#7 end of day

vignettes/07_reproducable_research.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "A Biostatistician's Introduction to Reproducible Research and Reporting"
+title: "Introduction to Reproducible Research and Reporting"
 author: "Paul Stevenson"
 date: "`r format(Sys.time(), '%d %B %Y')`"
 output:
@@ -18,6 +18,9 @@ vignette: >
 
 ```{r init, include = FALSE, echo = FALSE}
 library(biometrics)
+library(knitr)
+
+source("assets/R/hooks.R")
 
 ```
 
@@ -32,19 +35,19 @@ library(biometrics)
 
 <div class = "col2 small">
 
-  - Convention for how you organise your research artefacts into directories
-  - A standard and easily recognisable way for organising a reproducible research project
-  - Simplifies file management and streamlines analytical workflows
-  - Ideal for projects that result in the publication of a paper
-  - Easier to communicate your work with other researchers (and your future self)
-  - "Project as a Package"
-  - R and beyond
+- Convention for how you organise your research artefacts into directories
+- A standard and easily recognisable way for organising a reproducible research project
+- Simplifies file management and streamlines analytical workflows
+- Ideal for projects that result in the publication of a paper
+- Easier to communicate your work with other researchers (and your future self)
+- "Project as a Package"
+- R and beyond
 
 </div>
 
 &nbsp;
 
-<div class = "small">[https://github.com/ropensci/rrrpkg](https://github.com/ropensci/rrrpkg)</div>
+<div class = "small"><https://github.com/ropensci/rrrpkg></div>
 
 ## Definition
 
@@ -55,118 +58,119 @@ library(biometrics)
 
 <div class = "col2 small">
 
-  >- Convention for how you organise your research artefacts into directories
-  >- A standard and easily recognisable way for organising a reproducible research project
-  >- Simplifies file management and streamlines analytical workflows
-  >- Ideal for projects that result in the publication of a paper
-  >- Easier to communicate your work with other researchers (and your future self)
-  >- "Project as a Package"
-  >- R and beyond
+>- Convention for how you organise your research artefacts into directories
+>- A standard and easily recognisable way for organising a reproducible research project
+>- Simplifies file management and streamlines analytical workflows
+>- Ideal for projects that result in the publication of a paper
+>- Easier to communicate your work with other researchers (and your future self)
+>- "Project as a Package"
+>- R and beyond
   
 </div>
 
 &nbsp;
 
-<div class = "small">[https://github.com/ropensci/rrrpkg](https://github.com/ropensci/rrrpkg)</div>
+<div class = "small"><https://github.com/ropensci/rrrpkg></div>
 
 ## Example Project Directory | *The Container*
 
-```{r, echo = F, out.extra = "class='centre'", out.width = "50%"}
-knitr::include_graphics(file.path("assets", "images", "Slide1.JPG"))
+```{r, echo = F, out.extra = "figure", out.width = "50%"}
+knitr::include_graphics(file.path("assets", "images", "07_Slide1.JPG"))
 
 ```
 
 # Example Template Project
 
 ## Project meta data
 
- >- README.md
-   >- a synopsis of the project
-   >- very useful for your future self and colleges/collaborators
-   
- >- NEWS.md
-   >- Communicate change to the project files/data
-   
- >- DESCRIPTION (R specific - Python requirements.txt)
- >- LICENSE
- >- .gitIgnore (Will talk about Git later)
+>- README.md
+  >- a synopsis of the project
+  >- very useful for your future self and colleges/collaborators
+ 
+>- NEWS.md
+  >- Communicate change to the project files/data
+ 
+>- DESCRIPTION (R specific - Python requirements.txt)
+>- LICENSE
+>- .gitIgnore (Will talk about Git later)
 
 # Project Administration
 
 ## Project Administration
 
-```{r, echo = F, out.extra = "class='centre'", out.width = "50%"}
-knitr::include_graphics(file.path("assets", "images", "Slide2.JPG"))
+```{r, echo = F, out.extra = "figure", out.width = "50%"}
+knitr::include_graphics(file.path("assets", "images", "07_Slide2.JPG"))
 
 ```
 
 ## admin \*
 
- - Project meta data
- - Legal documents (e.g. contracts)
- - Communications
- - Ethics documentation
- - Indirect resources (e.g. papers)
- - Project management resources
- - etc.
+- Project meta data
+- Legal documents (e.g. contracts)
+- Communications
+- Ethics documentation
+- Indirect resources (e.g. papers)
+- Project management resources
+- etc.
 
