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add read delays episode #5

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merged 208 commits into from
Mar 25, 2024
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b4d5af1
add first draft to solve #70
avallecam Nov 22, 2023
61eab21
add introduction episode for lesson_build
avallecam Nov 22, 2023
8dfc626
fix writing of objectives
avallecam Nov 22, 2023
72e2dd2
add structure of questions to last two sections
avallecam Nov 22, 2023
4a52fc3
remove temporally setup logs chunk
avallecam Nov 22, 2023
a49028c
reduce object names and visible arguments
avallecam Nov 22, 2023
4e7ffd7
change heading level
avallecam Nov 22, 2023
bcb2bc8
replace episode title
avallecam Nov 23, 2023
e58131e
add template and questions for read data episode
avallecam Nov 23, 2023
4d4e487
add draft chunk for discussion or challenge
avallecam Nov 23, 2023
e8e5121
add template and questions for describe data episode
avallecam Nov 23, 2023
e393b3c
add new episodes for build review
avallecam Nov 23, 2023
21b9fd9
update heading titles
avallecam Nov 23, 2023
1d937de
add paragraphs to the what and how
avallecam Nov 23, 2023
5d0eae8
add keypoints from episode
avallecam Nov 23, 2023
d03c70c
arrange text in what and how sections
avallecam Nov 23, 2023
cc8e33b
clear template content
avallecam Nov 23, 2023
5c1b6f9
rename figure
avallecam Nov 24, 2023
19cfe2b
remove space within epinow function
avallecam Nov 24, 2023
a770ac2
fix intro line to et1
avallecam Nov 24, 2023
7da8706
rewrite intro sentence
avallecam Nov 24, 2023
eb5cd1b
add prerequisites
avallecam Nov 24, 2023
b52eee9
replace prerequisite
avallecam Nov 24, 2023
1b4bdce
add clear wording
avallecam Nov 24, 2023
90ee9b1
add text on why and epinow2 steps
avallecam Nov 24, 2023
9354eaf
add definitions for delays
avallecam Nov 24, 2023
fce9c84
replace link with new R0 definition
avallecam Nov 24, 2023
47509bb
specify the task as a point of reference
avallecam Nov 24, 2023
dfe1f40
edits after first review with grammarly
avallecam Nov 24, 2023
bd769d2
relocate discussion after why section
avallecam Nov 24, 2023
be4d6d9
rename episode for delays previous to read data
avallecam Nov 29, 2023
65468d9
add placeholder for episoap episode
avallecam Nov 29, 2023
16af7b3
rename episode for read cases data
avallecam Nov 29, 2023
184dd8b
use a simpler epinow2 with generation time only
avallecam Nov 30, 2023
fdcbe1a
add summative code content
avallecam Nov 30, 2023
3e7288a
add sections content and names
avallecam Nov 30, 2023
9565255
add placeholder for describe cases episode
avallecam Nov 30, 2023
d2894c0
replace serial interval with generation time
avallecam Nov 30, 2023
c988567
add figure and references
avallecam Nov 30, 2023
0a8ae0b
expand argument detail in intro episode
avallecam Nov 30, 2023
3dc840b
update key points
avallecam Nov 30, 2023
6366b13
replace license file content to epiverse-trace
avallecam Dec 2, 2023
8a5d740
amend change in license by error
avallecam Dec 2, 2023
2b2f8dd
Revert "amend change in license by error"
Dec 2, 2023
51fb5fc
Revert "replace license file content to epiverse-trace"
Dec 2, 2023
ad2b9b9
add callout draft for delays from data
avallecam Dec 2, 2023
cf729e3
add placeholder to show how to get delays from contact data
avallecam Dec 2, 2023
a3263a6
add period delay figures
avallecam Dec 7, 2023
bcc3bff
edit text after review
avallecam Dec 7, 2023
bc1eabc
add symptom onset for reporting delay definition
avallecam Dec 7, 2023
4d3239f
remove figures replaced in previous commit
avallecam Dec 7, 2023
9aab370
add infectiousness to glossary
avallecam Dec 7, 2023
242a883
add new distribution delays figures
avallecam Dec 7, 2023
9e9a8a5
add more definitions
avallecam Dec 7, 2023
5d795b9
add figures and text for first section
avallecam Dec 7, 2023
69f244b
add callout on reminder about the adjustments for Rt
avallecam Dec 8, 2023
c676d92
add episode et1 content
avallecam Dec 8, 2023
9cc660b
fix and extend the definitions
avallecam Dec 11, 2023
55e9671
add objectives
avallecam Dec 11, 2023
37f7c0c
add an explanation on serial interval biases
avallecam Dec 11, 2023
c37a506
add content about growth rate curve
avallecam Dec 11, 2023
945d5b9
write text for epiparameter epidist_db
avallecam Dec 11, 2023
027ffae
add text before about exploring the epidist class object
avallecam Dec 11, 2023
a72eeb8
add challenge format
avallecam Dec 11, 2023
385fab9
complete with the max argument for dist_spec
avallecam Dec 11, 2023
6f1d3b1
add spoiler on distribution plus explore output
avallecam Dec 11, 2023
2f37372
add offspring distribution to glossary
avallecam Dec 12, 2023
24c9d79
add formative assessments on distributions
avallecam Dec 12, 2023
c863754
add text and assessment about continuous
avallecam Dec 14, 2023
958ede2
add normal distribution figure
avallecam Dec 14, 2023
5008827
