From bb2bb6b6e795c80d301115407ba6d253a4e7d2b1 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 14 May 2024 20:00:00 +0000
Subject: [PATCH] markdown source builds

Auto-generated via {sandpaper}
Source  : b22497cb97fa18a9f56b9b5c57dcd41879efc3e2
Branch  : main
Author  : Naupaka Zimmerman <naupaka@gmail.com>
Time    : 2024-05-14 19:58:23 +0000
Message : Merge pull request #275 from datacarpentry/update/packages

Update 13 packages
---
 00-introduction.md                            |   8 +-
 01-r-basics.md                                |  90 +-
 03-basics-factors-dataframes.md               |  96 +-
 05-dplyr.md                                   |  56 +-
 06-data-visualization.md                      |   8 +-
 07-r-help.md                                  |   2 +-
 config.yaml                                   |  88 --
 depth.pdf                                     | Bin 45059 -> 45059 bytes
 ...dataframes-rendered-unnamed-chunk-10-1.png | Bin 362 -> 0 bytes
 ...dataframes-rendered-unnamed-chunk-14-1.png | Bin 3685 -> 0 bytes
 md5sum.txt                                    |  36 +-
 renv.lock                                     | 974 ------------------
 12 files changed, 148 insertions(+), 1210 deletions(-)
 delete mode 100644 config.yaml
 delete mode 100644 fig/03-basics-factors-dataframes-rendered-unnamed-chunk-10-1.png
 delete mode 100644 fig/03-basics-factors-dataframes-rendered-unnamed-chunk-14-1.png
 delete mode 100644 renv.lock

diff --git a/00-introduction.md b/00-introduction.md
index b90c9b860..de76a2c98 100644
--- a/00-introduction.md
+++ b/00-introduction.md
@@ -428,7 +428,7 @@ with a decimal:
 round(3.14)
 ```
 
-```{.output}
+```output
 [1] 3
 ```
 
@@ -455,7 +455,7 @@ You can also see a function's argument using the `args()` function:
 args(round)
 ```
 
-```{.output}
+```output
 function (x, digits = 0) 
 NULL
 ```
@@ -473,7 +473,7 @@ function:
 round(3.14159, digits = 2)
 ```
 
-```{.output}
+```output
 [1] 3.14
 ```
 
@@ -487,7 +487,7 @@ digits is 2.
 round(3.14159, 2)
 ```
 
-```{.output}
+```output
 [1] 3.14
 ```
 
diff --git a/01-r-basics.md b/01-r-basics.md
index 45c17b2d0..9f02c60a6 100644
--- a/01-r-basics.md
+++ b/01-r-basics.md
@@ -338,7 +338,7 @@ their modes. Try to guess what the mode will be before you look at the solution
 mode(chromosome_name)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -346,7 +346,7 @@ mode(chromosome_name)
 mode(od_600_value)
 ```
 
-```{.output}
+```output
 [1] "numeric"
 ```
 
@@ -354,7 +354,7 @@ mode(od_600_value)
 mode(chr_position)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -362,7 +362,7 @@ mode(chr_position)
 mode(spock)
 ```
 
-```{.output}
+```output
 [1] "logical"
 ```
 
@@ -371,7 +371,7 @@ mode(spock)
 mode(pilot)
 ```
 
-```{.error}
+```error
 Error in eval(expr, envir, enclos): object 'pilot' not found
 ```
 
@@ -399,7 +399,7 @@ to check their classes.
 class(chromosome_name)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -407,7 +407,7 @@ class(chromosome_name)
 class(od_600_value)
 ```
 
-```{.output}
+```output
 [1] "numeric"
 ```
 
@@ -415,7 +415,7 @@ class(od_600_value)
 class(chr_position)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -423,7 +423,7 @@ class(chr_position)
 class(spock)
 ```
 
-```{.output}
+```output
 [1] "logical"
 ```
 
@@ -432,7 +432,7 @@ class(spock)
 class(pilot)
 ```
 
-```{.error}
+```error
 Error in eval(expr, envir, enclos): object 'pilot' not found
 ```
 
@@ -458,7 +458,7 @@ pilot <- "Earhart"
 mode(pilot)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -468,7 +468,7 @@ pilot <- "Earhart"
 typeof(pilot)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -496,7 +496,7 @@ These can be used with literal numbers:
 (1 + (5 ** 0.5))/2
 ```
 
-```{.output}
+```output
 [1] 1.618034
 ```
 
@@ -512,7 +512,7 @@ by R) a numeric object:
 human_chr_number * 2
 ```
 
-```{.output}
+```output
 [1] 46
 ```
 
@@ -534,7 +534,7 @@ functions. Hint: remember the `round()` function can take 2 arguments.
 round((1 + sqrt(5))/2, digits = 3)
 ```
 
-```{.output}
+```output
 [1] 1.618
 ```
 
@@ -574,7 +574,7 @@ Another useful function that gives both of these pieces of information is the
 mode(snp_genes)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -582,7 +582,7 @@ mode(snp_genes)
 length(snp_genes)
 ```
 
-```{.output}
+```output
 [1] 4
 ```
 
@@ -590,7 +590,7 @@ length(snp_genes)
 str(snp_genes)
 ```
 
-```{.output}
+```output
  chr [1:4] "OXTR" "ACTN3" "AR" "OPRM1"
 ```
 
@@ -624,7 +624,7 @@ we place the index (e.g. a number) in that bracket as follows:
 snps[3]
 ```
 
-```{.output}
+```output
 [1] "rs6152"
 ```
 
@@ -639,7 +639,7 @@ range of numbers:
 snps[1:3]
 ```
 
-```{.output}
+```output
 [1] "rs53576"   "rs1815739" "rs6152"   
 ```
 
