add episodes on introduction and read delays #104

avallecam · 2023-12-23T07:57:53Z

Fix #88
Fix #67

For context: I wrote two episodes, "introduction" and "read delays", as starting episodes around {EpiNow2} and {epiparameter} as a motivational example:

{epiparameters} fit as an authentic task: quick to master and immediately useful once mastered.
quantifying transmissibility is a familiar task to learners that immediately benefits from {epiparameter} as input (reference)
this joint presentation could also contribute to the vision of connecting packages to build a pipeline.
The {epiparameter} + {EpiNow2} interoperability code was based on recent code updates in Update {epiparameter} usage episoap#100

I'll appreciate your specific feedback providing a clear next step to remove, change or add content to this PR.

Some questions to guide this are:

Should we cut the episode on "read delays" in two or three? Where? (possibly between continuous distribution and Adjusting for reporting delays)
Should we briefly warn about biases of the {EpiNow2} demo in "introduction" episode and redirect to "quantify-transmissibility" (#58) after "read-delays"?
Should we add and adapt the {epiparameter} concept map as in #103?

For review, you can:

try to render locally the lesson, or
read the pre-rendered md files:
- introduction.md
- read_delays.md

github-actions · 2023-12-23T07:58:07Z

Thank you!

Thank you for your pull request 😃

🤖 This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

🎯 correct output
🖼️ correct figures
❓ new warnings
‼️ new errors

Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials/compare/md-outputs..md-outputs-PR-104

The following changes were observed in the rendered markdown documents:

 config.yaml (gone)                                 |   84 -
 create-forecast.md                                 |   45 +-
 ...create-forecast-rendered-unnamed-chunk-11-1.png |  Bin 8461 -> 8320 bytes
 fig/create-forecast-rendered-unnamed-chunk-3-1.png |  Bin 49982 -> 50619 bytes
 fig/create-forecast-rendered-unnamed-chunk-9-1.png |  Bin 10363 -> 10338 bytes
 fig/disease-reporting.jpg (new)                    |  Bin 0 -> 44277 bytes
 fig/fig5a-normaldistribution.png (new)             |  Bin 0 -> 111729 bytes
 fig/incubation-period-serial-interval.jpg (new)    |  Bin 0 -> 231856 bytes
 fig/infectiousness-covid19.jpg (new)               |  Bin 0 -> 720176 bytes
 ...troduction-rendered-unnamed-chunk-5-1.png (new) |  Bin 0 -> 51068 bytes
 fig/model-choices-rendered-unnamed-chunk-3-1.png   |  Bin 13458 -> 13483 bytes
 fig/model-choices-rendered-unnamed-chunk-4-1.png   |  Bin 9206 -> 9063 bytes
 fig/pkgs-hexlogos.png (new)                        |  Bin 0 -> 590622 bytes
 ...ransmissibility-rendered-unnamed-chunk-15-1.png |  Bin 31592 -> 30774 bytes
 ...ransmissibility-rendered-unnamed-chunk-16-1.png |  Bin 30628 -> 30666 bytes
 ...ransmissibility-rendered-unnamed-chunk-19-1.png |  Bin 84498 -> 84456 bytes
 ...ad-delays-rendered-unnamed-chunk-20-1.png (new) |  Bin 0 -> 11595 bytes
 fig/reproduction-generation-time.png (new)         |  Bin 0 -> 725371 bytes
 fig/reproduction-number-pre-symptomatic.png (new)  |  Bin 0 -> 721253 bytes
 fig/rt-adjusting-delays.png (new)                  |  Bin 0 -> 34455 bytes
 fig/seria-interval-fitted-distributions.jpg (new)  |  Bin 0 -> 200736 bytes
 fig/serial-interval-covid-sars.jpg (new)           |  Bin 0 -> 122860 bytes
 fig/serial-interval-observed.jpeg (new)            |  Bin 0 -> 319571 bytes
 fig/serial-interval-pairs.jpg (new)                |  Bin 0 -> 923818 bytes
 fig/simulating-transmission-rendered-plot-1.png    |  Bin 16469 -> 16390 bytes
 fig/time-periods.jpg (new)                         |  Bin 0 -> 300672 bytes
 introduction.md (new)                              |  210 ++
 md5sum.txt                                         |   34 +-
 quantify-transmissibility.md                       |  116 +-
 read-delays.md (new)                               | 1675 +++++++++++++++
 reference.md                                       |   58 +-
 renv.lock (gone)                                   | 2262 --------------------
 32 files changed, 2034 insertions(+), 2450 deletions(-)

What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible.

