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diff --git a/...s/figure-html/1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA_g21a84b32106_0_0.png b/...s/figure-html/1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA_g21a84b32106_0_0.png
diff --git a/docs/05-setting-up.md b/docs/05-setting-up.md
@@ -4,3 +4,49 @@
 
 
 ![](resources/images/05-setting-up_files/figure-docx//1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA_g21a84b32106_0_13.png){width=100%}
+
+
+
+## Understand why project organization is key to reproducible analyses
+
+![](resources/images/05-setting-up_files/figure-docx//1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA_g2fea8805c08_0_1121.png){width=100%}
+
+## Understand general principles of project organization
+
+![](resources/images/05-setting-up_files/figure-docx//1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA_g2fea8805c08_0_421.png){width=100%}
+
+![](resources/images/05-setting-up_files/figure-docx//1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA_g2fea8805c08_0_426.png){width=100%}
+
+![](resources/images/05-setting-up_files/figure-docx//1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA_g2fea8805c08_0_442.png){width=100%}
+
+https://github.com/jhudsl/reproducible-r-example
+
+## Navigate file paths
+
+![](resources/images/05-setting-up_files/figure-docx//1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA_g2fea8805c08_0_1337.png){width=100%}
+
+## Handy R Tools
+
+### here package
+
+<blockquote class="twitter-tweet"><p lang="en" dir="ltr">The only two things that make <a href="https://twitter.com/JennyBryan?ref_src=twsrc%5Etfw">@JennyBryan</a> 😤😠🤯. Instead use projects + here::here() <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> <a href="https://t.co/GwxnHePL4n">pic.twitter.com/GwxnHePL4n</a></p>&mdash; Hadley Wickham (@hadleywickham) <a href="https://twitter.com/hadleywickham/status/940021008764846080?ref_src=twsrc%5Etfw">December 11, 2017</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
+
+https://here.r-lib.org/
+
+https://www.tidyverse.org/blog/2017/12/workflow-vs-script/
+
+### RProj files
+
+https://bookdown.org/ndphillips/YaRrr/projects-in-rstudio.html
+
+### ProjectTemplate
+
+http://projecttemplate.net/
+
+### R Markdown files
+
+https://rmarkdown.rstudio.com/articles_intro.html
+
+### Quarto files
+
+https://quarto.org/docs/get-started/hello/rstudio.html
diff --git a/docs/06-rmarkdown.md b/docs/06-rmarkdown.md
diff --git a/docs/09-software-versions.md b/docs/09-software-versions.md
@@ -64,15 +64,19 @@ sessionInfo()
 ## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] vctrs_0.6.5      httr_1.4.7       cli_3.6.2        knitr_1.47.3    
-##  [5] rlang_1.1.4      xfun_0.44.4      jsonlite_1.8.8   glue_1.7.0      
-##  [9] openssl_2.1.1    askpass_1.2.0    htmltools_0.5.7  hms_1.1.3       
-## [13] fansi_1.0.6      rmarkdown_2.27.1 evaluate_0.23    tibble_3.2.1    
-## [17] tzdb_0.4.0       fastmap_1.1.1    yaml_2.3.8       lifecycle_1.0.4 
-## [21] bookdown_0.39.1  compiler_4.3.2   ottrpal_1.2.1    fs_1.6.3        
-## [25] pkgconfig_2.0.3  digest_0.6.34    R6_2.5.1         utf8_1.2.4      
-## [29] readr_2.1.5      curl_5.2.0       pillar_1.9.0     magrittr_2.0.3  
-## [33] tools_4.3.2      xml2_1.3.6
+##  [1] jsonlite_1.8.8   dplyr_1.1.4      compiler_4.3.2   promises_1.2.1  
+##  [5] Rcpp_1.0.12      tidyselect_1.2.0 xml2_1.3.6       webshot2_0.1.1  
+##  [9] stringr_1.5.1    snakecase_0.11.1 later_1.3.2      yaml_2.3.8      
+## [13] fastmap_1.1.1    readr_2.1.5      R6_2.5.1         generics_0.1.3  
+## [17] curl_5.2.0       knitr_1.48       tibble_3.2.1     bookdown_0.41   
+## [21] janitor_2.2.0    rprojroot_2.0.4  openssl_2.1.1    lubridate_1.9.3 
+## [25] pillar_1.9.0     tzdb_0.4.0       rlang_1.1.4      websocket_1.4.2 
+## [29] utf8_1.2.4       stringi_1.8.3    xfun_0.48        timechange_0.3.0
+## [33] cli_3.6.2        magrittr_2.0.3   ps_1.7.6         processx_3.8.3  
+## [37] digest_0.6.34    hms_1.1.3        askpass_1.2.0    lifecycle_1.0.4 
+## [41] chromote_0.3.1   vctrs_0.6.5      ottrpal_1.3.0    evaluate_0.23   
+## [45] glue_1.7.0       fansi_1.0.6      rmarkdown_2.25   httr_1.4.7      
+## [49] tools_4.3.2      pkgconfig_2.0.3  htmltools_0.5.7
 ```
 
 Now we have recorded what some key aspects of our computing environment looked like at the time that this book was rendered last.