-\* I Would consider adding directories/files marked with an asterisk to .gitIgnore
+\* Consider adding directories/files marked with an asterisk to .gitIgnore
 
 ## archive \*
 
- - Old code that might be redundant, but is precious
- - Helps to keep project folders tidy
+- Old code that might be redundant, but is precious
+- Helps to keep project folders tidy
 
 # Data Directories
 
 ## Data Directories
 
-```{r, echo = F, out.extra = "class='centre'", out.width = "50%"}
-knitr::include_graphics(file.path("assets", "images", "Slide3.JPG"))
+```{r, echo = F, out.extra = "figure", out.width = "50%"}
+knitr::include_graphics(file.path("assets", "images", "07_Slide3.JPG"))
 
 ```
 
 ## data-raw \*
 
- - a "read-only" directory to store raw data (e.g. Excel, STATA, SAS, .csv)
- - recommend changing the file to read only in operating system
- - The heart of reproducible research, all actions are traceable from raw data to report
+- A "read-only" directory to store raw data (e.g. Excel, STATA, SAS, .csv)
+- Recommend changing the file to read only in operating system
+- The heart of reproducible research, all actions are traceable from raw data to report
 
 ## data \*
 
- - Data is converted from the raw format in to the software's preferred structure (e.g. .RData, .rds)
- - Minimal operations are performed on data
-   - correcting variable names
-   - data cleaning
-   - data harmonisation/standardisation/coding
-   - table joining/splitting
+- Data is converted from the raw format in to the software's preferred structure (e.g. .RData, .rds)
+- Minimal operations are performed on data
+  - correcting variable names
+  - data cleaning
+  - data harmonisation/standardisation/coding
+  - table joining/splitting
 
 ## cache \*
 
- >- Store manipulated data here for statistical analysis
+>- Store manipulated data here for statistical analysis
    
 # Script/Algorithm Directories
 
 ## Script/Algorithm Directories
 
-```{r, echo = F, out.extra = "class='centre'", out.width = "50%"}
-knitr::include_graphics(file.path("assets", "images", "Slide4.JPG"))
+```{r, echo = F, out.extra = "figure", out.width = "50%"}
+knitr::include_graphics(file.path("assets", "images", "07_Slide4.JPG"))
 
 ```
 
 ## ProjectTemplate Package
 
- >- Automates data initiation
-   >- Loads library
-   >- Runs munge scripts
-   >- Loads data
+```{r eval = F}
+library('ProjectTemplate')
+load.project()
+
+```
 
- >- <http://projecttemplate.net/getting_started.html>
+>- Automates data initiation
+  >- Loads library
+  >- Runs munge scripts
+  >- Loads data
 
-<code>
-library('ProjectTemplate')<br />
-load.project()
-</code>
+>- <http://projecttemplate.net/getting_started.html>
 
 ## munge
 
@@ -176,50 +180,50 @@ load.project()
   <footer class="blockquote-footer">www.dictionary.com</footer>
 </blockquote>
 
- - A ProjectTemplate directory
- - Order numerically in the order the scripts should be run:
-   - 01-munge.R
-   - 02-Lexis.R
+- A ProjectTemplate directory
+- Order numerically in the order the scripts should be run:
+  - 01-munge.R
+  - 02-Lexis.R
 
 ## R | (src, py, cpp, or whatever)
 
- - <code>00-cleaner.R</code> - read in raw data and save in <em>data</em>
- - <code>01-main.R</code> - main script file
- - <code>99-helper.R</code> - custom functions to be read in at start of script
- - <code>data.R</code> - How you can create a data dictionary in R!
+- <code>00-cleaner.R</code> - read in raw data and save in <em>data</em>
+- <code>01-main.R</code> - main script file
+- <code>99-helper.R</code> - custom functions to be read in at start of script
+- <code>data.R</code> - How you can create a data dictionary in R!
 