This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

⏱️ Updated at 2024-02-06 13:41:38 +0000

joshwlambert · 2024-01-15T16:01:37Z

The error I get when trying to run sandpaper::manage_deps() is:

clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [Matrix.so] Error 1
ERROR: compilation failed for package ‘Matrix’

joshwlambert · 2024-01-15T16:10:59Z

I have {Matrix} installed:

> library(Matrix)
> packageVersion("Matrix")
[1] ‘1.5.3’

I've updated to the latest version, which installs correctly:

> install.packages("Matrix")
trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/Matrix_1.6-5.tgz'
Content type 'application/x-gzip' length 5348209 bytes (5.1 MB)
==================================================
downloaded 5.1 MB


The downloaded binary packages are in
	/var/folders/c2/bn46nm4j7mj2_zyktygmfnk40000gp/T//RtmpAofVU8/downloaded_packages
> library(Matrix)
> packageVersion("Matrix")
[1] ‘1.6.5’

These are the versions of the carpentries packages I have installed:

library(sandpaper)
library(varnish)
library(pegboard)
library(tinkr)
sessionInfo()
#> R version 4.2.3 (2023-03-15)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS 14.1.2
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] tinkr_0.2.0           pegboard_0.7.1.9000   varnish_0.3.3.9000   
#> [4] sandpaper_0.14.1.9000
#> 
#> loaded via a namespace (and not attached):
#>  [1] rstudioapi_0.14   xml2_1.3.3        knitr_1.44        magrittr_2.0.3   
#>  [5] R.cache_0.16.0    R6_2.5.1          rlang_1.1.2       fastmap_1.1.1    
#>  [9] styler_1.10.0     tools_4.2.3       xfun_0.40         R.oo_1.25.0      
#> [13] cli_3.6.2         withr_2.5.2       htmltools_0.5.6   yaml_2.3.7       
#> [17] digest_0.6.33     assertthat_0.2.1  lifecycle_1.0.4   processx_3.8.2   
#> [21] purrr_1.0.2       callr_3.7.3       ps_1.7.5          vctrs_0.6.5      
#> [25] R.utils_2.12.2    fs_1.6.3          glue_1.6.2        evaluate_0.23    
#> [29] rmarkdown_2.25    reprex_2.0.2      compiler_4.2.3    R.methodsS3_1.8.2

^{Created on 2024-01-15 with reprex v2.0.2}

joshwlambert · 2024-01-15T16:22:15Z

I've updated the carpentries packages to see if that was the issue:

library(sandpaper)
library(varnish)
library(pegboard)
library(tinkr)
sessionInfo()
#> R version 4.2.3 (2023-03-15)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS 14.1.2
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] tinkr_0.2.0      pegboard_0.7.3   varnish_1.0.1    sandpaper_0.16.2
#> 
#> loaded via a namespace (and not attached):
#>  [1] rstudioapi_0.14   xml2_1.3.3        knitr_1.44        magrittr_2.0.3   
#>  [5] R.cache_0.16.0    R6_2.5.1          rlang_1.1.2       fastmap_1.1.1    
#>  [9] styler_1.10.0     tools_4.2.3       xfun_0.40         R.oo_1.25.0      
#> [13] cli_3.6.2         withr_2.5.2       htmltools_0.5.6   yaml_2.3.7       
#> [17] digest_0.6.33     assertthat_0.2.1  lifecycle_1.0.4   processx_3.8.2   
#> [21] purrr_1.0.2       callr_3.7.3       ps_1.7.5          vctrs_0.6.5      
#> [25] R.utils_2.12.2    fs_1.6.3          glue_1.6.2        evaluate_0.23    
#> [29] rmarkdown_2.25    reprex_2.0.2      compiler_4.2.3    R.methodsS3_1.8.2

^{Created on 2024-01-15 with reprex v2.0.2}

However, the same issue persists:

clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [Matrix.so] Error 1
ERROR: compilation failed for package ‘Matrix’

This could be due to compiling the package on apple silicon. As the package version required by {tutorials} is v1.6-4, and I'm unsure where {sandpaper}/{renv} is installing from, but if a binary is not available it may cause issues with code requiring compilation, especially on Macs.

