Merge pull request #460 from jhudsl/clif-reproducibility

Clif reproducibility

.github/workflows/pull_request.yml

@@ -474,7 +474,7 @@ jobs:
           echo "changes=$changes" >> $GITHUB_OUTPUT 
           git add . --force
           git commit -m 'Render preview' || echo "No changes to commit"
-          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
+          git pull --rebase --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
           git push --force || echo "No changes to commit"
         shell: bash
 

docs/_schedule_table.Rmd

@@ -4,7 +4,7 @@
 |                                        |                             |                                                                                                                                                                                                                                          |                                                                                                                                                    |                                                                                                                                                                                                                                                                          |                                                                                    |
 | [Day 1](docs/module_details/day1.html) | Intro                       | [HTML](modules/Intro/Intro.html), [PDF](modules/Intro/Intro.pdf)                                                                                                                                                                         | [Rmd](modules/Intro/Intro.Rmd)                                                                                                                     |                                                                                                                                                                                                                                                                          | [Day 1 Cheatsheet](modules/cheatsheets/Day-1.pdf)                                  |
 |                                        | RStudio                     | [HTML](modules/RStudio/RStudio.html), [PDF](modules/RStudio/RStudio.pdf)                                                                                                                                                                 | [Rmd](modules/RStudio/RStudio.Rmd)                                                                                                                 | [Lab](modules/RStudio/lab/RStudio_Lab.Rmd), [Key](modules/RStudio/lab/RStudio_Lab_Key.Rmd), [Key HTML](modules/RStudio/lab/RStudio_Lab_Key.html)                                                                                                                         |                                                                                    |
-|                                        | Reproducibility             | [HTML](modules/Reproducibility/Reproducibility.html), [PDF](modules/Reproducibility/Reproducibility.pdf)                                                                                                                                  | [Rmd](modules/Reproducibility/Reproducibility.Rmd)                                                                                                 |                                                                                                                                                                                                                                                                          | [Good scientific coding practices](resources/good-scientific-coding-practices.pdf) |
+|                                        | Reproducibility             | [HTML](modules/Reproducibility/Reproducibility.html), [PDF](modules/Reproducibility/Reproducibility.pdf)                                                                                                                                  | [Rmd](modules/Reproducibility/Reproducibility.Rmd)                                                                                                 | [Lab](modules/Reproducibility/lab/Reproducibility_Lab.Rmd), [Key](modules/Reproducibility/lab/Reproducibility_Lab_Key.Rmd), [Key HTML](modules/Reproducibility/lab/Reproducibility_Lab_Key.html)                                                                                                                         | [Good scientific coding practices](resources/good-scientific-coding-practices.pdf) |
 |                                        |                             |                                                                                                                                                                                                                                          |                                                                                                                                                    |                                                                                                                                                                                                                                                                          |                                                                                    |
 | [Day 2](docs/module_details/day2.html) | Basic R                     | [HTML](modules/Basic_R/Basic_R.html), [PDF](modules/Basic_R/Basic_R.pdf)                                                                                                                                                                 | [Rmd](modules/Basic_R/Basic_R.Rmd)                                                                                                                 | [Lab](modules/Basic_R/lab/Basic_R_Lab.Rmd), [Key](modules/Basic_R/lab/Basic_R_Lab_Key.Rmd), [Key HTML](modules/Basic_R/lab/Basic_R_Lab_Key.html)                                                                                                                         | [Day 2 Cheatsheet](modules/cheatsheets/Day-2.pdf)                                  |
 |                                        | Data Input                  | [HTML](modules/Data_Input/Data_Input.html), [PDF](modules/Data_Input/Data_Input.pdf)                                                                                                                                                     | [Rmd](modules/Data_Input/Data_Input.Rmd)                                                                                                           | [Lab](modules/Data_Input/lab/Data_Input_Lab.Rmd), [Key](modules/Data_Input/lab/Data_Input_Lab_Key.Rmd), [Key HTML](modules/Data_Input/lab/Data_Input_Lab_Key.html)                                                                                                       | [Debugging tips guide](resources/debugging_guide.pdf)                              |

modules/Intro/Intro.Rmd

@@ -535,3 +535,7 @@ knitr::include_graphics(here::here("images/the-end-g23b994289_1280.jpg"))
 
 Image by <a href="https://pixabay.com/users/geralt-9301/?utm_source=link-attribution&amp;utm_medium=referral&amp;utm_campaign=image&amp;utm_content=812226">Gerd Altmann</a> from <a href="https://pixabay.com//?utm_source=link-attribution&amp;utm_medium=referral&amp;utm_campaign=image&amp;utm_content=812226">Pixabay</a>
 
+
+
+
+

modules/Reproducibility/Reproducibility.Rmd

@@ -6,9 +6,11 @@ output:
     widescreen: yes
 --- 
 
+```{r include=FALSE}
+knitr::opts_chunk$set(echo = FALSE, message = FALSE, comment=FALSE, warning=FALSE)
+```
 