@@ -654,7 +654,7 @@ positions you wish to retrieve.
 snps[c(1, 3, 4)]
 ```
 
-```{.output}
+```output
 [1] "rs53576"   "rs6152"    "rs1799971"
 ```
 
@@ -670,7 +670,7 @@ Also, several of these subsetting expressions can be combined:
 snps[c(1:3,4)]
 ```
 
-```{.output}
+```output
 [1] "rs53576"   "rs1815739" "rs6152"    "rs1799971"
 ```
 
@@ -693,7 +693,7 @@ We can verify that "snp\_genes" contains the new gene entry
 snp_genes
 ```
 
-```{.output}
+```output
 [1] "OXTR"   "ACTN3"  "AR"     "OPRM1"  "CYP1A1" "APOA5" 
 ```
 
@@ -705,7 +705,7 @@ value removed:
 snp_genes[-6]
 ```
 
-```{.output}
+```output
 [1] "OXTR"   "ACTN3"  "AR"     "OPRM1"  "CYP1A1"
 ```
 
@@ -717,7 +717,7 @@ snp_genes <- snp_genes[-6]
 snp_genes
 ```
 
-```{.output}
+```output
 [1] "OXTR"   "ACTN3"  "AR"     "OPRM1"  "CYP1A1"
 ```
 
@@ -729,7 +729,7 @@ snp_genes[6]<- "APOA5"
 snp_genes
 ```
 
-```{.output}
+```output
 [1] "OXTR"   "ACTN3"  "AR"     "OPRM1"  "CYP1A1" "APOA5" 
 ```
 
@@ -774,7 +774,7 @@ There is one last set of cool subsetting capabilities we want to introduce. It i
 snp_positions[snp_positions > 100000000]
 ```
 
-```{.output}
+```output
 [1] 154039662
 ```
 
@@ -805,7 +805,7 @@ evaluates to:
 snp_positions > 100000000
 ```
 
-```{.output}
+```output
 [1] FALSE FALSE FALSE  TRUE
 ```
 
@@ -817,7 +817,7 @@ you pass a logical vector as an index, R will return the true values:
 snp_positions[c(FALSE, FALSE, FALSE, TRUE)]
 ```
 
-```{.output}
+```output
 [1] 154039662
 ```
 
@@ -840,7 +840,7 @@ evaluates as TRUE in our comparison:
 which(snp_positions > 100000000)
 ```
 
-```{.output}
+```output
 [1] 4
 ```
 
@@ -857,7 +857,7 @@ snp_marker_cutoff <- 100000000
 snp_positions[snp_positions > snp_marker_cutoff]
 ```
 
-```{.output}
+```output
 [1] 154039662
 ```
 
@@ -883,7 +883,7 @@ value:
 is.na(snp_genes)
 ```
 
-```{.output}
+```output
 [1] FALSE FALSE FALSE FALSE FALSE FALSE
 ```
 
@@ -903,7 +903,7 @@ the vector you are searching:
 c("ACTN3","APOA5") %in% snp_genes
 ```
 
-```{.output}
+```output
 [1] TRUE TRUE
 ```
 
@@ -942,7 +942,7 @@ c. `snp_positions`
 mode(snps)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -950,7 +950,7 @@ mode(snps)
 mode(snp_chromosomes)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -958,7 +958,7 @@ mode(snp_chromosomes)
 mode(snp_positions)
 ```
 
-```{.output}
+```output
 [1] "numeric"
 ```
 
@@ -985,7 +985,7 @@ snps <- c(snps, "rs662799")
 snps
 ```
 
-```{.output}
+```output
 [1] "rs53576"   "rs1815739" "rs6152"    "rs1799971" "rs662799" 
 ```
 
@@ -994,7 +994,7 @@ snp_chromosomes <- c(snp_chromosomes, "11") # did you use quotes?
 snp_chromosomes
 ```
 
-```{.output}
+```output
 [1] "3"  "11" "X"  "6"  "11"
 ```
 
@@ -1003,7 +1003,7 @@ snp_positions <- c(snp_positions, 116792991)
 snp_positions
 ```
 
-```{.output}
+```output
 [1]   8762685  66560624  67545785 154039662 116792991
 ```
 
@@ -1036,7 +1036,7 @@ snp_genes <- c(snp_genes, NA, NA)
 snp_genes
 ```
 
-```{.output}
+```output
 [1] "OXTR"  "ACTN3" "AR"    "OPRM1" "APOA5" NA      NA     
 ```
 
@@ -1065,7 +1065,7 @@ combined <- c(snp_genes[1], snps[1], snp_chromosomes[1], snp_positions[1])
 combined
 ```
 
-```{.output}
+```output
 [1] "OXTR"    "rs53576" "3"       "8762685"
 ```
 
@@ -1088,7 +1088,7 @@ What type of data is `combined`?
 typeof(combined)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -1125,7 +1125,7 @@ snp_data <- list(genes = snp_genes,
 str(snp_data)
 ```
 
-```{.output}
+```output
 List of 4
  $ genes         : chr [1:7] "OXTR" "ACTN3" "AR" "OPRM1" ...
  $ refference_snp: chr [1:5] "rs53576" "rs1815739" "rs6152" "rs1799971" ...
@@ -1142,7 +1142,7 @@ To get all the values for the `position` object in the list, we use the `$` nota
 snp_data$position
 ```
 
-```{.output}
+```output
 [1]   8762685  66560624  67545785 154039662 116792991
 ```
 
@@ -1155,7 +1155,7 @@ To get the first value in the `position` object, use the `[]` notation to index:
 snp_data$position[1]
 ```
 
-```{.output}
+```output
 [1] 8762685
 ```
 :::::::::::::::::::::::::::::::::::::::::
diff --git a/03-basics-factors-dataframes.md b/03-basics-factors-dataframes.md
index fde632e48..70b9c5681 100644
--- a/03-basics-factors-dataframes.md
+++ b/03-basics-factors-dataframes.md
@@ -198,7 +198,7 @@ frame. Let's examine what each of these functions can tell us:
 summary(variants)
 ```
 