Bisaloo · 2024-01-15T16:38:47Z

Do you have the full install log from the failing Matrix installation please?

joshwlambert · 2024-01-15T16:40:21Z

Do you have the full install log from the failing Matrix installation please?

What is the best way to share this? Paste a reprex of sandpaper::manage_deps()?

Bisaloo · 2024-01-15T16:50:44Z

I suspect you're missing a fortran compiler / R doesn't find it. Can you try installing https://github.com/coatless-mac/macrtools first please? Carmen has had success with this in the past.

joshwlambert · 2024-01-19T13:42:00Z

I've used {macrtools} to install gfortran. Running sandpaper::manage_deps() now gets further (i.e. installs more packages including {Matrix}) but now fails when trying to install {ragg}.

The head and tail of the error message are:

Error: 
! in callr subprocess.
Caused by error: 
! Error installing package 'ragg':
================================

** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘ragg’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Users/lshjl15/Documents/LSHTM_code/tutorials/renv/profiles/lesson-requirements/renv/library/R-4.2/aarch64-apple-darwin20/.renv/1/00LOCK-ragg/00new/ragg/libs/ragg.so':
  dlopen(/Users/lshjl15/Documents/LSHTM_code/tutorials/renv/profiles/lesson-requirements/renv/library/R-4.2/aarch64-apple-darwin20/.renv/1/00LOCK-ragg/00new/ragg/libs/ragg.so, 0x0006): symbol not found in flat namespace '_WebPConfigInitInternal'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/lshjl15/Documents/LSHTM_code/tutorials/renv/profiles/lesson-requirements/renv/library/R-4.2/aarch64-apple-darwin20/.renv/1/ragg’
install of package 'ragg' failed [error code 1]
ℹ See `$stdout` and `$stderr` for standard output and error.

Bisaloo · 2024-01-22T08:53:14Z

It looks like you're probably missing system dependencies for ragg. Can you try running:

pak::sysreqs_check_installed("ragg")

please?

joshwlambert · 2024-01-22T10:09:08Z

pak::sysreqs_check_installed("ragg")
#> Error: ! error in pak subprocess
#> Caused by error in `sysreqs2_command(sysreqs_platform, "query")`:
#> ! Unknown OS. Don't know how to query or install system packages for
#> aarch64-apple-darwin20.

^{Created on 2024-01-22 with reprex v2.0.2}

joshwlambert · 2024-01-22T10:11:54Z

r-lib/pak#563

Bisaloo · 2024-01-22T11:16:31Z

That's unfortunate. Could you then look manually into ragg system dependencies and search if they are installed / how to install them on macOS?

joshwlambert · 2024-01-22T11:50:23Z

4 system dependencies for {ragg}: https://cran.r-project.org/web/packages/ragg/index.html

I seem to have all system dependencies installed. Some possible problems:

freetype2 is specified as the system dependency but brew only has freetype (https://formulae.brew.sh/formula/freetype) so this might be an issue recognising the right program
libjpeg might not be recognised by the compiler toolchain in R due for reasons outlined by brew info libjpeg

brew info libjpeg
==> jpeg: stable 9f (bottled) [keg-only]
Image manipulation library
https://www.ijg.org/
/opt/homebrew/Cellar/jpeg/9f (21 files, 900.9KB)
  Poured from bottle using the formulae.brew.sh API on 2024-01-22 at 11:48:13
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/j/jpeg.rb
License: IJG
==> Caveats
jpeg is keg-only, which means it was not symlinked into /opt/homebrew,
because it conflicts with `jpeg-turbo`.