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/About.md b/docs/About.md
@@ -51,12 +51,12 @@ These credits are based on our [course contributors table guidelines](https://ww
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       Etc/UTC
-##  date     2024-09-11
+##  date     2024-11-13
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date (UTC) lib source
-##  bookdown      0.39.1  2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
+##  bookdown      0.41    2024-10-16 [1] CRAN (R 4.3.2)
 ##  cachem        1.0.8   2023-05-01 [1] RSPM (R 4.3.0)
 ##  cli           3.6.2   2023-12-11 [1] RSPM (R 4.3.0)
 ##  devtools      2.4.5   2022-10-11 [1] RSPM (R 4.3.0)
@@ -69,7 +69,7 @@ These credits are based on our [course contributors table guidelines](https://ww
 ##  htmltools     0.5.7   2023-11-03 [1] RSPM (R 4.3.0)
 ##  htmlwidgets   1.6.4   2023-12-06 [1] RSPM (R 4.3.0)
 ##  httpuv        1.6.14  2024-01-26 [1] RSPM (R 4.3.0)
-##  knitr         1.47.3  2024-06-11 [1] Github (yihui/knitr@e1edd34)
+##  knitr         1.48    2024-07-07 [1] CRAN (R 4.3.2)
 ##  later         1.3.2   2023-12-06 [1] RSPM (R 4.3.0)
 ##  lifecycle     1.0.4   2023-11-07 [1] RSPM (R 4.3.0)
 ##  magrittr      2.0.3   2022-03-30 [1] RSPM (R 4.3.0)
@@ -85,15 +85,15 @@ These credits are based on our [course contributors table guidelines](https://ww
 ##  Rcpp          1.0.12  2024-01-09 [1] RSPM (R 4.3.0)
 ##  remotes       2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0)
 ##  rlang         1.1.4   2024-06-04 [1] CRAN (R 4.3.2)
-##  rmarkdown     2.27.1  2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9)
+##  rmarkdown     2.25    2023-09-18 [1] RSPM (R 4.3.0)
 ##  sessioninfo   1.2.2   2021-12-06 [1] RSPM (R 4.3.0)
 ##  shiny         1.8.0   2023-11-17 [1] RSPM (R 4.3.0)
 ##  stringi       1.8.3   2023-12-11 [1] RSPM (R 4.3.0)
 ##  stringr       1.5.1   2023-11-14 [1] RSPM (R 4.3.0)
 ##  urlchecker    1.0.1   2021-11-30 [1] RSPM (R 4.3.0)
 ##  usethis       2.2.3   2024-02-19 [1] RSPM (R 4.3.0)
 ##  vctrs         0.6.5   2023-12-01 [1] RSPM (R 4.3.0)
-##  xfun          0.44.4  2024-06-11 [1] Github (yihui/xfun@9da62cc)
+##  xfun          0.48    2024-10-03 [1] CRAN (R 4.3.2)
 ##  xtable        1.8-4   2019-04-21 [1] RSPM (R 4.3.0)
 ##  yaml          2.3.8   2023-12-11 [1] RSPM (R 4.3.0)
 ## 

diff --git a/docs/Tools-for-Reproducibility-in-R.docx b/docs/Tools-for-Reproducibility-in-R.docx