Clean up cheatsheets

modules/cheatsheets/Day-1.md

@@ -1,35 +1,42 @@
 ---
-classoption:
-- landscape
+classoption: landscape
+output:
+  pdf_document: default
+  html_document:
+    df_print: paged
 ---
 
 # Day 1 Cheatsheet
 
-## Intro
+## Basic R
 
 ### Major concepts
 
-- **Package** - a package in R is a bundle or “package” of code (and or possibly data)
-that can be loaded together for easy repeated use or for sharing with others.
-- **Function** - a function is a particular piece of code that allows you to do
-something in R. You can write your own, use functions that come directly from
-installing R, or use functions from additional packages.
+- **Package** - a package in R is a bundle or “package” of code (and or possibly data) that can be loaded together for easy repeated use or for sharing with others. Like an "expansion pack".
+- **Function** - a function is a particular piece of code that allows you to dosomething in R. You can write your own, use functions that come directly from installing R, or use functions from additional packages.
 - **Argument** - an option that you specify to a function.
-- **Object** - an object is something that can be worked with in R - can be lots of
-different things!
-- **Variable** something measured or counted that is a characteristic about a
-sample.
-- **Sample** individuals that you have data about - e.g. people, houses, viruses etc.\
-- **Data frames** A collection of variables and samples in a row/column format. Sample = Row, Variable = Column
-- [**Tidyverse**](https://tidyverse.tidyverse.org/articles/paper.html) - This is a newer set of packages designed for data science that can make your
-code more intuitive as compared to the original older Base R.
-
+- **Object** - an object is something that can be worked with in R - can be lots of different things!
+- [**Tidyverse**](https://tidyverse.tidyverse.org/articles/paper.html) - This is a newer set of packages designed for data science that can make your code more intuitive as compared to the original older Base R.
+- The R console is a full calculator:
+  - `+`, `-`, `/`, `*` are add, subtract, divide and multiply
+  - `^` or `**` is power
+  - parentheses – ( and ) – work with order of operations
+  - %% finds the remainder
+- `#` is the comment symbol; nothing to its right is evaluated.
 
 ### Functions
 |Library/Package|Piece of code|Example of usage|What it does|
 |---------------|-------------|----------------|-------------|
-|Base `R`|[`install.packages()`](https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/install.packages)| `install.packages("remotes")`| Installs packages|
-|Base `R`| [`library()`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/library)|`library(remotes)`| Loads and attaches additional packages to the R environment.|
+| Base `R`| [`<-`](https://stat.ethz.ch/R-manual/R-devel/library/base/html/assignOps.html)| `x <- 1`| Assigns a name `x` to something in the R environment.|
+| Base `R`| [`c()`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/c)| `x <- c(1, 3)`| Combines values into a vector. |
+| Base `R`| [`str()`](https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/str)|`str(x)`| Gets a summary of the object `x` structure.|
+| Base `R`| [`class()`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/class)|`class(x)`| Returns the type of the values in object `x`.|
+| Base `R`| [`length()`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/length)|`length(x)`| Returns how long the object `x` is. |
+| Base `R`| [`seq()`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/seq)|`seq(from = 0, to = 100, by = 5)`| Generate regular sequences. |
+| Base `R`| [`rep()`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/rep)|`rep(1, times = 10)`| Replicates the values in x. Can take `times` or `length.out` argument.|
+| Base `R`| [`sample()`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/sample)|`sample(1:12)`| Takes a sample of the specified size from the elements of x using either with or without replacement. `replace = TRUE` samples with replacement. |
+| Base `R`| [`install.packages()`](https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/install.packages)| `install.packages("tidyverse")`| Installs packages|
+| Base `R`| [`library()`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/library)|`library(tidyverse)`| Loads and attaches additional packages to the R environment. Done every time you start R.|
 
 <div style="page-break-after: always;"></div>
 
@@ -56,26 +63,4 @@ output.
 