If you need to have jpeg first in your PATH, run:
  echo 'export PATH="/opt/homebrew/opt/jpeg/bin:$PATH"' >> ~/.zshrc

For compilers to find jpeg you may need to set:
  export LDFLAGS="-L/opt/homebrew/opt/jpeg/lib"
  export CPPFLAGS="-I/opt/homebrew/opt/jpeg/include"
==> Analytics
install: 25,267 (30 days), 41,108 (90 days), 97,414 (365 days)
install-on-request: 8,179 (30 days), 16,181 (90 days), 40,597 (365 days)
build-error: 0 (30 days)

Bisaloo · 2024-01-23T12:56:08Z

I'm not really sure how to help. This is very specific to macOS and my knowledge is limited, as are my options to test potential fixes.

If I was in this situation, my gut feeling would be to try and install webp related libraries that you may(???) be missing. No idea if that will help but probably worth a try.

Otherwise:

we can clarify that rendering the materials is not expected from reviewers and improve the online preview mechanism.
we can set up a Docker container for this repo so we at least all have the same setup, which makes it easier to debug potential issues.

sbfnk · 2024-01-23T15:53:58Z

symbol not found in flat namespace '_WebPConfigInitInternal'

I presume you've got webp installed?
brew info webp

joshwlambert · 2024-01-23T18:47:29Z

Reinstalled webp:

brew info webp
==> webp: stable 1.3.2 (bottled), HEAD
Image format providing lossless and lossy compression for web images
https://developers.google.com/speed/webp/
/opt/homebrew/Cellar/webp/1.3.2 (63 files, 2.3MB) *
  Poured from bottle using the formulae.brew.sh API on 2024-01-23 at 18:25:21
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/w/webp.rb
License: BSD-3-Clause
==> Dependencies
Build: cmake ✘
Required: giflib ✔, jpeg-turbo ✘, libpng ✔, libtiff ✔
==> Options
--HEAD
	Install HEAD version
==> Analytics
install: 75,767 (30 days), 250,667 (90 days), 1,036,950 (365 days)
install-on-request: 18,342 (30 days), 69,549 (90 days), 336,029 (365 days)
build-error: 65 (30 days)

However, the {ragg} install still fails:

** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘ragg’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Users/lshjl15/Documents/LSHTM_code/tutorials/renv/profiles/lesson-requirements/renv/library/R-4.2/aarch64-apple-darwin20/.renv/1/00LOCK-ragg/00new/ragg/libs/ragg.so':
  dlopen(/Users/lshjl15/Documents/LSHTM_code/tutorials/renv/profiles/lesson-requirements/renv/library/R-4.2/aarch64-apple-darwin20/.renv/1/00LOCK-ragg/00new/ragg/libs/ragg.so, 0x0006): symbol not found in flat namespace '_WebPConfigInitInternal'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/lshjl15/Documents/LSHTM_code/tutorials/renv/profiles/lesson-requirements/renv/library/R-4.2/aarch64-apple-darwin20/.renv/1/ragg’
install of package 'ragg' failed [error code 1]
ℹ See `$stdout` and `$stderr` for standard output and error.

chartgerink · 2024-01-24T09:39:42Z

For what it's worth - I just went through the install steps on a macOS (Intel-based) device, with no major issues (I only had to manually install pak::pak("epiverse-trace/epidemics")). Might it be worth to open up a separate issue to track this problem?

avallecam · 2024-01-24T10:54:45Z

(I only had to manually install pak::pak("epiverse-trace/epidemics")). Might it be worth to open up a separate issue to track this problem?

I think yes. That's a step we can add to the guidelines. I also noticed that for a successful local run of sandpaper::build_lesson(), we need to install any new package used in the lesson manually. This happened to me while working in epimodelac, where, for a moment, I did not have {vaccineff} and {serofoi} locally.

joshwlambert · 2024-01-24T14:10:43Z

Might it be worth to open up a separate issue to track this problem?

