeggo assigned amanda-minter Oct 5, 2023

amanda-minter added a commit that referenced this issue Oct 16, 2023

Add greek letters to flow diagrams

ca59168

Fixes #29

avallecam mentioned this issue Oct 20, 2023

add diagram representations of the set of equations #21

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avallecam closed this as completed Oct 20, 2023

avallecam reopened this Oct 20, 2023

avallecam closed this as completed Oct 20, 2023

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

Add greek letters to flow diagrams

6f43ba7

Fixes #29

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Add greek letters to model figure #29

Add greek letters to model figure #29

rozeggo commented Oct 5, 2023

amanda-minter commented Oct 9, 2023

rozeggo commented Oct 16, 2023

Bisaloo commented Oct 16, 2023

amanda-minter commented Oct 16, 2023

avallecam commented Oct 20, 2023

Add greek letters to model figure #29

Add greek letters to model figure #29

Comments

rozeggo commented Oct 5, 2023

amanda-minter commented Oct 9, 2023

rozeggo commented Oct 16, 2023

Bisaloo commented Oct 16, 2023

amanda-minter commented Oct 16, 2023

avallecam commented Oct 20, 2023