Home
Francisco Bischoff
on August 21, 2022
Last updated: 2022-08-21
Checks: 7 0
Knit directory:
false.alarm_2submodels/docs/
This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20201020) was run prior to running the code in the R Markdown file.
Setting a seed ensures that any results that rely on randomness, e.g.
subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 1b337ae. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the
analysis have been committed to Git prior to generating the results (you can
use wflow_publish or wflow_git_commit). workflowr only
checks the R Markdown file, but you know if there are other scripts or data
files that it depends on. Below is the status of the Git repository when the
results were generated:
Ignored files:
Ignored: .Renviron
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: .docker/
Ignored: .httr-oauth
Ignored: R/RcppExports.R
Ignored: _regime_change/meta/process
Ignored: _regime_change/meta/progress
Ignored: _regime_change/objects/
Ignored: _regime_change/user/
Ignored: _regime_optimize/meta/meta2
Ignored: _regime_optimize/meta/process
Ignored: _regime_optimize/meta/progress
Ignored: _regime_optimize/objects/
Ignored: _regime_optimize/user/
Ignored: analysis/shiny_land/rsconnect/
Ignored: dev
Ignored: inst/extdata/
Ignored: papers/epia2022/epia2022.md
Ignored: renv/python/
Ignored: renv/staging/
Ignored: src/RcppExports.cpp
Ignored: src/RcppExports.o
Ignored: src/contrast.o
Ignored: src/false.alarm.so
Ignored: src/fft.o
Ignored: src/mass.o
Ignored: src/math.o
Ignored: src/mpx.o
Ignored: src/scrimp.o
Ignored: src/stamp.o
Ignored: src/stomp.o
Ignored: src/windowfunc.o
Ignored: tests/testthat/_snaps/
Ignored: tmp
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made
to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html)
files. If you’ve configured a remote Git repository (see
?wflow_git_remote), click on the hyperlinks in the table below to
view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | d603ece | Francisco Bischoff | 2022-07-23 | lint |
| html | 5943a09 | Francisco Bischoff | 2022-07-21 | Build site. |
| html | 3328477 | Francisco Bischoff | 2022-07-21 | Build site. |
| Rmd | f86f334 | Francisco Bischoff | 2022-07-19 | new article |
| Rmd | 441629f | Francisco Bischoff | 2022-05-31 | begining analysis |
| html | 5927668 | Francisco Bischoff | 2022-04-17 | Build site. |
| html | 96dd528 | Francisco Bischoff | 2022-03-15 | Build site. |
| html | 1006f27 | Francisco Bischoff | 2022-03-15 | Build site. |
| html | c340b46 | GitHub Actions | 2022-03-15 | Build site. |
| Rmd | c155156 | Francisco Bischoff | 2022-03-14 | workflowr asd |
| Rmd | 5f35362 | Francisco Bischoff | 2022-03-14 | rekniting |
| html | 0aefdd1 | Francisco Bischoff | 2022-03-14 | workflowr 2 |
| html | 5f35362 | Francisco Bischoff | 2022-03-14 | rekniting |
| html | 6004462 | Francisco Bischoff | 2022-03-11 | workflowr |
| Rmd | 0f2f487 | Francisco Bischoff | 2022-03-03 | spellchecking |
| html | 0f2f487 | Francisco Bischoff | 2022-03-03 | spellchecking |
| Rmd | 4884ec1 | Francisco Bischoff | 2022-02-02 | work |
| html | 4884ec1 | Francisco Bischoff | 2022-02-02 | work |
| html | 867bcf2 | Francisco Bischoff | 2022-01-16 | workflowr |
| Rmd | 95ae431 | Francisco Bischoff | 2022-01-05 | blogdog |
| html | 95ae431 | Francisco Bischoff | 2022-01-05 | blogdog |
| Rmd | 7278108 | Francisco Bischoff | 2021-12-21 | update dataset on zenodo |
| html | 7278108 | Francisco Bischoff | 2021-12-21 | update dataset on zenodo |
| html | ca1941e | GitHub Actions | 2021-10-12 | Build site. |
| Rmd | 6b03f43 | Francisco Bischoff | 2021-10-11 | Squashed commit of the following: |
| html | c19ec01 | Francisco Bischoff | 2021-08-17 | Build site. |
| html | a5ec160 | Francisco Bischoff | 2021-08-17 | Build site. |
| html | e7e5d48 | GitHub Actions | 2021-07-15 | Build site. |
| Rmd | 1473a05 | Francisco Bischoff | 2021-07-15 | report |
| html | 1473a05 | Francisco Bischoff | 2021-07-15 | report |
| html | bf772a5 | GitHub Actions | 2021-03-24 | Build site. |
| Rmd | b869025 | Francisco Bischoff | 2021-03-24 | targets and workflowr |
| html | 52e7f0b | GitHub Actions | 2021-03-24 | Build site. |
| Rmd | c87e8e1 | Francisco Bischoff | 2021-03-24 | targets and workflowr |
| Rmd | 7c3cc31 | Francisco Bischoff | 2021-03-23 | Targets |
| html | 7c3cc31 | Francisco Bischoff | 2021-03-23 | Targets |
| html | 01a7ace | Francisco Bischoff | 2020-07-23 | Refactor |
| html | 5f450d2 | Francisco Bischoff | 2020-05-05 | gh-pages placeholder |
Dataset hosted by:
TLDR;
This website contains all the necessary for reproducibility of this Ph.D. It is built joining three frameworks:
- workflowr, the main infrastructure that organizes every analysis step as Github versions. But instead of showing all commits, it just keeps the important ones.