-```{.output}
+```output
   sample_id            CHROM                POS             ID         
  Length:801         Length:801         Min.   :   1521   Mode:logical  
  Class :character   Class :character   1st Qu.:1115970   NA's:801      
@@ -284,7 +284,7 @@ at how data frames work:
 str(subset)
 ```
 
-```{.output}
+```output
 'data.frame':	801 obs. of  4 variables:
  $ sample_id: chr  "SRR2584863" "SRR2584863" "SRR2584863" "SRR2584863" ...
  $ CHROM    : chr  "CP000819.1" "CP000819.1" "CP000819.1" "CP000819.1" ...
@@ -323,7 +323,7 @@ Ok, thats a lot up unpack! Some things to notice.
   mode(variants)
   ```
   
-  ```{.output}
+  ```output
   [1] "list"
   ```
 
@@ -334,7 +334,7 @@ Ok, thats a lot up unpack! Some things to notice.
   class(variants)
   ```
   
-  ```{.output}
+  ```output
   [1] "data.frame"
   ```
 
@@ -374,7 +374,7 @@ Let's look at the first few items in our factor using `head()`:
 head(alt_alleles)
 ```
 
-```{.output}
+```output
 [1] "G"         "T"         "T"         "CTTTTTTTT" "CCGCGC"    "T"        
 ```
 
@@ -401,19 +401,19 @@ now:
 plot(snps)
 ```
 
-```{.warning}
+```warning
 Warning in xy.coords(x, y, xlabel, ylabel, log): NAs introduced by coercion
 ```
 
-```{.warning}
+```warning
 Warning in min(x): no non-missing arguments to min; returning Inf
 ```
 
-```{.warning}
+```warning
 Warning in max(x): no non-missing arguments to max; returning -Inf
 ```
 
-```{.error}
+```error
 Error in plot.window(...): need finite 'ylim' values
 ```
 
@@ -434,7 +434,7 @@ Let's learn a little more about this new type of vector:
 str(factor_snps)
 ```
 
-```{.output}
+```output
  Factor w/ 4 levels "A","C","G","T": 1 1 1 1 1 1 1 1 1 1 ...
 ```
 
@@ -458,7 +458,7 @@ We can see how many items in our vector fall into each category:
 summary(factor_snps)
 ```
 
-```{.output}
+```output
   A   C   G   T 
 211 139 154 203 
 ```
@@ -552,9 +552,9 @@ it will look for a CRAN repository to install from. So, for example, to install
 install.packages("ggplot2")
 ```
 
-```{.output}
+```output
 The following package(s) will be installed:
-- ggplot2 [3.5.0]
+- ggplot2 [3.5.1]
 These packages will be installed into "~/work/genomics-r-intro/genomics-r-intro/renv/profiles/lesson-requirements/renv/library/R-4.3/x86_64-pc-linux-gnu".
 
 # Installing packages --------------------------------------------------------
@@ -614,7 +614,7 @@ a.
 variants[1, 1]
 ```
 
-```{.output}
+```output
 [1] "SRR2584863"
 ```
 
@@ -625,7 +625,7 @@ b.
 variants[2, 4]
 ```
 
-```{.output}
+```output
 [1] NA
 ```
 
@@ -636,7 +636,7 @@ c.
 variants[801, 29]
 ```
 
-```{.output}
+```output
 [1] "T"
 ```
 
@@ -647,7 +647,7 @@ d.
 variants[2, ]
 ```
 
-```{.output}
+```output
    sample_id      CHROM    POS ID REF ALT QUAL FILTER INDEL IDV IMF DP      VDB
 2 SRR2584863 CP000819.1 263235 NA   G   T   85     NA FALSE  NA  NA  6 0.096133
   RPB MQB BQB MQSB       SGB     MQ0F ICB HOB AC AN     DP4 MQ
@@ -666,7 +666,7 @@ variants[-1, ]
 ```
 
 
-```{.output}
+```output
    sample_id      CHROM     POS ID      REF       ALT QUAL FILTER INDEL IDV IMF
 2 SRR2584863 CP000819.1  263235 NA        G         T   85     NA FALSE  NA  NA
 3 SRR2584863 CP000819.1  281923 NA        G         T  217     NA FALSE  NA  NA
@@ -704,7 +704,7 @@ f.
 variants[1:4, 1]
 ```
 
-```{.output}
+```output
 [1] "SRR2584863" "SRR2584863" "SRR2584863" "SRR2584863"
 ```
 
@@ -715,7 +715,7 @@ g.
 variants[1:10, c("REF", "ALT")]
 ```
 
-```{.output}
+```output
                                 REF
 1                                 T
 2                                 G
@@ -748,7 +748,7 @@ variants[, c("sample_id")]
 ```
 
 
-```{.output}
+```output
 [1] "SRR2584863" "SRR2584863" "SRR2584863" "SRR2584863" "SRR2584863"
 [6] "SRR2584863"
 ```
@@ -760,7 +760,7 @@ i.
 head(variants)
 ```
 
-```{.output}
+```output
    sample_id      CHROM    POS ID      REF       ALT QUAL FILTER INDEL IDV IMF
 1 SRR2584863 CP000819.1   9972 NA        T         G   91     NA FALSE  NA  NA
 2 SRR2584863 CP000819.1 263235 NA        G         T   85     NA FALSE  NA  NA
@@ -798,7 +798,7 @@ j.
 tail(variants)
 ```
 
