• Friday February 7, 2020 - “Best Practices of Maintaining a Lab Notebook to improve Accountability”, Melissa Ishler, Ph.D. Department of Entomology, The Pennsylvania State University, 11:15 am to 12:05 pm. 127 Noll Laboratory, Host: Department of Kinesiology
• Institute for Computational and Data Science (ICDS) events
• “The Data Deluge”, ICDS Symposium, March 16-17, 2020, NLI.

• Registration
  • What, why, who, how?
• Tools for reproducible workflows
  • Introduction to RStudio
  • Introduction to R Markdown
• Doing real work with R Markdown

• What are they?
• Why are they a thing?
• Who’s doing them?
• How they work and how to get involved

• Peer review and provisional acceptance of methodologically sound study proposals

• Results (positive or null) don’t determine publication (prevent publication bias)
• Reduce questionable practices
  • p-hacking
  • HARKing

• Restrict creativity in reporting “un-registered”/exploratory analyses?
  • Clearer communication about confirmatory vs. exploratory
• Mandatory vs. optional
• Clinical trials vs. fundamental research
• Exploration is not a dirty word

• Journals with Registered Reports from COS
• How do they work?
  • Google sheet comparing features https://docs.google.com/spreadsheets/d/1D4_k-8C_UENTRtbPzXfhjEyu3BfLxdOsn9j-otrO870/edit#gid=0

• Standardized preregistration tool
• Separate confirmatory from exploratory analyses
• One author completes checklist, others receive email to approve
• Unique (private) URL to pdf
• Share when you like or never

• An integrated development environment (IDE) for R

• Code editor
• R console
• Integrated help
• Image viewer
• Integration with git and other version-control packages
• Project management

• Markdown
  • Mark-up language to make it easy to write HTML
• R Markdown a special type of Markdown
  • Allows for “literate” programming, mixing text, analysis, figures
  • Adds to Markdown syntax

• Open up RStudio
• Create a new R Markdown document
  • File/New File/R Markdown...

• Select Document, call it something sensible like psy-525-rmarkdown-testbed
  • NB: This is the document’s title not the name of the file.

• Save the file as testbed.Rmd

• Header
• Chunks
• Text, etc.

• Text formatting
  • italics by surrounding text with single asterisks or underscores: *italics* or _italics_
  • boldface by surrounding text with double asterisks or underscores: **boldface** or __boldface__

• Text formatting
  • strikethrough by surrounding text with double tildes: ~~strikethrough~~
  • Clickable URLs by surrounding link text with square brackets and URL with parentheses:
  • [Clickable URLs](http://www.psu.edu)

• Paragraph formatting
  • Headings with level specified by the number of hash (#) marks
  • Lists (bullet and enumerated)
  • Block quotes
  • Code blocks

# This is a Heading 1
## This is a Heading 2
### This is a Heading 3

Code:

- An item
    - A nested item
        - A doubly-nested item
- Another item

• An item
  • A nested item
    • A doubly-nested item
• Another item

Code:

1. An enumerated item
    - A nested item
1. A second enumerated item

1. An enumerated item
   • A nested item
2. A second enumerated item

Notice how the numbers are incremented automatically!

• <CTRL>+2 goes to console
• <CTRL>+1 goes to source
• <UP-ARROW> <RETURN>
• <COMMAND><ALT>+I (Mac OS); <CTRL><ALT>+I (Windows) inserts a chunk
• Train your fingers now!

Code:

> Four score and seven years ago, some famous President 
> spoke infamous words that would live on throughout history.
> These words are famous enough that I want to highlight them with a block quote.

Four score and seven years ago, some famous President spoke infamous words that would live on throughout history. These words are famous enough that I want to highlight them with a block quote.

• Images can be inserted using this syntax ![Alt text](/path/to/img.jpg)
• Comments – won’t print in rendered output –
• <!- This is a comment ->

• .Rmd extension
• Combine text, code, images, figures, video
• “Computable” reports, documents, slide shows, notebooks
• Code in “chunks”
• Output in multiple formats from the same file

Code (in a chunk):

```{r}
x = rnorm(n = 100, mean = 0, sd = 1)   # N(0,1)
y = rnorm(n = 100, mean = 2, sd = 0.5) # N(2, 0.5)
```

Code (in a chunk):

```{r}
summary(x)
summary(y)
```

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
## -2.1435 -0.6226  0.1075  0.1305  0.8273  2.5863

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7052  1.6464  1.9712  1.9492  2.2385  2.8509

Code (in a chunk):

```{r}
hist(x)
```

Code (in a chunk):

```{r}
hist(y)
```

Code (in a chunk):

```{r}
plot(x,y)
```

Code (in a chunk):

```{r rog, fig.cap="Rick's pic from Databrary"}
knitr::include_graphics("https://nyu.databrary.org/party/6/avatar")
```

Code (outside a chunk):

<img src="img/sleic.jpg" height=500px>

Height parameter (or, e.g. height=500px) is optional, but useful. Remember Markdown -> HTML.