complete with assessments until epiparam + epinow2
avallecam Dec 14, 2023
14d0ed1
relevel titles to isolate content index
avallecam Dec 14, 2023
7071036
add formative assessment + block all epinow2
avallecam Dec 14, 2023
8750f81
write the structure of content
avallecam Dec 14, 2023
7d18b4f
move questions to section on from your data
avallecam Dec 14, 2023
7c95333
translate questions to cases
avallecam Dec 14, 2023
5171cd0
update title
avallecam Dec 14, 2023
620b050
update questions and objectives
avallecam Dec 16, 2023
4343673
add question on serial interval from data
avallecam Dec 16, 2023
066f839
move read-cases file to separate branch
avallecam Dec 16, 2023
634680b
move describe-cases to separate branch
avallecam Dec 16, 2023
f70b634
move create-report to separate branch
avallecam Dec 16, 2023
785c52b
add chunk placeholder for reactive hexwall
avallecam Dec 17, 2023
b98964a
rephrase questions, move one to other branch
avallecam Dec 17, 2023
10a1134
add rcompendium paths to data as suggested in #90
avallecam Dec 17, 2023
f2f5aa5
add idea callout to move from lollipop chart to distribution
avallecam Dec 20, 2023
cbdd149
add one more figure on infectiousness
avallecam Dec 20, 2023
5c1a72d
add figure tags to url links
avallecam Dec 18, 2023
2f6b175
add reference on sampling and censoring bias to si
avallecam Dec 21, 2023
11c1fab
add distributions affected by censoring
avallecam Dec 21, 2023
eeb468f
add figures to callout on cases to distributions
avallecam Dec 21, 2023
67f0591
remove episodes out of feature branch
avallecam Dec 21, 2023
502a2af
fix text and references on distrib params
avallecam Dec 21, 2023
3974ee0
add figure of observed serial intervals
avallecam Dec 21, 2023
7951813
relocate bias section to generation time
avallecam Dec 21, 2023
8da35c9
remove figures from infectious period
avallecam Dec 21, 2023
113f1d6
edit text with grammarly
avallecam Dec 22, 2023
0d1fcdf
fix links to figures and tables in distribution presentation
avallecam Dec 22, 2023
963eae1
add presymptomatic line and reference
avallecam Dec 22, 2023
2cdbb66
edit challenge writing
avallecam Dec 22, 2023
5dc838d
remove installation code from episodes
avallecam Dec 22, 2023
1b7e1c5
replace ver to express calculation
avallecam Dec 22, 2023
9b03bff
add delay word for generation time
avallecam Dec 22, 2023
2f4d96a
review intro with grammarly
Dec 22, 2023
5f5fa69
add specific objectives and keypoints
avallecam Dec 23, 2023
7e3d759
homogenize reference to delays
avallecam Dec 23, 2023
e501160
complete introduction section
avallecam Dec 23, 2023
9ddd3f7
relocate episode goal to introduction
avallecam Dec 23, 2023
59b3256
complete content writing
avallecam Dec 23, 2023
beb25b8
separate linelist
avallecam Dec 23, 2023
8340f35
complete editing of episode
avallecam Dec 23, 2023
a032a60
add definitions on biases
avallecam Dec 23, 2023
cd50c56
reduce to lower keys on subtitle
avallecam Dec 23, 2023
08cd413
edit with grammarly
avallecam Dec 23, 2023
ec116ce
edits after visual inspection of render website
avallecam Dec 23, 2023
435141d
relocate one challenge, remove eval in solutions
avallecam Dec 23, 2023
9a57d24
add renv file for early task 1 episodes
avallecam Dec 23, 2023
d399c8f
add eval false to hints, edit one question and sol
avallecam Dec 23, 2023
9d3139b
fix typo to use incubation instead of serial
avallecam Jan 19, 2024
62530b0
remove redundant "delays" separator
avallecam Jan 23, 2024
a938f76
update renv after resolve conflicts
Jan 24, 2024
c422164
add install.R file to solve RcppParallel gh action
avallecam Jan 24, 2024
cb73f6e
install RcppParallel from RSPM to renv.lock
avallecam Jan 25, 2024
e170c63
fix lintr warnings and move hexwall code to issue
avallecam Feb 1, 2024
ec49081
fix partially lintr warnings
avallecam Feb 1, 2024
029b4c4
edits to reduce lintr warnings
avallecam Feb 1, 2024
0d88a8c
edits to reduce lintr warnings
avallecam Feb 2, 2024
fa030c8
relocate hint as extension of solution challenge
avallecam Feb 2, 2024
b630d60
remove discrete distribution plot output
avallecam Feb 2, 2024
08a73e4
remove cache from chunk options
avallecam Feb 6, 2024
4b92374
[actions] update 23 packages
Bisaloo Feb 6, 2024
8dcbabf
Keep only parts related to early tasks
Bisaloo Feb 8, 2024
d589ffb
runing for the first time
Degoot-AM Feb 15, 2024
f1f0be8
adding sections of read case data
Degoot-AM Feb 15, 2024
a534352
adding rio package to read from files.
Degoot-AM Feb 16, 2024
07b0a5c
Reading from databases
Degoot-AM Feb 16, 2024
c57a73b
block in-development episode + move to new branch
avallecam Feb 17, 2024
b8c04c4
remove read-cases content + now in-dev branch
avallecam Feb 17, 2024
99c019c
add step to show get_parameters function
avallecam Feb 20, 2024
bfb76bd
fix all epiparameter and epinow2 connections
avallecam Feb 20, 2024
4638705
change solutions to TRUE
avallecam Feb 20, 2024
4fad8d7
