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Additional inference howto posts #57

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8665fe9
Add 2 examples
adamkucharski Mar 19, 2024
5ba670e
Add inference with finalsize
adamkucharski Mar 19, 2024
ba0ced1
Convert to howto format
adamkucharski Apr 13, 2024
ec10c17
Add real-time R_t estimate
adamkucharski Apr 26, 2024
111b531
Update reproduction_number_effective_intervention.qmd
adamkucharski Apr 26, 2024
7401895
Update infection file
adamkucharski May 25, 2024
ca96a3c
Update reproduction_number_serological_data.qmd
adamkucharski May 25, 2024
1f609b9
Add 2 examples
adamkucharski Mar 19, 2024
a83a054
Add inference with finalsize
adamkucharski Mar 19, 2024
37e2665
Add real-time R_t estimate
adamkucharski Apr 26, 2024
6636a22
Update reproduction_number_effective_intervention.qmd
adamkucharski Apr 26, 2024
710f18d
Update infection file
adamkucharski May 25, 2024
a03f85c
add epichains to renv lock
avallecam Jun 5, 2024
e524407
Update package loading
adamkucharski Jun 21, 2024
2bfd574
Add cores
adamkucharski Jun 21, 2024
94b7d09
Update heading
adamkucharski Jun 21, 2024
efa20c9
Load data from incidence2
adamkucharski Jun 21, 2024
4bde2a0
Remove ordering step
adamkucharski Jun 21, 2024
98eee72
Simplify print output
adamkucharski Jun 21, 2024
7fd06f5
Add epiparameter dependency
adamkucharski Jun 21, 2024
85832e2
Remove API call
adamkucharski Jun 21, 2024
67f9fbb
Remove stan argument
adamkucharski Jun 21, 2024
ac3e265
Use withr for cores
adamkucharski Jun 21, 2024
3ad192d
Use ggplot for lines
adamkucharski Jun 21, 2024
47de77a
Update Lognormal() inputs
adamkucharski Jun 21, 2024
083b135
Tidy pipe for Ebola data
adamkucharski Jun 21, 2024
e6af40c
Apply epiparameter suggestions from code review
adamkucharski Jun 21, 2024
02814a1
Update index.qmd
adamkucharski Jun 21, 2024
2318f70
Add EpiNow2 plotting
adamkucharski Jun 21, 2024
0681175
add namespace to avoid error in code run
avallecam Sep 26, 2024
7830c75
add template features and authorship
avallecam Oct 3, 2024
825413a
fixed line breaks + added package namespace
avallecam Oct 3, 2024
d9f86f5
add line breaks + add brackets for package linking
avallecam Oct 3, 2024
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Use withr for cores
Co-authored-by: Andree Valle Campos <avallecam@gmail.com>
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adamkucharski and avallecam committed Oct 3, 2024

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commit ac3e265d6aa8a641f0f03caae31fcc7e3c4e4af0
6 changes: 1 addition & 5 deletions analyses/reconstruct_transmission/estimate_infections.qmd
Original file line number Diff line number Diff line change
@@ -133,11 +133,7 @@ epinow_estimates <- epinow(
reported_cases = incidence_data, # time series data
generation_time = generation_time_opts(serial_interval_covid), # assume generation time = serial interval
delays = delay_opts(infection_to_death), # delay from infection-to-death
rt = NULL, # no Rt estimation
stan = stan_opts( # set up options for inference
cores = 4, samples = 1000, chains = 3,
control = list(adapt_delta = 0.99)
)
rt = NULL # no Rt estimation
)

# Extract infection estimates from the model output