markdown source builds

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Source  : 76b12f0
Branch  : main
Author  : Naupaka Zimmerman <[email protected]>
Time    : 2024-11-09 03:49:22 +0000
Message : Merge pull request #303 from JasonJWilliamsNY/patch-for-299

Patch for #299

Author: actions-user

01-r-basics.md

@@ -518,10 +518,13 @@ human_chr_number * 2
 
 ## Exercise: Compute the golden ratio
 
+The [golden ratio](https://en.wikipedia.org/wiki/Golden_ratio) is a famous
+mathematical constant associated with beauty, architecture, and [art](https://www.mos.org/leonardo/activities/golden-ratio.html).
+
 One approximation of the golden ratio (φ) can be found by taking the sum of 1
-and the square root of 5, and dividing by 2 as in the example above. Compute
+and the square root of 5, and dividing that sum by 2, as in the example above. Compute
 the golden ratio to 3 digits of precision using the `sqrt()` and `round()`
-functions. Hint: remember the `round()` function can take 2 arguments.
+functions. Hint: the `round()` function can take 2 arguments.
 
 :::::::::::::::  solution
 
@@ -536,7 +539,8 @@ round((1 + sqrt(5)) / 2, digits = 3)
 [1] 1.618
 ```
 
-Notice that you can place one function inside of another.
+Notice that you can place one function inside of another, and that you can use
+the 'digits' argument to return the desired precision.
 
 
 
@@ -605,6 +609,7 @@ Let's create a few more vectors to play around with:
 ``` r
 # Some interesting human SNPs
 # while accuracy is important, typos in the data won't hurt you here
+# feel free to copy and paste
 
 snps <- c("rs53576", "rs1815739", "rs6152", "rs1799971")
 snp_chromosomes <- c("3", "11", "X", "6")
@@ -910,8 +915,8 @@ c("ACTN3","APOA5") %in% snp_genes
 ## Tip: What's the difference between the `%in% and the `==` operators?
 
 The `%in%` operator is used to test if the elements of a vector are
-present in another vector. In the example above, if both "ACTN3" and "APOA5" are in 
-the vector `snp_genes`, then R will return `TRUE TRUE` since they are both present. 
+present in another vector. In the example above, if both "ACTN3" and "APOA5" are in
+the vector `snp_genes`, then R will return `TRUE TRUE` since they are both present.
 If "ACTN3" is but "APOA5" is not in `snp_genes`, then R will return `TRUE FALSE`. The `==` operator
 is used to test if two vectors are exactly equal. For example, if you wanted to know if the vector `c(1, 2, 3)`
 was equal to the vector `c(1, 2, 3)`, you could use the `==` operator. One trick people sometimes

config.yaml

@@ -0,0 +1,88 @@
+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Which carpentry is this (swc, dc, lc, or cp)?
+# swc: Software Carpentry
+# dc: Data Carpentry
+# lc: Library Carpentry
+# cp: Carpentries (to use for instructor training for instance)
+# incubator: The Carpentries Incubator
+carpentry: 'dc'
+
+# Overall title for pages.
+title: 'Intro to R and RStudio for Genomics'
+
+# Date the lesson was created (YYYY-MM-DD, this is empty by default)
+created: '2018-03-12'
+
+# Comma-separated list of keywords for the lesson
+keywords: 'software, data, lesson, The Carpentries'
+
+# Life cycle stage of the lesson
+# possible values: pre-alpha, alpha, beta, stable
+life_cycle: 'beta'
+
+# License of the lesson materials (recommended CC-BY 4.0)
+license: 'CC-BY 4.0'
+
+# Link to the source repository for this lesson
+source: 'https://github.com/datacarpentry/genomics-r-intro'
+
+# Default branch of your lesson
+branch: 'main'
+
+# Who to contact if there are any issues
+contact: '[email protected]'
+
+# Navigation ------------------------------------------------
+#
+# Use the following menu items to specify the order of
+# individual pages in each dropdown section. Leave blank to
+# include all pages in the folder.
+#
+# Example -------------
+#
+# episodes:
+# - introduction.md
+# - first-steps.md
+#
+# learners:
+# - setup.md
+#
+# instructors:
+# - instructor-notes.md
+#
+# profiles:
+# - one-learner.md
+# - another-learner.md
+
+# Order of episodes in your lesson
+episodes: 
+- 00-introduction.Rmd
+- 01-r-basics.Rmd
+- 02-data-prelude.Rmd
+- 03-basics-factors-dataframes.Rmd
+- 04-bioconductor-vcfr.Rmd
+- 05-dplyr.Rmd
+- 06-data-visualization.Rmd
+- 07-r-help.Rmd
+
+# Information for Learners
+learners: 
+
+# Information for Instructors
+instructors: 
+
+# Learner Profiles
+profiles: 
+
+# Customisation ---------------------------------------------
+#
+# This space below is where custom yaml items (e.g. pinning
+# sandpaper and varnish versions) should live
+
+
+url: 'https://datacarpentry.github.io/genomics-r-intro'
+analytics: carpentries
+lang: en

md5sum.txt

@@ -4,7 +4,7 @@
 "config.yaml" "b91cd97fa3b408bd1ac0a00e67ab3219" "site/built/config.yaml" "2024-11-05"
 "index.md" "7f9c30e6487338a0c3f8ecc4018873ab" "site/built/index.md" "2024-11-05"
 "episodes/00-introduction.Rmd" "03f55a33cafd3e5f3b407315c509a389" "site/built/00-introduction.md" "2024-11-05"
-"episodes/01-r-basics.Rmd" "f20944fd715ab905cb243f6a15ccff75" "site/built/01-r-basics.md" "2024-11-05"
+"episodes/01-r-basics.Rmd" "b45f835c7d4314da15066f1f2cb86b21" "site/built/01-r-basics.md" "2024-11-09"
 "episodes/02-data-prelude.Rmd" "ab2b1fd3cdaae919f9e409f713a0a8ad" "site/built/02-data-prelude.md" "2024-11-05"
 "episodes/03-basics-factors-dataframes.Rmd" "0bb7c8d7807eea75f14ce8ca3d22febf" "site/built/03-basics-factors-dataframes.md" "2024-11-05"
 "episodes/04-bioconductor-vcfr.Rmd" "10eb69b4697d7ecb9695d36c0d974208" "site/built/04-bioconductor-vcfr.md" "2024-11-05"