-```{.output}
+```output
      sample_id      CHROM     POS ID REF ALT QUAL FILTER INDEL IDV IMF DP
 796 SRR2589044 CP000819.1 3444175 NA   G   T  184     NA FALSE  NA  NA  9
 797 SRR2589044 CP000819.1 3481820 NA   A   G  225     NA FALSE  NA  NA 12
@@ -837,7 +837,7 @@ variants$sample_id
 ```
 
 
-```{.output}
+```output
 [1] "SRR2584863" "SRR2584863" "SRR2584863" "SRR2584863" "SRR2584863"
 [6] "SRR2584863"
 ```
@@ -850,7 +850,7 @@ variants[variants$REF == "A", ]
 ```
 
 
-```{.output}
+```output
     sample_id      CHROM     POS ID REF ALT QUAL FILTER INDEL IDV IMF DP
 11 SRR2584863 CP000819.1 2407766 NA   A   C  104     NA FALSE  NA  NA  9
 12 SRR2584863 CP000819.1 2446984 NA   A   C  225     NA FALSE  NA  NA 20
@@ -916,7 +916,7 @@ SRR2584863_variants <- variants[variants$sample_id == "SRR2584863", ]
 dim(SRR2584863_variants)
 ```
 
-```{.output}
+```output
 [1] 25 29
 ```
 
@@ -926,7 +926,7 @@ dim(SRR2584863_variants)
 summary(SRR2584863_variants)
 ```
 
-```{.output}
+```output
   sample_id            CHROM                POS             ID         
  Length:25          Length:25          Min.   :   9972   Mode:logical  
  Class :character   Class :character   1st Qu.:1331794   NA's:25       
@@ -1017,7 +1017,7 @@ snp_chromosomes <- c('3', '11', 'X', '6')
 typeof(snp_chromosomes)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -1031,7 +1031,7 @@ snp_chromosomes_2 <- c(3, 11, 'X', 6)
 typeof(snp_chromosomes_2)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -1039,7 +1039,7 @@ typeof(snp_chromosomes_2)
 snp_chromosomes_2[1]
 ```
 
-```{.output}
+```output
 [1] "3"
 ```
 
@@ -1053,7 +1053,7 @@ snp_positions_2 <- c("8762685", "66560624", "67545785", "154039662")
 typeof(snp_positions_2)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -1061,7 +1061,7 @@ typeof(snp_positions_2)
 snp_positions_2[1]
 ```
 
-```{.output}
+```output
 [1] "8762685"
 ```
 
@@ -1073,7 +1073,7 @@ snp_positions_2 <- as.numeric(snp_positions_2)
 typeof(snp_positions_2)
 ```
 
-```{.output}
+```output
 [1] "double"
 ```
 
@@ -1081,7 +1081,7 @@ typeof(snp_positions_2)
 snp_positions_2[1]
 ```
 
-```{.output}
+```output
 [1] 8762685
 ```
 
@@ -1093,7 +1093,7 @@ using `as.numeric()` on `snp_chromosomes_2`
 snp_chromosomes_2 <- as.numeric(snp_chromosomes_2)
 ```
 
-```{.warning}
+```warning
 Warning: NAs introduced by coercion
 ```
 
@@ -1105,7 +1105,7 @@ data) has been introduced.
 snp_chromosomes_2
 ```
 
-```{.output}
+```output
 [1]  3 11 NA  6
 ```
 
@@ -1118,7 +1118,7 @@ look at the result:
 as.numeric(factor_snps)
 ```
 
-```{.output}
+```output
   [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
  [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
  [75] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
@@ -1160,7 +1160,7 @@ variants$REF <- as.character(variants$REF)
 typeof(variants$REF)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -1213,7 +1213,7 @@ reads that support each of the reported variants.
 max(variants$DP)
 ```
 
-```{.output}
+```output
 [1] 79
 ```
 
@@ -1225,7 +1225,7 @@ sorted_by_DP <- variants[order(variants$DP), ]
 head(sorted_by_DP$DP)
 ```
 
-```{.output}
+```output
 [1] 2 2 2 2 2 2
 ```
 
@@ -1247,7 +1247,7 @@ variants with the greatest filtered depth ("DP").
    head(sorted_by_DP$DP)
 ```
 
-```{.output}
+```output
 [1] 79 46 41 29 29 27
 ```
 
@@ -1265,7 +1265,7 @@ colnames(variants)[colnames(variants) == "sample_id"] <- "strain"
 colnames(variants)
 ```
 
-```{.output}
+```output
  [1] "strain"        "CHROM"         "POS"           "ID"           
  [5] "REF"           "ALT"           "QUAL"          "FILTER"       
  [9] "INDEL"         "IDV"           "IMF"           "DP"           
@@ -1339,7 +1339,7 @@ frame:
 head(Ecoli_metadata)
 ```
 
-```{.output}
+```output
 # A tibble: 6 × 7
   sample   generation clade   strain cit     run       genome_size
   <chr>         <dbl> <chr>   <chr>  <chr>   <chr>           <dbl>
@@ -1386,7 +1386,7 @@ H) Save the edited Ecoli\_metadata data frame as "exercise\_solution.csv" in you
 dim(Ecoli_metadata)
 ```
 
-```{.output}
+```output
 [1] 30  7
 ```
 
@@ -1394,7 +1394,7 @@ dim(Ecoli_metadata)
 levels(as.factor(Ecoli_metadata$cit))
 ```
 
-```{.output}
+```output
 [1] "minus"   "plus"    "unknown"
 ```
 
@@ -1402,7 +1402,7 @@ levels(as.factor(Ecoli_metadata$cit))
 table(as.factor(Ecoli_metadata$cit))
 ```
 
-```{.output}
+```output
 
   minus    plus unknown 
       9       9      12 
@@ -1412,7 +1412,7 @@ table(as.factor(Ecoli_metadata$cit))
 Ecoli_metadata[7, 7]
 ```
 
-```{.output}
+```output
 # A tibble: 1 × 1
   genome_size
         <dbl>
@@ -1423,7 +1423,7 @@ Ecoli_metadata[7, 7]
 median(Ecoli_metadata$genome_size)
 ```
 
