Updating transmissibility template

[CarmenTamayo]

Changes in this branch:
 

• Overall, making changes to the text so it addresses the external reader of the report rather than the user of the package Changing content of the output of episoap templates #120
• A brief description of what each chunk of code is doing has been included as well, addressing mainly the user of the package, to facilitate the process if they decide to make any changes to the template
• Added missing information about the explanation for the different methods used to estimate Rt, to standardise the content of the rmd chunks Missing info in EpiNow2 chunk #141
• Updated description of some report parameters (incomplete_days r_estim_window, data_file)
• Changed description from "This report provides a template for estimating tx" to "This report estimates disease tx" since this is what the reader will see (a report rather than a template, which is seen by the user instead)
• Provided description of types of file that are suitable as input data Allowed input file types for {episoap}? #146
• Moving instructions about the code from main text of the report to rmd chunks (e.g., info about which packages need to be loaded, instructions on how to change input data)
• Swapping description of example data (COVID-19 hospitalisations in the UK in 2020) to a template so that users can describe their own data to match the outputs of the report.
• Correcting name of dataset from "dat" to "dat_raw"
• Updating the description of the dataset used as input data so that it contains only the variables needed for the analysis (date/region/incidence), and allowing users to input their own description of these variables.
• Adding chunk of code to visualise the heading of this dataset
• Adding code to plot global epicurve before stratified epicurves
• Serial interval
  • Removing text about hard-coded gamma distribution in the description of the serial interval
  • Plotting SI using quantiles rather than starting from 1 to allow negative values (only for plotting, not for GT estimation), for diseases with pre-symptomatic transmission Plotting SI with negative values in {episoap} templates #107
  • Allowing user to define whether si mean and sd were provided manually or obtained from {epiparameter} Description of serial interval in transmissibility report #138
• Updated use of incidence2 (interval from "daily" to 1L)
• EpiNow2
  • Moving info about template parameters within code chunks and adding context for readers about which data are used in Rt estimation Referring to template parameters in the text of the transmissibility report #140
  • Updating generation_time_opts() Distributions in Rt estimation using {EpiNow2} #113 and replace EpiNow2::dist_spec() with EpiNow2::pmf() when appropriate #131
  • Simplification of the distribution by passing pmf directly when estimating generation times Distributions in Rt estimation using {EpiNow2} #113
  • Fixing issues with regional epinow by specifying column date class and keeping only relevant columns  Errors with regional_epinow #118

[Bisaloo]

Thanks!

I browsed through the changes and it looks all good to me. Only comment is that I wouldn't put include = FALSE on any chunks.
In my opinion, we should display or hide all chunks, not just some of them.

I confirm the reports render without issues on my local computer.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 30.00%. Comparing base (a44eda5) to head (7508c47).
Report is 15 commits behind head on main.

❗ Current head 7508c47 differs from pull request most recent head c2dcaf9

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Additional details and impacted files

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- Coverage   73.07%   30.00%   -43.08%     
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  Files           4        3        -1     
  Lines          26       10       -16     
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- Hits           19        3       -16     
  Misses          7        7               

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