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‎docs/03-writing_code.md‎

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## collate en_US.UTF-8
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## ctype en_US.UTF-8
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## tz Etc/UTC
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## date 2024-09-04
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## date 2024-12-18
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## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
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##
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## ─ Packages ───────────────────────────────────────────────────────────────────
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## package * version date (UTC) lib source
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## askpass 1.2.0 2023-09-03 [1] RSPM (R 4.3.0)
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## bookdown 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
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## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2)
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## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0)
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## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0)
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## chromote 0.3.1 2024-08-30 [1] CRAN (R 4.3.2)
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## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0)
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## curl 5.2.0 2023-12-08 [1] RSPM (R 4.3.0)
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## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0)
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## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0)
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## dplyr 1.1.4 2023-11-17 [1] RSPM (R 4.3.0)
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## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0)
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## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0)
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## fansi 1.0.6 2023-12-08 [1] RSPM (R 4.3.0)
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## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0)
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## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0)
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## generics 0.1.3 2022-07-05 [1] RSPM (R 4.3.0)
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## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0)
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## highr 0.10 2022-12-22 [1] RSPM (R 4.3.0)
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## highr 0.11 2024-05-26 [1] CRAN (R 4.3.2)
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## hms 1.1.3 2023-03-21 [1] RSPM (R 4.3.0)
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## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0)
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## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0)
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## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0)
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## httr 1.4.7 2023-08-15 [1] RSPM (R 4.3.0)
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## janitor 2.2.0 2023-02-02 [1] RSPM (R 4.3.0)
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## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0)
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## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0)
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## knitr 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34)
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## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2)
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## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0)
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## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0)
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## lubridate 1.9.3 2023-09-27 [1] RSPM (R 4.3.0)
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## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0)
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## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0)
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## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0)
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## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0)
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## openssl 2.1.1 2023-09-25 [1] RSPM (R 4.3.0)
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## ottrpal 1.2.1 2024-06-11 [1] Github (jhudsl/ottrpal@828539f)
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## ottrpal 1.3.0 2024-10-23 [1] Github (jhudsl/ottrpal@2e19782)
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## pillar 1.9.0 2023-03-22 [1] RSPM (R 4.3.0)
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## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0)
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## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.3.0)
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## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0)
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## processx 3.8.3 2023-12-10 [1] RSPM (R 4.3.0)
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## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0)
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## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0)
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## ps 1.7.6 2024-01-18 [1] RSPM (R 4.3.0)
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## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0)
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## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0)
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## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0)
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## readr 2.1.5 2024-01-10 [1] RSPM (R 4.3.0)
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## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0)
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## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2)
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## rmarkdown 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9)
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## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0)
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## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.3.2)
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## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0)
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## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0)
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## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0)
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## snakecase 0.11.1 2023-08-27 [1] RSPM (R 4.3.0)
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## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0)
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## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0)
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## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.2)
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## tidyselect 1.2.0 2022-10-10 [1] RSPM (R 4.3.0)
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## timechange 0.3.0 2024-01-18 [1] RSPM (R 4.3.0)
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## tzdb 0.4.0 2023-05-12 [1] RSPM (R 4.3.0)
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## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0)
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## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0)
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## utf8 1.2.4 2023-10-22 [1] RSPM (R 4.3.0)
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## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0)
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## xfun 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc)
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## webshot2 0.1.1 2023-08-11 [1] CRAN (R 4.3.2)
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## websocket 1.4.2 2024-07-22 [1] CRAN (R 4.3.2)
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## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2)
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## xml2 1.3.6 2023-12-04 [1] RSPM (R 4.3.0)
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## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0)
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## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0)