• Don’t change your working directory…EVAH!
• Give R Markdown document “local” paths
• Projects (next week) make this MUCH easier
• Talk to R inside chunks; talk to RStudio outside chunks
• Save your R Markdown file often

HTML Code (outside a chunk–not talking to R)

<iframe width="420" height="315" 
src="https://www.youtube.com/embed/9hUy9ePyo6Q" 
frameborder="0" allowfullscreen>
</iframe>

• YouTube gives you code to cut and paste to ‘embed’ a video.
• Just copy and paste

Code (in a chunk):

```{r}
summ.x = summary(x)
summ.y = summary(y)
names(summ.x) # Figure out variable names for indexing
```

## [1] "Min."    "1st Qu." "Median"  "Mean"    "3rd Qu."
## [6] "Max."

• Prefix inline code bits with “`r”
• Terminate inline code bits with single backtick “`”
• No more copying and pasting statistical results!

• Format numeric outputs with sprintf()
• sprintf("%2.3f", 14.7666) gives 14.77
• See help("sprintf")

Index by variable name: X lies within the range of [-2.1434695, 2.5862562].

Index by numeric index: The (y-x) difference in means is 1.8187584.

Calculate and report: The correlation between x and y is -0.2262571.

Markdown (not in a chunk–not talking to R) using LaTex syntax.

$$e=mc^{2}$$

\[e=mc^{2}\]

• You want to give a talk based on your analysis
• You want to give a collaborator a report on your analysis in a format they prefer
• You don’t want to duplicate effort

• Document
  • HTML
    • Embedded or non-embedded figures
  • MS Word
  • PDF

• Presentation
  • HTML (ioslides)
  • HTML (Slidy)
  • PDF (Beamer)

• Shiny (interactive document)
  • Document
  • Presentation (ioslides)
• A website!

• R Markdown documents have header text written in YAML
• YAML = YAML Ain’t Markup Language

---
title: "psy-525-rmarkdown-testbed"
author: "Rick Gilmore"
date: "2020-02-27 12:28:14"
output:
  html_document:
    self_contained: true
  word_document:
    fig_width: 5
    fig_height: 5
    fig_caption: false
    df_print: kable
  pdf_document: default
  ioslides_presentation: default
  powerpoint_presentation: default
---

• YAML syntax is specific
• Yes, the tabs and colons matter
• You can have fun/waste a lot of time exploring YAML options

• OTOH, chunk options are super useful
  • echo=TRUE prints your R code
  • echo=FALSE runs but does not print your code; include=FALSE does also.
  • eval=FALSE prevents a chunk from executing

• Pressing the knit button converts your document to the default format
• That is, the first format after your output: parameter
• Pressing and holding the knit button gives other options
• knitr is an R package that R Markdown depends upon heavily

In the console (not your R Markdown document):

> rmarkdown::render("testbed.Rmd")

• Saves time when editing interactively
  • Render, then switch to browser (alt-tab or command-tab)
  • Refresh browser
• Give documents parameters, like which output(s) you want

In the console:

> rmarkdown::render("testbed.Rmd", 
output_format = c("html_document", "word_document", "pdf_document"))

Makes copies in three different formats: testbed.html, testbed.docx, and testbed.pdf.

• output_file = myslides.ioslides.html or output_file = myslides.slidy.html to specify different output file targets.
• output_dir = reports or output_dir = docx to direct output to a specific directory.
• parameterized reports using params:

In your header:

---
title: "psy-525-rmarkdown-testbed"
author: "Rick Gilmore"
date: "2020-02-27 12:28:14"
output:
  html_document: default
params:
  name: Joe
  quest: "to find the Holy Grail"
---

• Single words don’t require quotes; phrases with spaces do

In the console (for example):

> rmarkdown::render("testbed.Rmd", params=list(name="Francine"))

Make a self-contained HTML file that includes any plots you’ve made or graphics you’ve embedded. Great for sharing locally (i.e, as a document not over the web).

