Last updated: 2023-05-13

Checks: 7 0

Knit directory: pcarbo/analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0.3). 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(1) 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 71910a6. 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:    analysis/fit-scd-ex-k=10.rds
    Ignored:    sbatch/makefile_demo/sims/sim0001.csv
    Ignored:    sbatch/makefile_demo/sims/sim0002.csv
    Ignored:    sbatch/makefile_demo/sims/sim0003.csv
    Ignored:    sbatch/makefile_demo/sims/sim0004.csv
    Ignored:    sbatch/makefile_demo/sims/sim0005.csv
    Ignored:    sbatch/makefile_demo/sims/sim0006.csv
    Ignored:    sbatch/makefile_demo/sims/sim0007.csv
    Ignored:    sbatch/makefile_demo/sims/sim0008.csv
    Ignored:    sbatch/makefile_demo/sims/sim0009.csv
    Ignored:    sbatch/makefile_demo/sims/sim0010.csv
    Ignored:    sbatch/makefile_demo/sims/sim0011.csv
    Ignored:    sbatch/makefile_demo/sims/sim0012.csv
    Ignored:    sbatch/makefile_demo/sims/sim0013.csv
    Ignored:    sbatch/makefile_demo/sims/sim0014.csv
    Ignored:    sbatch/makefile_demo/sims/sim0015.csv
    Ignored:    sbatch/makefile_demo/sims/sim0016.csv
    Ignored:    sbatch/makefile_demo/sims/sim0017.csv
    Ignored:    sbatch/makefile_demo/sims/sim0018.csv
    Ignored:    sbatch/makefile_demo/sims/sim0019.csv
    Ignored:    sbatch/makefile_demo/sims/sim0020.csv
    Ignored:    sbatch/makefile_demo/sims/sim0021.csv
    Ignored:    sbatch/makefile_demo/sims/sim0022.csv
    Ignored:    sbatch/makefile_demo/sims/sim0023.csv
    Ignored:    sbatch/makefile_demo/sims/sim0024.csv
    Ignored:    sbatch/makefile_demo/sims/sim0025.csv
    Ignored:    sbatch/makefile_demo/sims/sim0026.csv
    Ignored:    sbatch/makefile_demo/sims/sim0027.csv
    Ignored:    sbatch/makefile_demo/sims/sim0028.csv
    Ignored:    sbatch/makefile_demo/sims/sim0029.csv
    Ignored:    sbatch/makefile_demo/sims/sim0030.csv
    Ignored:    sbatch/makefile_demo/sims/sim0031.csv
    Ignored:    sbatch/makefile_demo/sims/sim0032.csv
    Ignored:    sbatch/makefile_demo/sims/sim0033.csv
    Ignored:    sbatch/makefile_demo/sims/sim0034.csv
    Ignored:    sbatch/makefile_demo/sims/sim0035.csv
    Ignored:    sbatch/makefile_demo/sims/sim0036.csv
    Ignored:    sbatch/makefile_demo/sims/sim0037.csv
    Ignored:    sbatch/makefile_demo/sims/sim0038.csv
    Ignored:    sbatch/makefile_demo/sims/sim0039.csv
    Ignored:    sbatch/makefile_demo/sims/sim0040.csv
    Ignored:    sbatch/makefile_demo/sims/sim0041.csv
    Ignored:    sbatch/makefile_demo/sims/sim0042.csv
    Ignored:    sbatch/makefile_demo/sims/sim0043.csv
    Ignored:    sbatch/makefile_demo/sims/sim0044.csv
    Ignored:    sbatch/makefile_demo/sims/sim0045.csv
    Ignored:    sbatch/makefile_demo/sims/sim0046.csv
    Ignored:    sbatch/makefile_demo/sims/sim0047.csv
    Ignored:    sbatch/makefile_demo/sims/sim0048.csv
    Ignored:    sbatch/makefile_demo/sims/sim0049.csv
    Ignored:    sbatch/makefile_demo/sims/sim0050.csv
    Ignored:    sbatch/makefile_demo/sims/sim0051.csv
    Ignored:    sbatch/makefile_demo/sims/sim0052.csv
    Ignored:    sbatch/makefile_demo/sims/sim0053.csv
    Ignored:    sbatch/makefile_demo/sims/sim0054.csv
    Ignored:    sbatch/makefile_demo/sims/sim0055.csv
    Ignored:    sbatch/makefile_demo/sims/sim0056.csv
    Ignored:    sbatch/makefile_demo/sims/sim0057.csv
    Ignored:    sbatch/makefile_demo/sims/sim0058.csv