-```{.output}
+```output
 [1] 4.625
 ```
 
diff --git a/05-dplyr.md b/05-dplyr.md
index 571c6982a..2a04388bb 100644
--- a/05-dplyr.md
+++ b/05-dplyr.md
@@ -114,7 +114,7 @@ Now let's load our vcf .csv file using `read_csv()`:
 Similar to `str()`, which comes built into R, `glimpse()` is a `dplyr` function that (as the name suggests) gives a glimpse of the data frame.
 
 
-```{.output}
+```output
 Rows: 801
 Columns: 29
 $ sample_id     <chr> "SRR2584863", "SRR2584863", "SRR2584863", "SRR2584863", …
@@ -159,7 +159,7 @@ To select columns of a data frame, use `select()`. The first argument to this fu
 select(variants, sample_id, REF, ALT, DP)
 ```
 
-```{.output}
+```output
 # A tibble: 801 × 4
    sample_id  REF                              ALT                            DP
    <chr>      <chr>                            <chr>                       <dbl>
@@ -184,7 +184,7 @@ the variable to exclude it.
 select(variants, -CHROM)
 ```
 
-```{.output}
+```output
 # A tibble: 801 × 28
    sample_id      POS ID    REF      ALT    QUAL FILTER INDEL   IDV    IMF    DP
    <chr>        <dbl> <lgl> <chr>    <chr> <dbl> <lgl>  <lgl> <dbl>  <dbl> <dbl>
@@ -211,7 +211,7 @@ select(variants, -CHROM)
 select(variants, ends_with("B"))
 ```
 
-```{.output}
+```output
 # A tibble: 801 × 8
       VDB   RPB   MQB   BQB   MQSB    SGB ICB   HOB  
     <dbl> <dbl> <dbl> <dbl>  <dbl>  <dbl> <lgl> <lgl>
@@ -249,7 +249,7 @@ variants_result <- select(variants_subset, -Indiv, -FILTER)
 variants_result
 ```
 
-```{.output}
+```output
 # A tibble: 801 × 7
        POS sample_id  ID    INDEL   IDV    IMF ICB  
      <dbl> <chr>      <lgl> <lgl> <dbl>  <dbl> <lgl>
@@ -280,7 +280,7 @@ variants_result <- select(variants, POS, contains("i"), -Indiv, -FILTER)
 variants_result
 ```
 
-```{.output}
+```output
 # A tibble: 801 × 7
        POS sample_id  ID    INDEL   IDV    IMF ICB  
      <dbl> <chr>      <lgl> <lgl> <dbl>  <dbl> <lgl>
@@ -308,7 +308,7 @@ To choose rows, use `filter()`:
 filter(variants, sample_id == "SRR2584863")
 ```
 
-```{.output}
+```output
 # A tibble: 25 × 29
    sample_id  CHROM        POS ID    REF   ALT    QUAL FILTER INDEL   IDV    IMF
    <chr>      <chr>      <dbl> <lgl> <chr> <chr> <dbl> <lgl>  <lgl> <dbl>  <dbl>
@@ -338,7 +338,7 @@ Here are a few examples:
 filter(variants, REF %in% c("T", "G"))
 ```
 
-```{.output}
+```output
 # A tibble: 340 × 29
    sample_id CHROM    POS ID    REF   ALT    QUAL FILTER INDEL   IDV   IMF    DP
    <chr>     <chr>  <dbl> <lgl> <chr> <chr> <dbl> <lgl>  <lgl> <dbl> <dbl> <dbl>
@@ -363,7 +363,7 @@ filter(variants, REF %in% c("T", "G"))
 filter(variants, INDEL)
 ```
 
-```{.output}
+```output
 # A tibble: 101 × 29
    sample_id CHROM    POS ID    REF   ALT    QUAL FILTER INDEL   IDV   IMF    DP
    <chr>     <chr>  <dbl> <lgl> <chr> <chr> <dbl> <lgl>  <lgl> <dbl> <dbl> <dbl>
@@ -388,7 +388,7 @@ filter(variants, INDEL)
 filter(variants, !is.na(IDV))
 ```
 
-```{.output}
+```output
 # A tibble: 101 × 29
    sample_id CHROM    POS ID    REF   ALT    QUAL FILTER INDEL   IDV   IMF    DP
    <chr>     <chr>  <dbl> <lgl> <chr> <chr> <dbl> <lgl>  <lgl> <dbl> <dbl> <dbl>
@@ -420,7 +420,7 @@ have a QUAL score above a certain threshold:
 filter(variants, QUAL >= 100)
 ```
 
-```{.output}
+```output
 # A tibble: 666 × 29
    sample_id CHROM    POS ID    REF   ALT    QUAL FILTER INDEL   IDV   IMF    DP
    <chr>     <chr>  <dbl> <lgl> <chr> <chr> <dbl> <lgl>  <lgl> <dbl> <dbl> <dbl>
@@ -449,7 +449,7 @@ filter(variants, QUAL >= 100)
 filter(variants, sample_id == "SRR2584863", QUAL >= 100)
 ```
 
-```{.output}
+```output
 # A tibble: 19 × 29
    sample_id CHROM    POS ID    REF   ALT    QUAL FILTER INDEL   IDV   IMF    DP
    <chr>     <chr>  <dbl> <lgl> <chr> <chr> <dbl> <lgl>  <lgl> <dbl> <dbl> <dbl>
@@ -482,7 +482,7 @@ filter(variants, sample_id == "SRR2584863", QUAL >= 100)
 filter(variants, sample_id == "SRR2584863", (MQ >= 50 | QUAL >= 100))
 ```
 
-```{.output}
+```output
 # A tibble: 23 × 29
    sample_id  CHROM        POS ID    REF   ALT    QUAL FILTER INDEL   IDV    IMF
    <chr>      <chr>      <dbl> <lgl> <chr> <chr> <dbl> <lgl>  <lgl> <dbl>  <dbl>
@@ -521,7 +521,7 @@ Hint: to flip logical values such as TRUE to a FALSE, we can use to negation sym
 filter(variants, POS >= 1e6 & POS <= 2e6, QUAL > 200, !INDEL)
 ```
 