---
output:
  html_document:
    self_contained: true
---

Add a table of contents. toc_depth controls how “deep” into your header hierarchy the table of contents should go.

---
output:
  html_document:
    toc: true
    toc_depth: 2
---

Add toc_float: true to make the table of contents “float” to the side of your document.

---
output:
  html_document:
    toc: true
    toc_depth: 2
    toc_float: true
---

Add number_sections: true to make the table of contents automatically generate a hierarchical set of numbers–1.0, 1.2, 2.1, etc.–based on your header hierarchy. Remember, # is header 1, ## is header 2, etc.

---
output:
  html_document:
    toc: true
    toc_depth: 2
    toc_float: true
    number_sections: true
---

Include your code chunks (include = TRUE) but hide them until someone wants to see them by adding code_folding: hide to your YAML header.

---
output:
  html_document:
    toc: true
    toc_depth: 2
    toc_float: true
    number_sections: true
    code_folding: hide
---

• RStudio projects
• Version control using git and GitHub

This talk was produced on 2020-02-27 in RStudio using R Markdown. The code and materials used to generate the slides may be found at https://github.com/psu-psychology/psy-525-reproducible-research-2020. Information about the R Session that produced the code is as follows:

## R version 3.6.2 (2019-12-12)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Mojave 10.14.6
## 
## Matrix products: default
## BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.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 
## [6] methods   base     
## 
## other attached packages:
##  [1] DiagrammeR_1.0.5 forcats_0.4.0    stringr_1.4.0   
##  [4] dplyr_0.8.3      purrr_0.3.3      readr_1.3.1     
##  [7] tidyr_1.0.0      tibble_2.1.3     ggplot2_3.2.1   
## [10] tidyverse_1.3.0  seriation_1.2-8 
## 
## loaded via a namespace (and not attached):
##  [1] viridis_0.5.1      httr_1.4.1        
##  [3] tufte_0.5          jsonlite_1.6      
##  [5] viridisLite_0.3.0  foreach_1.4.8     
##  [7] modelr_0.1.5       gtools_3.8.1      
##  [9] assertthat_0.2.1   highr_0.8         
## [11] cellranger_1.1.0   yaml_2.2.0        
## [13] pillar_1.4.3       backports_1.1.5   
## [15] lattice_0.20-38    glue_1.3.1        
## [17] digest_0.6.23      RColorBrewer_1.1-2
## [19] rvest_0.3.5        colorspace_1.4-1  
## [21] htmltools_0.4.0    pkgconfig_2.0.3   
## [23] broom_0.5.3        haven_2.2.0       
## [25] scales_1.1.0       gdata_2.18.0      
## [27] farver_2.0.3       generics_0.0.2    
## [29] withr_2.1.2        lazyeval_0.2.2    
## [31] cli_2.0.1          magrittr_1.5      
## [33] crayon_1.3.4       readxl_1.3.1      
## [35] evaluate_0.14      fs_1.3.1          
## [37] fansi_0.4.1        nlme_3.1-142      
## [39] MASS_7.3-51.5      gplots_3.0.1.2    
## [41] xml2_1.2.2         tools_3.6.2       
## [43] registry_0.5-1     hms_0.5.3         
## [45] lifecycle_0.1.0    munsell_0.5.0     
## [47] reprex_0.3.0       cluster_2.1.0     
## [49] packrat_0.5.0      compiler_3.6.2    
## [51] caTools_1.18.0     rlang_0.4.4       
## [53] grid_3.6.2         iterators_1.0.12  
## [55] rstudioapi_0.10    visNetwork_2.0.9  
## [57] htmlwidgets_1.5.1  labeling_0.3      
## [59] bitops_1.0-6       rmarkdown_2.1     
## [61] gtable_0.3.0       codetools_0.2-16  
## [63] DBI_1.1.0          TSP_1.1-8         
## [65] R6_2.4.1           gridExtra_2.3     
## [67] lubridate_1.7.4    knitr_1.27        
## [69] pwr_1.2-2          utf8_1.1.4        
## [71] KernSmooth_2.23-16 dendextend_1.13.3 
## [73] stringi_1.4.5      Rcpp_1.0.3        
## [75] vctrs_0.2.2        gclus_1.3.2       
## [77] dbplyr_1.4.2       tidyselect_1.0.0  
## [79] xfun_0.12