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add episodes on estimate superspreading and simulate chains (trial 04) #29

Merged
merged 140 commits into from
May 1, 2024
Merged

add episodes on estimate superspreading and simulate chains (trial 04) #29

merged 140 commits into from
May 1, 2024

Commits on Apr 30, 2024

  1. add draft design content for superspreading and chains episodes

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  2. add episode on simulate

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  3. add empty lesson template

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  4. add packages and testimonial

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  5. add summative code to episode

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  6. add draft content to episodes

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  7. fix code output in build lesson

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  8. add episode specific packages

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  9. edit to pass lintr checks

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  10. add redirection to project cases

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  11. add text on contact tracing effords

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  12. add figures on contact tracing

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  13. specify chunk test on cluster size probability

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  14. edit text on superspreading + order content

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  15. add unit figures from SEE paper

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  16. edit code issues in output

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  17. fix code to pass lintr

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  18. select a minimal chain

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  19. clean simluation output to three generations only

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  20. add intro to estimate episode

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  21. clean entry content

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  22. add figures on see from hong kong sars cov 2 paper

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  23. solve lint checks

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  24. rephrase contact tracing justification

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  25. add purrr checkpoint callout as prerequisite

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  26. change number of simulation chain number id

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  27. add blog post content on the episode topic

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  28. expand on topics

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  29. typo addition

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  30. add empirica evidence of backward tracing

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  31. simplify epiparameter callout

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  32. fix lintr checks

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  33. clean individual reproduction number section

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  34. add callout to differentiate terminologies

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  35. clear content writing + add entry to estimate k

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  36. edit the fitted plot + add callout on pkg helper

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  37. fix heterogeneity call out text

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  38. rearrange after review

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  39. make estimation of sse as challenge

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  40. make epiparameter explicit

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  41. relocate and simplify text after review

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  42. add within challenges and prioritize content

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  43. move text on decision making to simulate episode

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  44. relocate complementary information chunk

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  45. fix typo

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  46. clarify relationship between poisson and nb

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  47. clarify challenge

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  48. clean all challenges

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  49. clean variation across diseases chunk

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  50. clean output after review

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  51. add keypoints

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  52. test plot from epiparameter and superspreading

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  53. fix text and figure after review

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  54. clarify challenges questions + text and subtitles

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  55. fix lintr checks

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  56. clear question writing 

    Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
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  57. fix code clarity

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  58. clean code output

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  59. pass lintr checks

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  60. update to not superseded functions

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  61. pass lintr edits

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  62. add spoiler on simulated over observed cases

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  63. add labels to ggplots

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  64. focus on map in the checkpoint callout

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  65. clean spoiler code

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  66. clear ggplot actions

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  67. increase visibility of chains size and length

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  68. introduce epichains class object

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  69. show distribution of outbreaks and null intros

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  70. make observed over simulated cases visible

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  71. add intro text to spoiler section

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  72. remove distribution chunk + text median outbreaks

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  73. pass lintr checks + complement explanation text

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  74. rephrase conclusion

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  75. relocated interpretation from simulations

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  76. add interpretation of observed over simulated

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  77. add figure introduce cases generations size length

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  78. use duration of chain instead of length

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  79. show why to transform chain ID to factor

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  80. rewrite referral to an explosive outbreal

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  81. use mean and sd from serial interval in text

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  82. clean offspring definition

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  83. homogenize term to reproduction over reproductive

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  84. homogenize reproduction number across episode

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  85. add text about argument

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  86. complete writing content

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  87. edit the challenges

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  88. clean challenge section writing

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  89. provide dosified reading of the epichains output

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  90. fix closing of tag callout

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  91. fill introduction

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  92. add figures for k and percent of large outbreaks

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  93. add preliminary time to 30 min

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  94. use grammarly with simulate episode

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  95. Clean writing of questions and objectives 

    Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
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  96. clean writing of introduction 

    Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
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  97. clean contact data callout 

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  98. clean writing of questions and objectives 

    Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
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  99. homogenize usage of individual-level variation

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  100. add detail on mers data

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  101. rewrite for clarity

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  102. homogenize usage of r nut

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  103. add R0 context for individual reproduction number

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  104. add explanation on the right-hand tail

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  105. add biological and environmental details

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  106. expand sentence on individual level of transmission

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  107. use potential for superspreading

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  108. add explanation on the 20/80 rule

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  109. fix one dot

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  110. rewrite intro on SSE definition

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  111. add suggested edit on backward contact strategy

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  112. use SARS-1 to differenciate it from SARS-CoV-2

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  113. apply suggestions for introduction 

    Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
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  114. apply suggestions for branching intro 

    Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
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  115. homogenise to use individual level variation

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  116. clear get offspring distribution section 

    Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
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  117. clear simulate single chain section 

    Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
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  118. fix number_chains typo

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  119. add chunk to make visible the number of chain

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  120. clear mention to number of chains 

    Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
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  121. fix print of number_chains

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  122. fix capitalization in solution subtitle

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  123. collect suggestions across text 

    Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
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  124. add discussion context to readers 

    Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
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  125. collect edits in viz and challenge 

    Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
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  126. collect edits on questions

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  127. apply suggestions from code review 

    Co-authored-by: Abdoelnaser M Degoot <degoot@aims.ac.za>
Co-authored-by: James Azam <james.m.azam@gmail.com>
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  128. apply suggestions from code review 

    Co-authored-by: James Azam <james.m.azam@gmail.com>
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  129. fix serial interval object naming

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  130. replace exclusive with customizable

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  131. add double colon checklist in introduction (#49)

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  132. add book link to the dot prefix

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  133. remove covidregional from setup

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  134. rename subtitle on backward strategy

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  135. connect number output with text

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  136. add set seed for same result always

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  137. annotate code and use simulation TRUE

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  138. add solutions to challenges

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  139. protect from conflicts

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  140. fix lintr checks

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