- targets, a Make-like pipeline toolkit for Statistics and data science in R. It supersedes drake package. This allows to keep track of every step of the data science workflow and helps understand what needs to be rebuilt and what has not changed since the last iteration. Every complete analysis shall be registered by one entry in the previous package (workflowr)
- thesisdown, inspired by the package bookdown helps write the thesis in rmarkdown that is easily compiled in PDF, Doc, EPUB, and allows to change the theme/format for several universities/journals.
Use the big button above 
to navigate through the older commits.
Use the top menu for further information and the thesis itself.
Last Targets Run network:
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23)
os Ubuntu 20.04.4 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Lisbon
date 2022-08-21
pandoc 2.17.0.1 @ /usr/bin/ (via rmarkdown)
─ Packages ───────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
askpass 1.1 2019-01-13 [1] CRAN (R 4.2.0)
assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.2.0)
backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0)
base64url 1.4 2018-05-14 [1] CRAN (R 4.2.0)
bookdown 0.28.1 2022-08-11 [1] Github (rstudio/bookdown@f52bdab)
bslib 0.4.0 2022-07-16 [1] CRAN (R 4.2.1)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0)
callr 3.7.1 2022-07-13 [1] CRAN (R 4.2.1)
cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.0)
codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.0)
crayon 1.5.1 2022-03-26 [1] CRAN (R 4.2.0)
credentials 1.3.2 2021-11-29 [1] CRAN (R 4.2.0)
data.table 1.14.2 2021-09-27 [1] CRAN (R 4.2.0)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
debugme 1.1.0 2017-10-22 [1] CRAN (R 4.2.0)
devtools 2.4.4 2022-07-20 [1] CRAN (R 4.2.1)
digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0)
dplyr 1.0.9 2022-04-28 [1] CRAN (R 4.2.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
evaluate 0.16 2022-08-09 [1] CRAN (R 4.2.1)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
gert 1.7.0 2022-08-07 [1] CRAN (R 4.2.1)
getPass 0.2-2 2017-07-21 [1] CRAN (R 4.2.0)
git2r 0.30.1.9000 2022-04-29 [1] Github (ropensci/git2r@80ba185)
gittargets * 0.0.4.9000 2022-08-14 [1] Github (wlandau/gittargets@64d5134)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
here * 1.0.1 2020-12-13 [1] CRAN (R 4.2.0)
htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.2.0)
httpuv 1.6.5 2022-01-05 [1] CRAN (R 4.2.0)
httr 1.4.3 2022-05-04 [1] CRAN (R 4.2.0)
igraph 1.3.4 2022-07-19 [1] CRAN (R 4.2.1)
jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.2.0)
jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.2.0)
knitr 1.39 2022-04-26 [1] CRAN (R 4.2.0)
later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.0)
magrittr * 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0)
openssl 2.0.2 2022-05-24 [1] CRAN (R 4.2.0)
pillar 1.8.0 2022-07-18 [1] CRAN (R 4.2.1)
pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.2.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
pkgload 1.3.0 2022-06-27 [1] CRAN (R 4.2.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0)
processx 3.7.0 2022-07-07 [1] CRAN (R 4.2.1)
profvis 0.3.7 2020-11-02 [1] CRAN (R 4.2.1)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0)
ps 1.7.1 2022-06-18 [1] CRAN (R 4.2.0)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.1)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0)
renv 0.15.5-49 2022-08-11 [1] Github (rstudio/renv@96d0a62)
rlang 1.0.4 2022-07-12 [1] CRAN (R 4.2.1)
rmarkdown 2.14.3 2022-07-28 [1] Github (rstudio/rmarkdown@63b7ecf)
rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.0)
sass 0.4.2 2022-07-16 [1] CRAN (R 4.2.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
shiny 1.7.2 2022-07-19 [1] CRAN (R 4.2.1)
stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.2.0)
sys 3.4 2020-07-23 [1] CRAN (R 4.2.0)
tarchetypes * 0.7.0 2022-08-05 [1] CRAN (R 4.2.1)
targets * 0.13.1 2022-08-05 [1] CRAN (R 4.2.1)
tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.2.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.1)
usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.0)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
uuid 1.1-0 2022-04-19 [1] CRAN (R 4.2.0)
vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0)
visNetwork 2.1.0 2021-09-29 [1] CRAN (R 4.2.0)
whisker 0.4 2019-08-28 [1] CRAN (R 4.2.0)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
workflowr * 1.7.0 2021-12-21 [1] CRAN (R 4.2.0)
xfun 0.32 2022-08-10 [1] CRAN (R 4.2.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0)
yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0)
[1] /workspace/.cache/R/renv/proj_libs/false.alarm_2submodels-0a931486/R-4.2/x86_64-pc-linux-gnu
[2] /usr/lib/R/library
──────────────────────────────────────────────────────────────────────────────