‎docs/03-writing_code_activity.md‎

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## collate en_US.UTF-8
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## ctype en_US.UTF-8
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## tz Etc/UTC
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## date 2024-09-04
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## date 2024-12-18
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## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
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##
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## ─ Packages ───────────────────────────────────────────────────────────────────
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## package * version date (UTC) lib source
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## askpass 1.2.0 2023-09-03 [1] RSPM (R 4.3.0)
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## bookdown 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
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## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2)
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## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0)
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## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0)
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## chromote 0.3.1 2024-08-30 [1] CRAN (R 4.3.2)
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## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0)
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## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0)
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## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0)
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## dplyr 1.1.4 2023-11-17 [1] RSPM (R 4.3.0)
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## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0)
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## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0)
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## fansi 1.0.6 2023-12-08 [1] RSPM (R 4.3.0)
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## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0)
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## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0)
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## generics 0.1.3 2022-07-05 [1] RSPM (R 4.3.0)
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## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0)
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## hms 1.1.3 2023-03-21 [1] RSPM (R 4.3.0)
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## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0)
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## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0)
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## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0)
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## httr 1.4.7 2023-08-15 [1] RSPM (R 4.3.0)
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## janitor 2.2.0 2023-02-02 [1] RSPM (R 4.3.0)
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## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0)
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## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0)
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## knitr 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34)
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## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2)
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## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0)
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## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0)
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## lubridate 1.9.3 2023-09-27 [1] RSPM (R 4.3.0)
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## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0)
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## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0)
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## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0)
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## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0)
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## openssl 2.1.1 2023-09-25 [1] RSPM (R 4.3.0)
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## ottrpal 1.2.1 2024-06-11 [1] Github (jhudsl/ottrpal@828539f)
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## ottrpal 1.3.0 2024-10-23 [1] Github (jhudsl/ottrpal@2e19782)
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## pillar 1.9.0 2023-03-22 [1] RSPM (R 4.3.0)
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## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0)
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## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.3.0)
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## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0)
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## processx 3.8.3 2023-12-10 [1] RSPM (R 4.3.0)
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## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0)
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## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0)
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## ps 1.7.6 2024-01-18 [1] RSPM (R 4.3.0)
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## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0)
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## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0)
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## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0)
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## readr 2.1.5 2024-01-10 [1] RSPM (R 4.3.0)
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## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0)
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## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2)
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## rmarkdown 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9)
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## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0)
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## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.3.2)
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## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0)
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## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0)
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## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0)
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## snakecase 0.11.1 2023-08-27 [1] RSPM (R 4.3.0)
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## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0)
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## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0)
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## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.2)
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## tidyselect 1.2.0 2022-10-10 [1] RSPM (R 4.3.0)
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## timechange 0.3.0 2024-01-18 [1] RSPM (R 4.3.0)
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## tzdb 0.4.0 2023-05-12 [1] RSPM (R 4.3.0)
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## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0)
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## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0)
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## utf8 1.2.4 2023-10-22 [1] RSPM (R 4.3.0)
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## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0)
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## xfun 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc)
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## webshot2 0.1.1 2023-08-11 [1] CRAN (R 4.3.2)
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## websocket 1.4.2 2024-07-22 [1] CRAN (R 4.3.2)
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## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2)
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## xml2 1.3.6 2023-12-04 [1] RSPM (R 4.3.0)
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## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0)
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## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0)

‎docs/04-refactoring.md‎

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```
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The `outer()` function performs the same calculation as the nested loop in the original code, but more efficiently. It returns a matrix of all possible combinations of x and y values, with each element of the matrix being the product of the corresponding x and y values. The `rowSums()` function is then used to sum the elements of each row of the matrix, which is equivalent to summing the products of x and y for each index `i` in the original loop. This method avoids the need for the nested loop, resulting in a faster and more efficient computation.
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One optimized way to perform the same calculation is by using the `%*%` operator to perform matrix multiplication. This can be done by converting x and y to matrices and transposing one of them so that their dimensions align for matrix multiplication. This code should be much faster than the original implementation because it takes advantage of highly optimized matrix multiplication algorithms in R.

‎docs/05-annotation.md‎

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## collate en_US.UTF-8
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## tz Etc/UTC
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## date 2024-09-04
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## date 2024-12-18
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## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
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##
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## ─ Packages ───────────────────────────────────────────────────────────────────
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## package * version date (UTC) lib source
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## askpass 1.2.0 2023-09-03 [1] RSPM (R 4.3.0)
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## bookdown 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
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## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2)
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## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0)
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## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0)
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## chromote 0.3.1 2024-08-30 [1] CRAN (R 4.3.2)
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## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0)
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## curl 5.2.0 2023-12-08 [1] RSPM (R 4.3.0)
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## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0)
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## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0)
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## dplyr 1.1.4 2023-11-17 [1] RSPM (R 4.3.0)
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## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0)
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## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0)
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## fansi 1.0.6 2023-12-08 [1] RSPM (R 4.3.0)
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## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0)
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## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0)
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## generics 0.1.3 2022-07-05 [1] RSPM (R 4.3.0)
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## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0)
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## highr 0.10 2022-12-22 [1] RSPM (R 4.3.0)
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## highr 0.11 2024-05-26 [1] CRAN (R 4.3.2)
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## hms 1.1.3 2023-03-21 [1] RSPM (R 4.3.0)
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## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0)
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## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0)
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## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0)
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## httr 1.4.7 2023-08-15 [1] RSPM (R 4.3.0)
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## janitor 2.2.0 2023-02-02 [1] RSPM (R 4.3.0)
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## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0)
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## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0)
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## knitr 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34)
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## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2)
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## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0)
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## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0)
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## lubridate 1.9.3 2023-09-27 [1] RSPM (R 4.3.0)
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## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0)
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## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0)
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## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0)
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## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0)
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## openssl 2.1.1 2023-09-25 [1] RSPM (R 4.3.0)
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## ottrpal 1.2.1 2024-06-11 [1] Github (jhudsl/ottrpal@828539f)
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## ottrpal 1.3.0 2024-10-23 [1] Github (jhudsl/ottrpal@2e19782)
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## pillar 1.9.0 2023-03-22 [1] RSPM (R 4.3.0)
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## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0)
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## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.3.0)
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## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0)
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## processx 3.8.3 2023-12-10 [1] RSPM (R 4.3.0)
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## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0)
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## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0)
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## ps 1.7.6 2024-01-18 [1] RSPM (R 4.3.0)
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## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0)
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‎docs/05-annotation_activity.md‎

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## collate en_US.UTF-8
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## tz Etc/UTC
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## date 2024-09-04
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## date 2024-12-18
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## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
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##
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## ─ Packages ───────────────────────────────────────────────────────────────────
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## package * version date (UTC) lib source
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## bookdown 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
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## rmarkdown 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9)
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## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0)
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## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0)
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## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0)
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## xfun 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc)
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## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2)
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##

‎docs/404.html‎

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