    Ignored:    sbatch/makefile_demo/sims/sim0059.csv
    Ignored:    sbatch/makefile_demo/sims/sim0060.csv
    Ignored:    sbatch/makefile_demo/sims/sim0061.csv
    Ignored:    sbatch/makefile_demo/sims/sim0062.csv
    Ignored:    sbatch/makefile_demo/sims/sim0063.csv
    Ignored:    sbatch/makefile_demo/sims/sim0064.csv
    Ignored:    sbatch/makefile_demo/sims/sim0065.csv
    Ignored:    sbatch/makefile_demo/sims/sim0066.csv
    Ignored:    sbatch/makefile_demo/sims/sim0067.csv
    Ignored:    sbatch/makefile_demo/sims/sim0068.csv
    Ignored:    sbatch/makefile_demo/sims/sim0069.csv
    Ignored:    sbatch/makefile_demo/sims/sim0070.csv
    Ignored:    sbatch/makefile_demo/sims/sim0071.csv
    Ignored:    sbatch/makefile_demo/sims/sim0072.csv
    Ignored:    sbatch/makefile_demo/sims/sim0073.csv
    Ignored:    sbatch/makefile_demo/sims/sim0074.csv
    Ignored:    sbatch/makefile_demo/sims/sim0075.csv
    Ignored:    sbatch/makefile_demo/sims/sim0076.csv
    Ignored:    sbatch/makefile_demo/sims/sim0077.csv
    Ignored:    sbatch/makefile_demo/sims/sim0078.csv
    Ignored:    sbatch/makefile_demo/sims/sim0079.csv
    Ignored:    sbatch/makefile_demo/sims/sim0080.csv
    Ignored:    sbatch/makefile_demo/sims/sim0081.csv
    Ignored:    sbatch/makefile_demo/sims/sim0082.csv
    Ignored:    sbatch/makefile_demo/sims/sim0083.csv
    Ignored:    sbatch/makefile_demo/sims/sim0084.csv
    Ignored:    sbatch/makefile_demo/sims/sim0085.csv
    Ignored:    sbatch/makefile_demo/sims/sim0086.csv
    Ignored:    sbatch/makefile_demo/sims/sim0087.csv
    Ignored:    sbatch/makefile_demo/sims/sim0088.csv
    Ignored:    sbatch/makefile_demo/sims/sim0089.csv
    Ignored:    sbatch/makefile_demo/sims/sim0090.csv
    Ignored:    sbatch/makefile_demo/sims/sim0091.csv
    Ignored:    sbatch/makefile_demo/sims/sim0092.csv
    Ignored:    sbatch/makefile_demo/sims/sim0093.csv
    Ignored:    sbatch/makefile_demo/sims/sim0094.csv
    Ignored:    sbatch/makefile_demo/sims/sim0095.csv
    Ignored:    sbatch/makefile_demo/sims/sim0096.csv
    Ignored:    sbatch/makefile_demo/sims/sim0097.csv
    Ignored:    sbatch/makefile_demo/sims/sim0098.csv
    Ignored:    sbatch/makefile_demo/sims/sim0099.csv
    Ignored:    sbatch/makefile_demo/sims/sim0100.csv
    Ignored:    sbatch/makefile_demo/sims/sim0101.csv
    Ignored:    sbatch/makefile_demo/sims/sim0102.csv
    Ignored:    sbatch/makefile_demo/sims/sim0103.csv
    Ignored:    sbatch/makefile_demo/sims/sim0104.csv
    Ignored:    sbatch/makefile_demo/sims/sim0105.csv
    Ignored:    sbatch/makefile_demo/sims/sim0106.csv
    Ignored:    sbatch/makefile_demo/sims/sim0107.csv
    Ignored:    sbatch/makefile_demo/sims/sim0108.csv
    Ignored:    sbatch/makefile_demo/sims/sim0109.csv
    Ignored:    sbatch/makefile_demo/sims/sim0110.csv
    Ignored:    sbatch/makefile_demo/sims/sim0111.csv
    Ignored:    sbatch/makefile_demo/sims/sim0112.csv
    Ignored:    sbatch/makefile_demo/sims/sim0113.csv
    Ignored:    sbatch/makefile_demo/sims/sim0114.csv
    Ignored:    sbatch/makefile_demo/sims/sim0115.csv
    Ignored:    sbatch/makefile_demo/sims/sim0116.csv
    Ignored:    sbatch/makefile_demo/sims/sim0117.csv
    Ignored:    sbatch/makefile_demo/sims/sim0118.csv
    Ignored:    sbatch/makefile_demo/sims/sim0119.csv
    Ignored:    sbatch/makefile_demo/sims/sim0120.csv
    Ignored:    sbatch/makefile_demo/sims/sim0121.csv
    Ignored:    sbatch/makefile_demo/sims/sim0122.csv