-```{.output}
+```output
 # A tibble: 77 × 29
    sample_id CHROM    POS ID    REF   ALT    QUAL FILTER INDEL   IDV   IMF    DP
    <chr>     <chr>  <dbl> <lgl> <chr> <chr> <dbl> <lgl>  <lgl> <dbl> <dbl> <dbl>
@@ -564,7 +564,7 @@ variants %>%
   select(REF, ALT, DP)
 ```
 
-```{.output}
+```output
 # A tibble: 25 × 3
    REF                              ALT                                       DP
    <chr>                            <chr>                                  <dbl>
@@ -613,7 +613,7 @@ the first six rows to confirm it's what we want:
 SRR2584863_variants
 ```
 
-```{.output}
+```output
 # A tibble: 25 × 3
    REF                              ALT                                       DP
    <chr>                            <chr>                                  <dbl>
@@ -637,7 +637,7 @@ Similar to `head()` and `tail()` functions, we can also look at the first or las
 SRR2584863_variants %>% slice(1:6)
 ```
 
-```{.output}
+```output
 # A tibble: 6 × 3
   REF      ALT          DP
   <chr>    <chr>     <dbl>
@@ -654,7 +654,7 @@ SRR2584863_variants %>% slice(1:6)
 SRR2584863_variants %>% slice(10:25)
 ```
 
-```{.output}
+```output
 # A tibble: 16 × 3
    REF   ALT      DP
    <chr> <chr> <dbl>
@@ -697,7 +697,7 @@ Showing only 5th through 11th rows of columns `REF`, `ALT`, and `POS`.
  select(sample_id, DP, REF, ALT, POS)
 ```
 
-```{.output}
+```output
 # A tibble: 7 × 5
   sample_id     DP REF   ALT       POS
   <chr>      <dbl> <chr> <chr>   <dbl>
@@ -734,7 +734,7 @@ variants %>%
   mutate(POLPROB = 1 - (10 ^ -(QUAL/10)))
 ```
 
-```{.output}
+```output
 # A tibble: 801 × 30
    sample_id  CHROM        POS ID    REF   ALT    QUAL FILTER INDEL   IDV    IMF
    <chr>      <chr>      <dbl> <lgl> <chr> <chr> <dbl> <lgl>  <lgl> <dbl>  <dbl>
@@ -774,7 +774,7 @@ variants %>%
  select(sample_id, POS, QUAL, POLPROB)
 ```
 
-```{.output}
+```output
 # A tibble: 801 × 4
    sample_id      POS  QUAL POLPROB
    <chr>        <dbl> <dbl>   <dbl>
@@ -812,7 +812,7 @@ variants %>%
   tally()
 ```
 
-```{.output}
+```output
 # A tibble: 3 × 2
   sample_id      n
   <chr>      <int>
@@ -829,7 +829,7 @@ variants %>%
   count(sample_id)
 ```
 
-```{.output}
+```output
 # A tibble: 3 × 2
   sample_id      n
   <chr>      <int>
@@ -854,7 +854,7 @@ variants %>%
   count(INDEL)
 ```
 
-```{.output}
+```output
 # A tibble: 2 × 2
   INDEL     n
   <lgl> <int>
@@ -901,7 +901,7 @@ variants %>%
     max_DP = max(DP))
 ```
 
-```{.output}
+```output
 # A tibble: 3 × 5
   sample_id  mean_DP median_DP min_DP max_DP
   <chr>        <dbl>     <dbl>  <dbl>  <dbl>
@@ -935,7 +935,7 @@ variants_wide <- variants %>%
   pivot_wider(names_from = sample_id, values_from = mean_DP)
 ```
 
-```{.output}
+```output
 `summarise()` has grouped output by 'sample_id'. You can override using the
 `.groups` argument.
 ```
@@ -944,7 +944,7 @@ variants_wide <- variants %>%
 variants_wide
 ```
 
-```{.output}
+```output
 # A tibble: 1 × 4
   CHROM      SRR2584863 SRR2584866 SRR2589044
   <chr>           <dbl>      <dbl>      <dbl>
@@ -959,7 +959,7 @@ variants_wide %>%
   pivot_longer(-CHROM, names_to = "sample_id", values_to = "mean_DP")
 ```
 
-```{.output}
+```output
 # A tibble: 3 × 3
   CHROM      sample_id  mean_DP
   <chr>      <chr>        <dbl>
diff --git a/06-data-visualization.md b/06-data-visualization.md
index 54987fd62..759c11333 100644
--- a/06-data-visualization.md
+++ b/06-data-visualization.md
@@ -70,18 +70,18 @@ library(readr)
 library(dplyr)
 ```
 
-```{.output}
+```output
 
 Attaching package: 'dplyr'
 ```
 
-```{.output}
+```output
 The following objects are masked from 'package:stats':
 
     filter, lag
 ```
 
-```{.output}
+```output
 The following objects are masked from 'package:base':
 
     intersect, setdiff, setequal, union
@@ -103,7 +103,7 @@ Explore the *structure* (types of columns and number of rows) of the dataset usi
 glimpse(variants) # Show a snapshot of the rows and columns
 ```
 
-```{.output}
+```output
 Rows: 801
 Columns: 29
 $ sample_id     <chr> "SRR2584863", "SRR2584863", "SRR2584863", "SRR2584863", …
diff --git a/07-r-help.md b/07-r-help.md
index db8c66fb1..7e4b469d0 100644
--- a/07-r-help.md
+++ b/07-r-help.md
@@ -155,7 +155,7 @@ they come up commonly:
 1:101 # generates the sequence of numbers from 1 to 101
 ```
 
