markdown source builds

Auto-generated via {sandpaper}
Source  : a3a27da
Branch  : main
Author  : Jason Williams <[email protected]>
Time    : 2024-10-02 15:28:06 +0000
Message : Merge pull request #274 from naupaka/main

Some minor clean up (style/spacing, remove unneeded chunk, etc)

Author: actions-user

01-r-basics.md

@@ -23,8 +23,6 @@ source: Rmd
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
-
-
 ## "The fantastic world of R awaits you" OR "Nobody wants to learn how to use R"
 
 Before we begin this lesson, we want you to be clear on the goal of the workshop
@@ -220,7 +218,7 @@ but R is "not sure"
 about how to assign the name to "human\_ chr\_number" when the object name we
 want is "human\_chr\_number".
 
-<img src="fig/rstudio_script_warning.png" alt="rstudio script warning" style="width: 600px;"/>
+![RStudio script warning]("fig/rstudio_script_warning.png")
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
@@ -493,7 +491,7 @@ These can be used with literal numbers:
 
 
 ``` r
-(1 + (5 ** 0.5))/2
+(1 + (5 ** 0.5)) / 2
 ```
 
 ``` output
@@ -531,7 +529,7 @@ functions. Hint: remember the `round()` function can take 2 arguments.
 
 
 ``` r
-round((1 + sqrt(5))/2, digits = 3)
+round((1 + sqrt(5)) / 2, digits = 3)
 ```
 
 ``` output
@@ -667,7 +665,7 @@ Also, several of these subsetting expressions can be combined:
 ``` r
 # get the 1st through the 3rd value, and 4th value in the snp vector
 # yes, this is a little silly in a vector of only 4 values.
-snps[c(1:3,4)]
+snps[c(1:3, 4)]
 ```
 
 ``` output
@@ -725,7 +723,7 @@ We can also explicitly rename or add a value to our index using double bracket n
 
 
 ``` r
-snp_genes[6]<- "APOA5"
+snp_genes[6] <- "APOA5"
 snp_genes
 ```
 

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" "2024-10-02"
 "index.md" "7f9c30e6487338a0c3f8ecc4018873ab" "site/built/index.md" "2024-10-02"
 "episodes/00-introduction.Rmd" "e1354ed92fb458179c8c00b00ee1cf55" "site/built/00-introduction.md" "2024-10-02"
-"episodes/01-r-basics.Rmd" "ba3faa27a6f2eb8087acf99679a7ac03" "site/built/01-r-basics.md" "2024-10-02"
+"episodes/01-r-basics.Rmd" "c9e52db6d25e0b716fce903bdf9d3ee8" "site/built/01-r-basics.md" "2024-10-02"
 "episodes/02-data-prelude.Rmd" "ab2b1fd3cdaae919f9e409f713a0a8ad" "site/built/02-data-prelude.md" "2024-10-02"
 "episodes/03-basics-factors-dataframes.Rmd" "109ed19fade231fe8e1da43903b06539" "site/built/03-basics-factors-dataframes.md" "2024-10-02"
 "episodes/04-bioconductor-vcfr.Rmd" "10eb69b4697d7ecb9695d36c0d974208" "site/built/04-bioconductor-vcfr.md" "2024-10-02"