-
-```{r, echo = FALSE, message = FALSE, comment=FALSE}
+```{r}
 # from these slides: https://docs.google.com/presentation/d/1-cauITbscmnDEDt5IqrZOLlCjyhzEOZY5fqwVY7l8tQ/edit?usp=sharing
 library(knitr)
 opts_chunk$set(comment = "")
@@ -17,7 +19,7 @@ suppressPackageStartupMessages(library(dplyr))
 library(tidyverse)
 library(devtools)
 library(remotes)
-install.packages("ottrpal")
+install.packages("ottrpal", repos = "https://cloud.r-project.org", quiet = TRUE)
 library(ottrpal)
 ```
 
@@ -174,6 +176,10 @@ sessionInfo()
 knitr::include_graphics("images/session_info.png")
 ```
 
+## Lab 1
+
+🏠 [Class Website](https://jhudatascience.org/intro_to_r/)    
+💻 [Lab](https://jhudatascience.org/intro_to_r/modules/Reproducibility/lab/Reproducibility_Lab.Rmd)
 
 ## More resources
 

modules/Reproducibility/lab/Reproducibility_Lab.Rmd

@@ -0,0 +1,34 @@
+---
+title: "Reproducibility Lab"
+output: html_document
+editor_options: 
+  chunk_output_type: console
+---
+
+1. Create two objects in your environment, `x` and `y`. Assign `x` as a vector of numbers 1, 2, and 3. Assign `y` as a vector of numbers 4, 5, and 6. Once complete, check that both objects are visible in your RStudio environment.
+```{r}
+
+```
+
+2. Clear your environment. Check that `x` and `y` are no longer in the environment by typing each letter in the console. What is the result?
+```{r}
+
+```
+
+3. Check your R session info. Which version of R are you running? Which version of the `knitr` package are you running? Write these details below.
+```{r}
+
+```
+
+- R version:
+- `knitr` version:
+
+**Bonus / Extra practice**: Create a vector `z` with the numbers 0 to 9. Set the seed for the R random number generator to 1234. Draw 5 numbers at random from `z` using the `sample()` function with `replace = TRUE`. Repeatedly run the code 3 times and note what you observe.
+```{r}
+
+```
+
+**Bonus / Extra practice**: Run the `sample()` statement again, but this time without running the `set.seed()` line. What do you notice about the 5 numbers?
+```{r}
+
+```

modules/Reproducibility/lab/Reproducibility_Lab_Key.Rmd

@@ -0,0 +1,39 @@
+---
+title: "Reproducibility Lab Key"
+output: html_document
+editor_options: 
+  chunk_output_type: console
+---
+
+1. Create two objects in your environment, `x` and `y`. Assign `x` as a vector of numbers 1, 2, and 3. Assign `y` as a vector of numbers 4, 5, and 6. Once complete, check that both objects are visible in your RStudio environment.
+```{r}
+x <- c(1, 2, 3)
+y <- c(4, 5, 6)
+x
+y
+```
+
+2. Clear your environment. Check that `x` and `y` are no longer in the environment by typing each letter in the console. What is the result?
+```{r}
+rm(list = ls())
+```
+
+3. Check your R session info. Which version of R are you running? Which version of the `knitr` package are you running? Write these details below.
+```{r}
+sessionInfo()
+```
+
+- R version:
+- `knitr` version:
+
+**Bonus / Extra practice**: Create a vector `z` with the numbers 0 to 9. Set the seed for the R random number generator to 1234. Draw 5 numbers at random from `z` using the `sample()` function with `replace = TRUE`. Repeatedly run the code 3 times and note what you observe.
+```{r}
+z <- 0:9
+set.seed(1234)
+sample(x = z, size = 5, replace = TRUE)
+```
+
+**Bonus / Extra practice**: Run the `sample()` statement again, but this time without running the `set.seed()` line. What do you notice about the 5 numbers?
+```{r}
+sample(x = z, size = 5, replace = TRUE)
+```

resources/dictionary.txt

@@ -98,6 +98,7 @@ jhur
 jitter
 Juneteenth
 Kaggle
+knitr
 Lawlor
 lefthand
 Leanpub

scripts/render_modules.R

@@ -50,17 +50,20 @@ if (length(lab_files) != 0) {
   for (i in 1:length(lab_files)) {
     module_name <- stringr::str_split(lab_files, pattern = '/')[[i]][2]
     rmarkdown::render(lab_files[i],
-                      output_dir = paste0("modules/", module_name, "/lab"))
+                      output_dir = paste0("modules/", module_name, "/lab"),
+                      envir = new.env())
   }
 }
 
 # loop thru and render all lecture files to html
 # Specific module name will be pulled out based on the dir name in modules/
+
 if (length(lecture_files) != 0) {
   for (i in 1:length(lecture_files)) {
     module_name <-
       stringr::str_split(lecture_files, pattern = '/')[[i]][2]
     rmarkdown::render(lecture_files[i],
-                      output_dir = paste0("modules/", module_name))
+                      output_dir = paste0("modules/", module_name),
+                      envir = new.env())
   }
 }