remove introduction to get_parameters
avallecam Feb 22, 2024
cf19a11
use mean sd max distrib for epinow2 connection
avallecam Feb 22, 2024
7b6206c
use convert from params to summary stats
avallecam Feb 22, 2024
6758f52
use pmf for a weibull distribution!
avallecam Feb 22, 2024
59f44bc
clean renv
avallecam Feb 22, 2024
4eb623f
remove usage of `$prob_dist$` from epidist objects
avallecam Feb 23, 2024
821edb9
simplify code to plot
avallecam Feb 23, 2024
d484eae
add detail to use summary stats for epinow2
avallecam Feb 23, 2024
e19a5dd
specify instructions to use pmf
avallecam Feb 23, 2024
8be16a9
add key tab to callout
avallecam Feb 23, 2024
f606f01
add lintr edits
avallecam Feb 23, 2024
58c8ef7
fix reference to calculate density values
avallecam Feb 23, 2024
9a1402d
add note on using serial interval for generation t
avallecam Feb 23, 2024
60d47c1
remix and edit challenge content + minor edits
avallecam Feb 24, 2024
4bc3817
split one episode content into three
avallecam Feb 24, 2024
b1b845e
add specification in hint
avallecam Feb 24, 2024
fb1e06e
rename read-delays episode
avallecam Feb 24, 2024
ac5241b
rename file with ordered numbers
avallecam Feb 24, 2024
33eace6
update config file with ordered episodes
avallecam Feb 24, 2024
eac8129
updated config file with episodes without numbers
avallecam Feb 24, 2024
01f4a24
update questions, objectives and keypoints on each
avallecam Feb 24, 2024
08ae27a
fix code issues after error
avallecam Feb 24, 2024
a98d2bb
update question and objectives + new subtitle
avallecam Feb 24, 2024
8e7d0ce
use grammarly
avallecam Feb 24, 2024
8704121
use lintr
avallecam Feb 24, 2024
40e68e1
emphasis to summary stats for epinow2
avallecam Feb 24, 2024
59a1d2e
use grammarly
avallecam Feb 24, 2024
ee3cea3
use grammarly
avallecam Feb 24, 2024
09ab3d5
add minor space at end
avallecam Feb 24, 2024
4bf44d1
use lintr
avallecam Feb 24, 2024
f6d1dbe
prefer literature search over systematic review
avallecam Mar 20, 2024
7106146
recover objective bullet
avallecam Mar 20, 2024
c2947a9
use comma-separated list in prereq
avallecam Mar 20, 2024
dd47ea8
locate glossary entry within right letter section
avallecam Mar 20, 2024
48c05c0
Merge branch 'add-read-delays' of https://github.com/epiverse-trace/t…
avallecam Mar 20, 2024
87694a4
rephrase contribution of epiparameter to modeling
avallecam Mar 20, 2024
3eea8c0
add hint + homogenise using database
avallecam Mar 21, 2024
5760f8c
add epinow2 context for challenge and hint info
avallecam Mar 21, 2024
d5dbd22
relocate plot and interactive distributions to ep1
avallecam Mar 21, 2024
e46d3aa
add reason behind distribution notation
avallecam Mar 21, 2024
4ff184f
relocate parametrise spoiler to episode 1
avallecam Mar 21, 2024
178d062
move uncertainty task from episode 1 to episode 2
avallecam Mar 21, 2024
dcfc264
epiparameter aids to choose rather than copy/paste
avallecam Mar 21, 2024
6611a89
relocate time periods callout to problem section
avallecam Mar 21, 2024
0597b42
add closure to episode on read delays
avallecam Mar 21, 2024
d5889c8
move the reporting delays challenge to previous ep
avallecam Mar 21, 2024
c54893a
simplify introduction to episode 2
avallecam Mar 21, 2024
bbfdd05
move sections from challenges episode to first two
avallecam Mar 21, 2024
c55f556
block delays challenges episode (#11)
avallecam Mar 21, 2024
ee7846c
replace to magrittr to load the pipe
avallecam Mar 21, 2024
22fe34c
move package loading at end of intro
avallecam Mar 21, 2024
38d474f
divide testimonial callout in two
avallecam Mar 21, 2024
3baf673
fix authorship tags
avallecam Mar 21, 2024
be47eb5
add package specification
avallecam Mar 21, 2024
96d0ec8
refer multi_epidist class as epidist objects
avallecam Mar 21, 2024
d76b712
Merge branch 'add-read-delays' of https://github.com/epiverse-trace/t…
avallecam Mar 21, 2024
a33b7d3
merge bullet points
avallecam Mar 21, 2024
47148b9
rephrase question
avallecam Mar 21, 2024
73e77db
rephrase for clarity
avallecam Mar 21, 2024
adc5055
update prereq for episode 2 after quantify Rt
avallecam Mar 21, 2024
9a7ec2a
rephrase summary statistics not as numbers
avallecam Mar 21, 2024
b9b836b
homogenize epinow2 code interface with quantify Rt
avallecam Mar 21, 2024
52899a0
add epiparameter get_parameters for epinow2 (#4)
avallecam Mar 21, 2024
2a7c8e8
fix na visibility in callout
avallecam Mar 21, 2024
cefbdb1
add rephrase of copy/paste
avallecam Mar 25, 2024
dbc5ce8
adding {tidyverse} due to dplyr use
avallecam Mar 25, 2024
87d7f61
add tidyverse to code chunk
avallecam Mar 25, 2024
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4 changes: 2 additions & 2 deletions CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -222,8 +222,8 @@ community listed at <https://github.com/epiverse-trace/> including via social
media, slack, newsletters, and email lists. You can also [reach us by
email][contact].