    Ignored:    sbatch/makefile_demo/sims/sim0123.csv
    Ignored:    sbatch/makefile_demo/sims/sim0124.csv
    Ignored:    sbatch/makefile_demo/sims/sim0125.csv
    Ignored:    sbatch/makefile_demo/sims/sim0126.csv
    Ignored:    sbatch/makefile_demo/sims/sim0127.csv
    Ignored:    sbatch/makefile_demo/sims/sim0128.csv
    Ignored:    sbatch/makefile_demo/sims/sim0129.csv
    Ignored:    sbatch/makefile_demo/sims/sim0130.csv
    Ignored:    sbatch/makefile_demo/sims/sim0131.csv
    Ignored:    sbatch/makefile_demo/sims/sim0132.csv
    Ignored:    sbatch/makefile_demo/sims/sim0133.csv
    Ignored:    sbatch/makefile_demo/sims/sim0134.csv
    Ignored:    sbatch/makefile_demo/sims/sim0135.csv
    Ignored:    sbatch/makefile_demo/sims/sim0136.csv
    Ignored:    sbatch/makefile_demo/sims/sim0137.csv
    Ignored:    sbatch/makefile_demo/sims/sim0138.csv
    Ignored:    sbatch/makefile_demo/sims/sim0139.csv
    Ignored:    sbatch/makefile_demo/sims/sim0140.csv
    Ignored:    sbatch/makefile_demo/sims/sim0141.csv
    Ignored:    sbatch/makefile_demo/sims/sim0142.csv
    Ignored:    sbatch/makefile_demo/sims/sim0143.csv
    Ignored:    sbatch/makefile_demo/sims/sim0144.csv
    Ignored:    sbatch/makefile_demo/sims/sim0145.csv
    Ignored:    sbatch/makefile_demo/sims/sim0146.csv
    Ignored:    sbatch/makefile_demo/sims/sim0147.csv
    Ignored:    sbatch/makefile_demo/sims/sim0148.csv
    Ignored:    sbatch/makefile_demo/sims/sim0149.csv
    Ignored:    sbatch/makefile_demo/sims/sim0150.csv
    Ignored:    sbatch/makefile_demo/sims/sim0151.csv
    Ignored:    sbatch/makefile_demo/sims/sim0152.csv
    Ignored:    sbatch/makefile_demo/sims/sim0153.csv
    Ignored:    sbatch/makefile_demo/sims/sim0154.csv
    Ignored:    sbatch/makefile_demo/sims/sim0155.csv
    Ignored:    sbatch/makefile_demo/sims/sim0156.csv
    Ignored:    sbatch/makefile_demo/sims/sim0157.csv
    Ignored:    sbatch/makefile_demo/sims/sim0158.csv
    Ignored:    sbatch/makefile_demo/sims/sim0159.csv
    Ignored:    sbatch/makefile_demo/sims/sim0160.csv
    Ignored:    sbatch/makefile_demo/sims/sim0161.csv
    Ignored:    sbatch/makefile_demo/sims/sim0162.csv
    Ignored:    sbatch/makefile_demo/sims/sim0163.csv
    Ignored:    sbatch/makefile_demo/sims/sim0164.csv
    Ignored:    sbatch/makefile_demo/sims/sim0165.csv
    Ignored:    sbatch/makefile_demo/sims/sim0166.csv
    Ignored:    sbatch/makefile_demo/sims/sim0167.csv
    Ignored:    sbatch/makefile_demo/sims/sim0168.csv
    Ignored:    sbatch/makefile_demo/sims/sim0169.csv
    Ignored:    sbatch/makefile_demo/sims/sim0170.csv
    Ignored:    sbatch/makefile_demo/sims/sim0171.csv
    Ignored:    sbatch/makefile_demo/sims/sim0172.csv
    Ignored:    sbatch/makefile_demo/sims/sim0173.csv
    Ignored:    sbatch/makefile_demo/sims/sim0174.csv
    Ignored:    sbatch/makefile_demo/sims/sim0175.csv
    Ignored:    sbatch/makefile_demo/sims/sim0176.csv
    Ignored:    sbatch/makefile_demo/sims/sim0177.csv
    Ignored:    sbatch/makefile_demo/sims/sim0178.csv
    Ignored:    sbatch/makefile_demo/sims/sim0179.csv
    Ignored:    sbatch/makefile_demo/sims/sim0180.csv
    Ignored:    sbatch/makefile_demo/sims/sim0181.csv
    Ignored:    sbatch/makefile_demo/sims/sim0182.csv
    Ignored:    sbatch/makefile_demo/sims/sim0183.csv
    Ignored:    sbatch/makefile_demo/sims/sim0184.csv
    Ignored:    sbatch/makefile_demo/sims/sim0185.csv
    Ignored:    sbatch/makefile_demo/sims/sim0186.csv