I agree, these problems are holding up this PR. I will unassign myself as a reviewer of this PR and will try to resolve these issues locally and with the team.

refer to #118

Bisaloo

Two comments that we should address after the split:

there is a cache/ folder in the output that probably shouldn't be here
most of the image should be converted to .png. .jpg is good for photographs but not for line art or scientific figures.

avallecam · 2024-02-06T10:51:43Z

Thank you for your feedback.

there is a cache/ folder in the output that probably shouldn't be here

Could it be because I used cache=TRUE in one epinow2 chunk in the intro file? I'll remove it to see how the md-outputs-PR-104 reacts to this change.

most of the image should be converted to .png. .jpg is good for photographs but not for line art or scientific figures.

Do you have a recommended method to do this conversion? I'll see if I can do this locally.

avallecam · 2024-02-06T11:17:21Z

most of the image should be converted to .png. .jpg is good for photographs but not for line art or scientific figures.

Do you have a recommended method to do this conversion? I'll see if I can do this locally.

I can do this locally 😅

Bisaloo · 2024-02-06T11:26:27Z

Do you have a recommended method to do this conversion? I'll see if I can do this locally.

Ideally, it shouldn't be a conversion since jpeg is a lossy format. The ideal solution would be to resave the images directly as png.

avallecam · 2024-02-06T11:28:03Z

Do you have a recommended method to do this conversion? I'll see if I can do this locally.

Ideally, it shouldn't be a conversion since jpeg is a lossy format. The ideal solution would be to resave the images directly as png.

thanks, hopefully, I did a direct resave as png.

Bisaloo

I see some quality issues with some images. Please leave me a moment to update them from my side.

avallecam · 2024-02-06T11:40:43Z

I see some quality issues with some images. Please leave me a moment to update them from my side.

thanks, after your update, it would be informative to refer to the changes you perceived and how you solved them in the update.

What I see when comparing the figures in the previous commit and the last commit is a brief increase in the file size.

Bisaloo · 2024-02-06T11:49:21Z

I didn't realize these figures were from articles, and they were provided as jpeg. This hurts my eyes 😭, and the proofing service should have fixed it before publication.

But I'll remove the last commit then. If a figure has been saved as jpeg, we should keep it this way, even though it should have been a png in the first place.

The idea of my first comment was that if we create a figure ourselves, it should be saved as png, not jpeg.

avallecam · 2024-02-06T11:55:47Z

The idea of my first comment was that if we create a figure ourselves, it should be saved as png, not jpeg.

Oh! now I understand. Yes, I did not create a figure yet. All jpeg and jpg files are original figures that I downloaded from papers.

I'd be happy if you remove the last commit, then.

avallecam · 2024-02-06T12:27:55Z

commit 0641875 is my worst commit ever! 🤣 I just realized I changed the figure's format but not change their names in the Rmd files, haha

avallecam · 2024-02-06T13:55:54Z

cache/ folder now is not present in md-outputs-PR-104. thank you @Bisaloo for flagging this!

avallecam requested review from joshwlambert and CarmenTamayo December 23, 2023 08:02

avallecam mentioned this pull request Jan 9, 2024

add: how to reuse distribution delays to quantify the time-varying reproduction number (Rt)? epiverse-trace/howto#34

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Configuration with {rprojroot} package. #106

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Add lesson dependency instruction #110

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avallecam force-pushed the early-task-1 branch from 0d5de1c to 6b127fc Compare January 24, 2024 16:42

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! Error installing package RcppParallel #111

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differences for PR #104

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differences for PR #104

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fix lintr warnings and move hexwall code to issue

6ceda33

refer to #118

fix partially lintr warnings

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edits to reduce lintr warnings

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edits to reduce lintr warnings

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relocate hint as extension of solution challenge

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remove discrete distribution plot output

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differences for PR #104

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remove cache from chunk options

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add complementary writing guidelines #75

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resave .jpg to .png epiverse-trace/git-rstudio-basics#42

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resave .jpg to .png epiverse-trace/research-compendium#31

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differences for PR #104

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Update 23 packages #126

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add read delays episode epiverse-trace/tutorials-early#5

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add episodes on introduction and read delays #104

add episodes on introduction and read delays #104

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avallecam commented Dec 23, 2023 • edited Loading

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Thank you!

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avallecam commented Dec 23, 2023 •

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