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Updating transmissibility template #144

Merged
merged 75 commits into from
May 28, 2024
Merged

Updating transmissibility template #144

merged 75 commits into from
May 28, 2024

Commits on Apr 26, 2024

  1. Removing text about hard-coded gamma distribution

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  2. Changing "dat" to actual name of file "dat_raw"

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  3. Update description of report parameters "incomplete_days" and "r_esti… 

    …m_window"
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  4. Updating description of parameter "data_file"

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  5. Updating description of report as seen when rendered

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  6. Moved description of code about loading libraries inside correspondin… 

    …g rmd chunk
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  7. Simplify and add flexibility to generation time definition 

    Fix #113
    @Bisaloo @CarmenTamayo
    Bisaloo authored and CarmenTamayo committed Apr 26, 2024
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  8. Moving code description about changing the data_file parameter inside… 

    … corresponding rmd chunk
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  9. Replacing description of data with template to be filled by users

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  10. Changing description of NHS data to template to be filled in by users

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  11. Adding visualisation of dataset heading

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  12. Changing count_var object to column name to fix error when estimating rt

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  13. Updating EpiNow2 generation time parameter

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  14. Fixing lintr indentation

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  15. Fixing lintr indentation

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  16. Updating use of density function with epiparameter from $d to density()

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  17. Fixing typo (duplicated "days")

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  18. Replacing "group" by "region" to match variables in the dataset

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  19. Updating si parameter description for user to choose between manually… 

    … provided mean/sd and when these are obtained from {epiparameter}
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  20. Updating description of time period included in table with Rt estimat… 

    …es so it's understandable by external readers
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  21. Adding description to the code chunk used to generate table with Rt e… 

    …stimates for days defined by "r_estim_window"
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  22. Keeping only columns needed by EpiNow2 to avoid errors

    @CarmenTamayo
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  23. Ensure the date column's class is correct to avoid errors with region… 

    …al epinow
    @CarmenTamayo
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  24. Plotting si allowing negative values (relevant mainly only for normal… 

    … dist)
    @CarmenTamayo
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  25. Updating use of incidence2 from "daily" to 1L

    @CarmenTamayo
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  26. Reverting description of grouping variable to "group" so users can gr… 

    …oup data according to different variables
    @CarmenTamayo
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  27. Adding code to specify that both epicurves are now included, and ment… 

    …ion grouping variable name
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    CarmenTamayo committed Apr 26, 2024
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  28. Adding code to plot global epicurve (as it appeared in episoap vignette)

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  29. Adding incidence2 to list of loaded packages

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  30. Removing redundant comma

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  31. Adding info about epicurves with stratification by group_var

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  32. Specifying that the data_file parameter should be a path and not just… 

    … the file name to avoid confusion
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  33. Adding specific details on how to select column for count_var so it's… 

    … easier to understand for users
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  34. Adding plot for epicurve with total cases (as it appears on episoap v… 

    …ignette)
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  35. Adding info about stratified epicurves and removing unnecessary labs … 

    …from plot
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  36. Reverting to saying "group" instead of "region" since users might wan… 

    …t to group their data by different variables
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  37. Adding info about supported file types

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  38. Removing code chunks from rendering that are not relevant for reader

    @CarmenTamayo
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  39. Adding brief explanation for package user of what the code in each ch… 

    …unk is doing
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  40. Removing "group_var" from table for reader, since the column "region"… 

    … is already included
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  41. Adding explanation for reader about transmissibility by group results… 

    … included in EpiEstim chunk
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  42. Removing "count_variable" from output table for reader as it's a colu… 

    …mn with "date" on each row, which isn't helpful or nice
    @CarmenTamayo
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  43. Adding small explanation about what each code chunk is doing for pack… 

    …age user
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  44. Adding Explanation section to EpiEstim to match i2extras chunk

    @CarmenTamayo
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  45. Adding myself as author of template

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  46. Adding explanation for EpiNow2 to match i2extras

    @CarmenTamayo
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  47. Adding explanations for the code for pkg users in EpiNow2 chunk

    @CarmenTamayo
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  48. Removing empty code chunk

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  49. Adding description of results for the transmissibility by group secti… 

    …on in EpiNow2 chunk
    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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  50. Updating incorrect description of table in global tx section of EpiNo… 

    …w2 chunk
    @CarmenTamayo
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  51. Adding code to automatically print whether the si has been provided b… 

    …y the author or obtained from {epiparameter}
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  52. Removing data preparation section as it didn't contain any text and t… 

    …he chunks of code are now hidden
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  53. Modifying Identifying key data section so that variables are only des… 

    …cribed once and objects can be knitted directly
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  54. Improve description of results in "Number of cases" section

    @CarmenTamayo
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  55. Replacing text with object that's rendered automatically to indicate … 

    …the grouping variable in the report
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  56. Changing description in "Importing the data" to address the reader

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  57. Removing text describing the data since this is now done at section "… 

    …Identifying key data"
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  58. Fixing typo in EpiEstim chunk

    @CarmenTamayo
    CarmenTamayo committed Apr 26, 2024
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Commits on Apr 30, 2024

  1. Removing note about {linelist} not being used

    @CarmenTamayo
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  2. Removing chunk where object "last_date" was created as it is not used… 

    … in the template
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  3. Updating EpiEstim explanation to mention effective Rt and clarify whi… 

    …ch dates are used in the analysis
    @CarmenTamayo
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  4. Updating Epinow2 explanation to mention effective Rt and clarify whic… 

    …h dates are used in the analysis
    @CarmenTamayo
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  5. Adding missing column with grouping variable to table displaying grow… 

    …th rates
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  6. Adding brief description of what each code section is doing in i2extr… 

    …as chunk
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  7. Adding info about grouping variable used to the descriptions of plots… 

    …/tables in i2extras chunk
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  8. Adding Explanation section to R0 chunk

    @CarmenTamayo
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  9. Adding code explanations for user to R0 chunk

    @CarmenTamayo
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  10. Adding row.names=FALSE when generating table since these were being p… 

    …rinted in the report
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  11. Updating description of Rt estimates per group with latest dates avai… 

    …lable
    @CarmenTamayo
    CarmenTamayo committed Apr 30, 2024
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  12. Adding brief description of transmissibility by group results in R0 c… 

    …hunk
    @CarmenTamayo
    CarmenTamayo committed Apr 30, 2024
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Commits on May 2, 2024

  1. Update inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd 

    Co-authored-by: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
    @CarmenTamayo @Bisaloo
    CarmenTamayo and Bisaloo committed May 2, 2024
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  2. Using kbl for better output of data heade

    @CarmenTamayo
    CarmenTamayo committed May 2, 2024
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  3. Removing include=FALSE to make all rmd chunks visible to reader again

    @CarmenTamayo
    CarmenTamayo committed May 2, 2024
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  4. Increasing fig.height for Rt estimates by group_var in RO chunk

    @CarmenTamayo
    CarmenTamayo committed May 2, 2024
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Commits on May 28, 2024

  1. Update inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/E… 

    …piNow2.Rmd

Co-authored-by: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
    @CarmenTamayo @Bisaloo
    CarmenTamayo and Bisaloo committed May 28, 2024
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