[repo]: https://github.com/epiverse-trace/tutorials
[repo-issues]: https://github.com/epiverse-trace/tutorials/issues
[repo]: https://github.com/epiverse-trace/tutorials-early
[repo-issues]: https://github.com/epiverse-trace/tutorials-early/issues
[contact]: mailto:[email protected]
[cp-site]: https://epiverse-trace.github.io/
[dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
Expand Down
28 changes: 13 additions & 15 deletions config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -11,29 +11,29 @@
carpentry: 'incubator'

# Overall title for pages.
title: 'Outbreak analytics with R'
title: 'Reading and cleaning data for outbreak analytics with R'

# Date the lesson was created (YYYY-MM-DD, this is empty by default)
created: ~
created:

# Comma-separated list of keywords for the lesson
keywords: 'forecasts, epidemic models, interventions' #FIXME
keywords:

# Life cycle stage of the lesson
# possible values: pre-alpha, alpha, beta, stable
life_cycle: 'pre-alpha'

# License of the lesson
license: 'CC-BY 4.0' #FIXME
# License of the lesson materials (recommended CC-BY 4.0)
license: 'CC-BY 4.0'

# Link to the source repository for this lesson
source: 'https://github.com/epiverse-trace/tutorials'
source: 'https://github.com/epiverse-trace/tutorials-early'

# Default branch of your lesson
branch: 'main'

# Who to contact if there are any issues
contact: '[email protected]' #FIXME
contact: '[email protected]'

# Navigation ------------------------------------------------
#
Expand All @@ -59,12 +59,9 @@ contact: '[email protected]' #FIXME

# Order of episodes in your lesson
episodes:
- quantify-transmissibility.Rmd
- create-forecast.Rmd
- simulating-transmission.Rmd
- model-choices.Rmd
- modelling-interventions.Rmd
- compare-interventions.Rmd
- delays-reuse.Rmd
- delays-functions.Rmd
#- delays-challenges.Rmd

# Information for Learners
learners:
Expand All @@ -79,6 +76,7 @@ profiles:
#
# This space below is where custom yaml items (e.g. pinning
# sandpaper and varnish versions) should live


varnish: epiverse-trace/varnish@epiversetheme
# this is carpentries/sandpaper#533 in our fork so we can keep it up to date with main
sandpaper: epiverse-trace/sandpaper@patch-renv-github-bug
sandpaper: epiverse-trace/sandpaper@patch-renv-github-bug
275 changes: 0 additions & 275 deletions episodes/compare-interventions.Rmd

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