Last updated: 2022-10-05
Checks: 7 0
Knit directory:
false.alarm/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 b79f104. 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: .devcontainer/exts/
Ignored: .docker/
Ignored: .github/ISSUE_TEMPLATE/
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_change2/meta/process
Ignored: _regime_change2/meta/progress
Ignored: _regime_change2/objects/
Ignored: _regime_change2/user/
Ignored: _regime_change3/meta/process
Ignored: _regime_change3/meta/progress
Ignored: _regime_change3/objects/
Ignored: _regime_change3/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: _targets/meta/process
Ignored: _targets/meta/progress
Ignored: _targets/objects/
Ignored: _targets/user/
Ignored: analysis/shiny/rsconnect/
Ignored: analysis/shiny_land/rsconnect/
Ignored: dev/
Ignored: inst/extdata/
Ignored: papers/aime2021/aime2021.md
Ignored: papers/epia2022/epia2022.md
Ignored: presentations/MEDCIDS21/MEDCIDS21-10min_files/
Ignored: presentations/MEDCIDS21/MEDCIDS21_files/
Ignored: presentations/Report/Midterm-Report_cache/
Ignored: presentations/Report/Midterm-Report_files/
Ignored: protocol/SecondReport_cache/
Ignored: protocol/SecondReport_files/
Ignored: protocol/_files/
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: thesis/Rplots.pdf
Ignored: thesis/_bookdown_files/
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/blog-202108.Rmd) and HTML (docs/blog-202108.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 |
|---|---|---|---|---|
| html | dbbd1d6 | Francisco Bischoff | 2022-08-22 | Squashed commit of the following: |
| html | de21180 | Francisco Bischoff | 2022-08-21 | Squashed commit of the following: |
| html | 5943a09 | Francisco Bischoff | 2022-07-21 | Build site. |
| html | 3328477 | Francisco Bischoff | 2022-07-21 | Build site. |
| Rmd | 03d1e68 | Francisco Bischoff | 2022-07-19 | Squashed commit of the following: |
| html | 5927668 | Francisco Bischoff | 2022-04-17 | Build site. |
| Rmd | ba0c9e1 | Francisco Bischoff | 2022-04-17 | refactor blog |
The first workflow presented in July has changed. Its purpose was to define a “big picture” of the process.
The main changes introduced were:
Initially, the data had been carried along the workflow, being copied at each new step. That obviously is not the way to handle it. Thus, the raw data is stored only on the “dataset” object and reused where needed.
Now, any modification to the raw data will create a new object, for example, “ds_filtered,” where the SQI filter is applied to the data.
The goal of this work is to operate with streaming data. Thus, the Matrix Profile computation algorithm has been rewritten to handle receiving data in chunks. The algorithm can simulate one observation at a time or a batch of observations (for efficiency). The result will always be as if one observation had been received individually by the model.
To avoid unnecessary recomputations for this analysis phase, the companion statistics needed by the model are pre-computed and fed alongside the data the algorithm needs to process. The pre-computation also allows experimenting with parameters during this process.
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23)
os Ubuntu 20.04.5 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Lisbon
date 2022-10-05
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 [1] 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 0.29.2 2022-09-26 [1] Github (rstudio/bookdown@dfe92a2)
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 3.7.2 2022-08-22 [1] CRAN (R 4.2.1)
cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.1)
codetools 0.2-18 2020-11-04 [2] CRAN (R 4.2.0)
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0)
conflicted 1.1.0 2021-11-26 [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 * 1.0.10 2022-09-01 [1] CRAN (R 4.2.1)
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 1.9.0 2022-09-15 [1] CRAN (R 4.2.1)
getPass 0.2-2 2017-07-21 [1] CRAN (R 4.2.0)
ggplot2 * 3.3.6 2022-05-03 [1] CRAN (R 4.2.0)
git2r 0.30.1.9000 2022-04-29 [1] Github (ropensci/git2r@80ba185)
gittargets * 0.0.5.9000 2022-09-26 [1] Github (wlandau/gittargets@a50dd58)
glue * 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.1)
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 1.6.6 2022-09-08 [1] CRAN (R 4.2.1)
httr 1.4.4 2022-08-17 [1] CRAN (R 4.2.1)
igraph 1.3.5 2022-09-22 [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)
kableExtra * 1.3.4 2021-02-20 [1] CRAN (R 4.2.0)
knitr 1.40 2022-08-24 [1] CRAN (R 4.2.1)
later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.2.0)
lifecycle 1.0.2 2022-09-09 [1] CRAN (R 4.2.1)
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)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
openssl 2.0.3 2022-09-14 [1] CRAN (R 4.2.1)
pillar 1.8.1 2022-08-19 [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)
plotly * 4.10.0 2021-10-09 [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 2022-05-26 [1] CRAN (R 4.2.0)
rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
rmarkdown 2.16.1 2022-09-26 [1] Github (rstudio/rmarkdown@9577707)
rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0)
rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
rvest 1.0.3 2022-08-19 [1] CRAN (R 4.2.1)
sass 0.4.2 2022-07-16 [1] CRAN (R 4.2.1)
scales 1.2.1 2022-08-20 [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 1.4.1 2022-08-20 [1] CRAN (R 4.2.1)
svglite 2.1.0.9000 2022-09-26 [1] Github (r-lib/svglite@8f30fc6)
sys 3.4 2020-07-23 [1] CRAN (R 4.2.0)
systemfonts 1.0.4 2022-02-11 [1] CRAN (R 4.2.0)
tarchetypes * 0.7.1 2022-09-07 [1] CRAN (R 4.2.1)
targets * 0.13.4 2022-09-15 [1] CRAN (R 4.2.1)
tibble * 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
tidyr 1.2.1 2022-09-08 [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 2.1.6.9000 2022-10-03 [1] Github (r-lib/usethis@8ecb7ab)
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)
viridisLite 0.4.1 2022-08-22 [1] CRAN (R 4.2.1)
webshot 0.5.3 2022-04-14 [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 0.33 2022-09-12 [1] CRAN (R 4.2.1)
xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0)
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-d6f1a0d1/R-4.2/x86_64-pc-linux-gnu
[2] /usr/lib/R/library
──────────────────────────────────────────────────────────────────────────────