-```{.output}
+```output
   [1]   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18
  [19]  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36
  [37]  37  38  39  40  41  42  43  44  45  46  47  48  49  50  51  52  53  54
diff --git a/config.yaml b/config.yaml
deleted file mode 100644
index d35bbb686..000000000
--- a/config.yaml
+++ /dev/null
@@ -1,88 +0,0 @@
-#------------------------------------------------------------
-# 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: 'team@carpentries.org'
-
-# 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
diff --git a/depth.pdf b/depth.pdf
index cd6caaef885e2b834c4e2c0e52fb706f6a0f5509..ec76f9ff524f2e6378255404254b7e69f1360c2c 100644
GIT binary patch
delta 50
ycmZpEz|{PJX@Z%msiBFXrKzQ<nI@OMZ+?nPVo9okhKrSvfsu&;TyA6ZiuC|@s}7L>

delta 50
ycmZpEz|{PJX@Z%miGhiMfsvuHi6)o6Z+?nPVo9okhKrSvfe}asDz`Cu#d-j90}fjN

diff --git a/fig/03-basics-factors-dataframes-rendered-unnamed-chunk-10-1.png b/fig/03-basics-factors-dataframes-rendered-unnamed-chunk-10-1.png
deleted file mode 100644
index a9cacb2958ddea79687b8f875abdc650da01fad4..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 362
zcmeAS@N?(olHy`uVBq!ia0y~yVEh5X9LzwGiQo8rffRFqPl)UP|NoaCkv;+Bau#?*
z7Bet#3xP1>rMq>1fEsu`T^vIy=Da;<$Ou$&Xu((iTpsxaK;{Sp5Aq+SGB7F%Uls&;
N-qY33Wt~$(695WHAk_c>