    Ignored:    sbatch/makefile_demo/sims/sim0187.csv
    Ignored:    sbatch/makefile_demo/sims/sim0188.csv
    Ignored:    sbatch/makefile_demo/sims/sim0189.csv
    Ignored:    sbatch/makefile_demo/sims/sim0190.csv
    Ignored:    sbatch/makefile_demo/sims/sim0191.csv
    Ignored:    sbatch/makefile_demo/sims/sim0192.csv
    Ignored:    sbatch/makefile_demo/sims/sim0193.csv
    Ignored:    sbatch/makefile_demo/sims/sim0194.csv
    Ignored:    sbatch/makefile_demo/sims/sim0195.csv
    Ignored:    sbatch/makefile_demo/sims/sim0196.csv
    Ignored:    sbatch/makefile_demo/sims/sim0197.csv
    Ignored:    sbatch/makefile_demo/sims/sim0198.csv
    Ignored:    sbatch/makefile_demo/sims/sim0199.csv
    Ignored:    sbatch/makefile_demo/sims/sim0200.csv
    Ignored:    sbatch/makefile_demo/sims/sim0201.csv
    Ignored:    sbatch/makefile_demo/sims/sim0202.csv
    Ignored:    sbatch/makefile_demo/sims/sim0203.csv
    Ignored:    sbatch/makefile_demo/sims/sim0204.csv
    Ignored:    sbatch/makefile_demo/sims/sim0205.csv
    Ignored:    sbatch/makefile_demo/sims/sim0206.csv
    Ignored:    sbatch/makefile_demo/sims/sim0207.csv
    Ignored:    sbatch/makefile_demo/sims/sim0208.csv
    Ignored:    sbatch/makefile_demo/sims/sim0209.csv
    Ignored:    sbatch/makefile_demo/sims/sim0210.csv
    Ignored:    sbatch/makefile_demo/sims/sim0211.csv
    Ignored:    sbatch/makefile_demo/sims/sim0212.csv
    Ignored:    sbatch/makefile_demo/sims/sim0213.csv
    Ignored:    sbatch/makefile_demo/sims/sim0214.csv
    Ignored:    sbatch/makefile_demo/sims/sim0215.csv
    Ignored:    sbatch/makefile_demo/sims/sim0216.csv
    Ignored:    sbatch/makefile_demo/sims/sim0217.csv
    Ignored:    sbatch/makefile_demo/sims/sim0218.csv
    Ignored:    sbatch/makefile_demo/sims/sim0219.csv
    Ignored:    sbatch/makefile_demo/sims/sim0220.csv
    Ignored:    sbatch/makefile_demo/sims/sim0221.csv
    Ignored:    sbatch/makefile_demo/sims/sim0222.csv
    Ignored:    sbatch/makefile_demo/sims/sim0223.csv
    Ignored:    sbatch/makefile_demo/sims/sim0224.csv
    Ignored:    sbatch/makefile_demo/sims/sim0225.csv
    Ignored:    sbatch/makefile_demo/sims/sim0226.csv
    Ignored:    sbatch/makefile_demo/sims/sim0227.csv
    Ignored:    sbatch/makefile_demo/sims/sim0228.csv
    Ignored:    sbatch/makefile_demo/sims/sim0229.csv
    Ignored:    sbatch/makefile_demo/sims/sim0230.csv
    Ignored:    sbatch/makefile_demo/sims/sim0231.csv
    Ignored:    sbatch/makefile_demo/sims/sim0232.csv
    Ignored:    sbatch/makefile_demo/sims/sim0233.csv
    Ignored:    sbatch/makefile_demo/sims/sim0234.csv
    Ignored:    sbatch/makefile_demo/sims/sim0235.csv
    Ignored:    sbatch/makefile_demo/sims/sim0236.csv
    Ignored:    sbatch/makefile_demo/sims/sim0237.csv
    Ignored:    sbatch/makefile_demo/sims/sim0238.csv
    Ignored:    sbatch/makefile_demo/sims/sim0239.csv
    Ignored:    sbatch/makefile_demo/sims/sim0240.csv
    Ignored:    sbatch/makefile_demo/sims/sim0241.csv
    Ignored:    sbatch/makefile_demo/sims/sim0242.csv
    Ignored:    sbatch/makefile_demo/sims/sim0243.csv
    Ignored:    sbatch/makefile_demo/sims/sim0244.csv
    Ignored:    sbatch/makefile_demo/sims/sim0245.csv
    Ignored:    sbatch/makefile_demo/sims/sim0246.csv
    Ignored:    sbatch/makefile_demo/sims/sim0247.csv
    Ignored:    sbatch/makefile_demo/sims/sim0248.csv
    Ignored:    sbatch/makefile_demo/sims/sim0249.csv
    Ignored:    sbatch/makefile_demo/sims/sim0250.csv