 ## Other Directories
 
- - config
-   - ProjectTemplate configuration files, e.g.:
-     - Auto-munge
-     - Auto-load packages
-     - Auto-import cache/data
- - inst
-   - Auto generated files used by some package-related functions
-   - Vignettes
+- config
+ - ProjectTemplate configuration files, e.g.:
+   - Auto-munge
+   - Auto-load packages
+   - Auto-import cache/data
+- inst
+ - Auto generated files used by some package-related functions
+ - Vignettes
 
-## Other Possibilities
+## More Directory Ideas
 
 <div class = "col2">
 
- - shiny
- - docker
- - logs
- - diagnostics
- - man/doc
- - graphs
- - tests
- - reports/vignettes
+- shiny
+- docker
+- logs
+- diagnostics
+- man/doc
+- graphs
+- tests
+- reports/vignettes
 
  </div>
 
 # Reporting | Biometrics R Markdown Templates
 
 ## Reporting
 
-```{r, echo = F, out.extra = "class='centre'", out.width = "50%"}
-knitr::include_graphics(file.path("assets", "images", "Slide5.JPG"))
+```{r, echo = F, out.extra = "figure", out.width = "50%"}
+knitr::include_graphics(file.path("assets", "images", "07_Slide5.JPG"))
 
 ```
 
@@ -237,8 +241,8 @@ knitr::include_graphics(file.path("assets", "images", "Slide5.JPG"))
   <footer class="blockquote-footer"><https://rmarkdown.rstudio.com/></footer>
 </blockquote>
 
-```{r, echo = F, out.extra = "class='centre'", out.width = "15%"}
-knitr::include_graphics(file.path("assets", "images", "rmarkdown.png"))
+```{r, echo = F, out.extra = "figure", out.width = "15%"}
+knitr::include_graphics(file.path("assets", "images", "07_rmarkdown.png"))
 
 ```
 
@@ -253,23 +257,23 @@ Live demo
 ## Version Control
 
 <div class = "col2"><p>
-```{r, echo = F, out.extra = "class='centre'", out.width = "75%"}
-knitr::include_graphics(file.path("assets", "images", "github_logo.png"))
+```{r, echo = F, out.extra = "figure", out.width = "75%"}
+knitr::include_graphics(file.path("assets", "images", "07_github_logo.png"))
 
 ```
 
-```{r, echo = F, out.extra = "class='centre'", out.width = "75%"}
-knitr::include_graphics(file.path("assets", "images", "gitlab.png"))
+```{r, echo = F, out.extra = "figure", out.width = "75%"}
+knitr::include_graphics(file.path("assets", "images", "07_gitlab.png"))
 
 ```
 
-```{r, echo = F, out.extra = "class='centre'", out.width = "75%"}
-knitr::include_graphics(file.path("assets", "images", "logos__Bitbucket.png"))
+```{r, echo = F, out.extra = "figure", out.width = "75%"}
+knitr::include_graphics(file.path("assets", "images", "07_logos__Bitbucket.png"))
 
 ```
 
-```{r, echo = F, out.extra = "class='centre'", out.width = "75%"}
-knitr::include_graphics(file.path("assets", "images", "cran.png"))
+```{r, echo = F, out.extra = "figure", out.width = "75%"}
+knitr::include_graphics(file.path("assets", "images", "07_cran.png"))
 
 ```
 
@@ -279,21 +283,21 @@ knitr::include_graphics(file.path("assets", "images", "cran.png"))
 
 ## Coding Tips
 
- - Be consistent:
-   - Values:
-     - "day1" vs "day_1" vs "Day 1"
-     - "5th May 1970" vs "01-05-1970" vs "05/01/1970" vs <mark>1970/05/01</mark>
-   - Variables:
-     - <code>FirstName</code> vs <mark><code>first_name</code></mark>
-     - <code>sex</code> vs <mark><code>female</code></mark>
- - Use variable names that a human can understand
- - Document/comment your code!
+- Be consistent:
+  - Values:
+    - "day1" vs "day_1" vs "Day 1"
+    - "5th May 1970" vs "01-05-1970" vs "05/01/1970" vs <mark>1970/05/01</mark>
+  - Variables:
+    - <code>FirstName</code> vs <mark><code>first_name</code></mark>
+    - <code>sex</code> vs <mark><code>female</code></mark>
+- Use variable names that a human can understand
+- Document/comment your code!
 
 ## Useful Tools/Packages
 
- >- R Studio IDE
- >- Tidyverse - data wrangling and visualisation
- >- repmis: Miscellaneous Tools for Reproducible Research
- >- captioner: Store figure and table captions and print them later
- >- devtools
- >- Telethon Kids Biometrics package <https://github.com/TelethonKids/biometrics>
+>- R Studio IDE
+>- Tidyverse - data wrangling and visualisation
+>- repmis: Miscellaneous Tools for Reproducible Research
+>- captioner: Store figure and table captions and print them later
+>- devtools
+>- Telethon Kids Biometrics package <https://github.com/TelethonKids/biometrics>