 <div style="page-break-after: always;"></div>
 
-## Reproducibility
-
-### Major concepts
-
-- **Reproducibility** - A different analyst re-performs the analysis with the same code and the same data and obtains the same
-result.
-- **Repeatable** - keeping everything the same but repeating the analysis - do we get the same results
-- **Reproducible** - using the same data and analysis but in the hands of another researcher - do we get the same results?
-- **Replicable** - with new data do we obtain the same inferences?
-
-### Functions
-|Library/Package|Piece of code|Example of usage|What it does|
-|---------------|-------------|----------------|-------------|
-| Base `R`| [`sessionInfo()`](https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/sessionInfo) |`sessionInfo()`| Returns the R version information, the OS, and the attached packages in the current R session.|
-
-### More resources
-- [The RMarkdown book](https://bookdown.org/yihui/rmarkdown/)
-- [Jenny Bryan's organizational strategies](https://www.stat.ubc.ca/~jenny/STAT545A/block19_codeFormattingOrganization.html).
-- [Write efficient R code for science](https://www.earthdatascience.org/courses/earth-analytics/automate-science-workflows/write-efficient-code-for-science-r/).
-- [Reproducibility in Cancer Informatics course](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/introduction.html)
-
-
 \* This format was adapted from the [cheatsheet format from AlexsLemonade](https://github.com/AlexsLemonade/training-modules/tree/master/module-cheatsheets).

modules/cheatsheets/Day-2.md

@@ -1,33 +1,30 @@
 ---
-classoption:
-- landscape
+classoption: landscape
+output: pdf_document
 ---
 
 # Day 2 Cheatsheet
 
-## Basic R
+## Reproducibility
 
 ### Major concepts
 
-- **Package** - a package in R is a bundle or “package” of code (and or possibly data)
-that can be loaded together for easy repeated use or for sharing with others.
-- The R console is a full calculator:
-  - `+`, `-`, `/`, `*` are add, subtract, divide and multiply
-  - `^` or `**` is power
-  - parentheses – ( and ) – work with order of operations
-  - %% finds the remainder
-- `#` is the comment symbol; nothing to its right is evaluated.
-
+- **Reproducibility** - A different analyst re-performs the analysis with the same code and the same data and obtains the same
+result.
+- **Repeatable** - keeping everything the same but repeating the analysis - do we get the same results
+- **Reproducible** - using the same data and analysis but in the hands of another researcher - do we get the same results?
+- **Replicable** - with new data do we obtain the same inferences?
 
 ### Functions
 |Library/Package|Piece of code|Example of usage|What it does|
 |---------------|-------------|----------------|-------------|
-| Base `R`| [`<-`](https://stat.ethz.ch/R-manual/R-devel/library/base/html/assignOps.html)| `x <- 1`| Assigns a name to something in the R environment.|
-| Base `R`| [`c()`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/c)| `x <- c(1, 3)`| Combines values into a vector or list. |
-| Base `R`| [`str(x)`](https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/str)|`str(x)`| Gets a summary of the object `x` structure.|
-| Base `R`| [`class(x)`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/class)|`class(x)`| Returns the type of the values in object `x`.|
-| Base `R`| [`print(x)`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/print)|`print(x)`| Prints out contents of `x`.|
-| Base `R`| [`length(x)`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/length)|`length(x)`| Returns how long the object `x` is. |
+| Base `R`| [`sessionInfo()`](https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/sessionInfo) |`sessionInfo()`| Returns the R version information, the OS, and the attached packages in the current R session.|
+
+### More resources
+- [The RMarkdown book](https://bookdown.org/yihui/rmarkdown/)
+- [Jenny Bryan's organizational strategies](https://www.stat.ubc.ca/~jenny/STAT545A/block19_codeFormattingOrganization.html).
+- [Write efficient R code for science](https://www.earthdatascience.org/courses/earth-analytics/automate-science-workflows/write-efficient-code-for-science-r/).
+- [Reproducibility in Cancer Informatics course](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/introduction.html)
 
 <div style="page-break-after: always;"></div>