Untracked files:
    Untracked:  R/demo.nmf.R
    Untracked:  R/nmfmu.R
    Untracked:  R/scd.R

Unstaged changes:
    Modified:   analysis/linreg_methods_demo.Rmd

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 71910a6 Peter Carbonetto 2023-05-13 workflowr::wflow_publish("index.Rmd", verbose = TRUE)
html cc66338 Peter Carbonetto 2022-06-15 Build site.
Rmd 046ca10 Peter Carbonetto 2022-06-15 workflowr::wflow_publish("index.Rmd")
html b30bc42 Peter Carbonetto 2020-10-12 Re-generated the overview page.
html 5c1307a Peter Carbonetto 2020-10-12 Added link to overview page.
Rmd 7a4bd96 Peter Carbonetto 2020-10-12 workflowr::wflow_publish("index.Rmd")
html debdc6f Peter Carbonetto 2020-01-14 Added more links to home page.
Rmd 0289f50 Peter Carbonetto 2020-01-14 wflow_publish("index.Rmd")
html 3357384 Peter Carbonetto 2020-01-14 Created home page.
Rmd 781b68e Peter Carbonetto 2020-01-14 Added/modified workflowr files.
Rmd 43ad1c3 Peter Carbonetto 2020-01-14 Added workflowr files.

Analyses

Other things

Emojis

Playing around with the R package emo:

library(emo)
cat(ji("truck"),
    ji("pencil"),
    ji("pushpin"),
    ji("pig"),
    "\n")
# 🚚 📝 📌 🐷

You can use emo::jis to get the full list of the several thousand available emojis.


sessionInfo()
# R version 3.6.2 (2019-12-12)
# Platform: x86_64-apple-darwin15.6.0 (64-bit)
# Running under: macOS Catalina 10.15.7
# 
# Matrix products: default
# BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] emo_0.0.0.9000
# 
# loaded via a namespace (and not attached):
#  [1] Rcpp_1.0.8        pillar_1.6.2      compiler_3.6.2    bslib_0.3.1      
#  [5] later_1.0.0       jquerylib_0.1.4   git2r_0.29.0      workflowr_1.7.0.3
#  [9] tools_3.6.2       digest_0.6.23     lubridate_1.7.10  jsonlite_1.7.2   
# [13] evaluate_0.14     lifecycle_1.0.3   tibble_3.1.3      pkgconfig_2.0.3  
# [17] rlang_1.0.6       cli_3.5.0         yaml_2.2.0        xfun_0.29        
# [21] fastmap_1.1.0     stringr_1.4.0     knitr_1.37        generics_0.0.2   
# [25] fs_1.5.2          vctrs_0.3.8       sass_0.4.0        rprojroot_2.0.3  
# [29] glue_1.4.2        R6_2.4.1          fansi_0.4.0       rmarkdown_2.11   
# [33] purrr_0.3.4       magrittr_2.0.1    whisker_0.4       promises_1.1.0   
# [37] ellipsis_0.3.2    htmltools_0.5.4   assertthat_0.2.1  httpuv_1.5.2     
# [41] utf8_1.1.4        stringi_1.4.3     crayon_1.4.1