diff --git a/fig/03-basics-factors-dataframes-rendered-unnamed-chunk-14-1.png b/fig/03-basics-factors-dataframes-rendered-unnamed-chunk-14-1.png
deleted file mode 100644
index 99e25c6db9a787bf1bd497e5ac6b7e6d5b251ea4..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 3685
zcmdT`X;71C5>AYOf)JI#2pR%|2O}al=)`aYITSD`h+tHlppF>iR<49#5*JZCfCWoY
zFtDKD0-A`3OfZ+AC@6;r2EiN*M>xcM+#%$cL}s?OYJcqhn60V#@pir4-}gS%)z8yi
zec6AXm!ZCyJ_rOd^zrr#0D-_V?O6iRM6zd~dqJQ@NPpkJT^bh*216ha9UUEAU0ppr
zJ$-$B0|Ns?Lqj7YBPbNQV#Nw$W8-hW`NqV=1O|hxUcK7X)YQz(Y|WZAYuB!Y!{O%U
z<_HAB!otGR((>DHzqPWm+OT26#*G`Tt*vcrY;0|9w`|#BZ*TA5;DAITckI}KLZKWT
z9i5z<oSmIrTwKs-^v<0--Q3*V-Q7JrJUl%;ckSA>d-rZHFE4LzZyz5Y3<l%t>$`XF
zUOzuSe}Dh|`}ZF>a3Cls=-|PFSS<GN;lshf!8jZ)BqZe6v16g3p{Gur!sGE_VPU6F
zpN@!#h>D7ej*gCvjXiVb%-OSN<KyEK5)u*<6O)pX2n0fMax#fTI(P0InM|foC{!vn
zH8u6Zg$rqEY3b?dmoHzwa^=d^t5>gGyOxoWk(rs9m6es9ot=}DbN%}D8#iv;ym>P>
zH~04K+j)6;1qB5~MMcHM#rN*rD=8@{EiJu&|9)9nS$TPRMMcGf2M-=Td`PF$84Sjw
zM~^BiE32xis;jG?K7CqKQ^RC3YinztJ$uGtvDj=jhr{7=xjY`PuCDIIix&+I4X<9k
zdj0x!V`F1eQ&USzOKWRuTU%Rud;9zM?>jm=Iy*c0e12C~*T;_^ySux4dU`&6`Xmqt
zL?TgdZ*N~;Uw?o9z`(%Z;Gjez85$ZI9v&VU85tcN{rvg!*x1;YFJGimDF6WD<Kq((
z6O)sZQ&UsZ)6=uFvoe`%Zf;I4m(S17D-;T)QmIm@)M|AhHZxTtou#qfhvPsXgO%C?
zZWoXhnoEa|r&}Q5&KQ3_$pmk5=}h|4D9bzPdxNtVl?9fsvcw(9(8Vx=cCOf3cEvN2
zeLRR|qGMt(w%_Jy(A|I~-#t8P=5g9PVx_SY<xXR7@$IVb@f5#PzDYBa3j3-Fj?|I#
z8lRSM%FW#}*q#sF8D|W*LC|45Jww?)z=&<)RNa&|D%9*x4Iaq^{FIy3!q?LAup_8C
z(e&J>;Q2^$me>2H6)HCO4cnFnGx^U9Hv@Oiv6X$*Szu{dHvn_WKXNm7RTMj5)B-3d
zHxvoCZzICH-tAv-xhIRyu8E*0EGPJNUJOZieAcF>({Txlt&&Pa4(-Mr7hQ#{<9s1)
z6f<x{?|jW{S1F@ksBAZ0&FO@~g(5**{Lh0Z@tDhp>uS3Q+SFoJOS6x;m`Jm+fC8P2
zxO&MZ8Zk=lCLSYF8DttMnN%`EAJza#z~lx#vtC3~IRG=xyjGc`UW$@PEgVlUlF8%1
z6!x289r0)@L@^Alj;^&Q#_Wj!g;31JB6W!?;?O&23Y|#hPK$ibo)}m!o_q^YG`afX
z$n7)V1E@i;3Ra^`8R@RIXM?q%ekw9~MBZIA<p@km7LiM-3|Da#1h<5s2QGvI?mVX@
zvd>i5BB2`(ug6*r7%f6OiPNY_%YlzzyTz<jYO4{!QVd_5lE^avOD+DAPpv7kcO0Q=
zd?fU1QD3%{-W({|70kGY)D!~>jQ!|woqrw<A2$5@Ip=ay)B_ZIYe=taQfnS7VsuY4
z0OF3E95@(_iFu2a+4>Etq_SSCGE;ML7BZ%*I!PiAK(WCrR4&li)~gh_cwMUaa2_c!
zCYMj9c1G~><Cb!_`s`ywM;@BrlMErmZRyR=IVrf?XC;7^BB@A;31?g0x;{({eeG#R
z$5WC<F!;ANirOlliFQp=s$ZI!7eXGzzkEE_SoQ&;$x`DZnDK*Yu<HgJ%YV=StW@o0
zl)^L@GtPHxkT#K2K7^w>T4xve^TAFZ?E_Jjw427&sB5XK@Lezy5<=P18xxPx{>=x1
zz%fRIts2@3LwWoqggD++4fl%85YBF1J_NUnP((E3K6IJ=q7Dkz1-9oI$P(sSyJl$}
z%fu0jSt#*Kjec+jgze&Hu$`_(Lq~WOzXS3Y;S7JnW32+h7vL<#)l@7*xE45}(G)|6
zWd;mVVOmMriaV)DJ=SWCEF-`S-9HO@;u2zPbPU13=?d>)WLIf>ZQo$7KE?UOfMQzK
zr;zw<{RzjsycU?u^$m>vsd<5vg$YukrF5l=FnRGuQWD+n#``r|1r#p(ZD54M332FN
zA}v2*i`Jg|-ByH1GM`|>dt8(jfWzR*0zUJj<ln8aD*2D$_%BHb^^eOMmG=K*SH?AX
z^~1qrQNgf;TDY|kI6y-v3K0$TK*#u4xv8eD*DD&<q1d&R$H#0mon4_33g`3$UpXZ6
zo=w$?h?r)Vv7u4cKBWr`vg#O4`RnWi*+P(3hdLPS=AME(;Vyq)@Ut;^9APUnwmAIj
zNWm}r%k|kGNa}wdJaPK2-TWR`9DA8|KK^Sl$XO`n485pvl$V*Qt-EGy-u~yOhP)WM
zv$}c@ltPq0{}9Ej8JsP<#I#eJBG9+;Dnk!^aX`~9QWQTiTf1i5@@3QE^$f?u%o{z?
z^gDJ~$HYYWb4k-2GAH>Kca{B5_S^f8f*o-CnpayNYY;{L!mlu-u!!|^wi7?Msa?|E
z<6K`OFRGt^M#?mTsW(qiB3DVr`%(Y%BKCwy<w^^RH?pQPZe-L@W|~jnojK)|Q)L`?
ze9FC|<8B@v_5NUliym;_TqcXt$&%GQD>Ow<zngK#f5z=MN2_0kVh!Lq>uOv>-bz})
ziUJQ;rEjIN?i%$D;<-MOdQ)rz&q?)tf)iGpzGqU8{EG`#O_YQcS!D`>hF)Ri&4QP$
zx58CC*J=NpNOZtZIzkYvjgRZ)^oL_GZ=m`G4iqs`_?R$mTWB5sqDs1Hs*llp2tB9#
z(q7Um+C*q!ou{z3-CWmatG14Bc*v!(GMxkZ`Eq_tMT&>Oh*i1KJg+udm00A#k++0E
zXI<J34_#x_6c8pSp1<^iIi56sE}HM}n9hyRhfjP!N~2j-qz7%Ljm8!Ed9HK!PvGBL
j5t2!Z|GdTai5i54*JXx%2Mg3J{UD!R`#kCH$Nu&!^L6?W

diff --git a/md5sum.txt b/md5sum.txt
index 08b2b8e41..028421a38 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -1,19 +1,19 @@
 "file" "checksum" "built" "date"
-"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2024-04-04"
-"LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2024-04-04"
-"config.yaml" "b91cd97fa3b408bd1ac0a00e67ab3219" "site/built/config.yaml" "2024-04-04"
-"index.md" "7f9c30e6487338a0c3f8ecc4018873ab" "site/built/index.md" "2024-04-04"
-"episodes/00-introduction.Rmd" "e1354ed92fb458179c8c00b00ee1cf55" "site/built/00-introduction.md" "2024-04-04"
-"episodes/01-r-basics.Rmd" "ba3faa27a6f2eb8087acf99679a7ac03" "site/built/01-r-basics.md" "2024-04-10"
-"episodes/02-data-prelude.Rmd" "ab2b1fd3cdaae919f9e409f713a0a8ad" "site/built/02-data-prelude.md" "2024-04-04"
-"episodes/03-basics-factors-dataframes.Rmd" "109ed19fade231fe8e1da43903b06539" "site/built/03-basics-factors-dataframes.md" "2024-04-10"
-"episodes/04-bioconductor-vcfr.Rmd" "10eb69b4697d7ecb9695d36c0d974208" "site/built/04-bioconductor-vcfr.md" "2024-04-04"
-"episodes/05-dplyr.Rmd" "f74055bd8677338a213e0a0c6c430119" "site/built/05-dplyr.md" "2024-04-04"
-"episodes/06-data-visualization.Rmd" "0b45534421bad05f040b24c40b6da71b" "site/built/06-data-visualization.md" "2024-04-04"
-"episodes/07-r-help.Rmd" "1a7610b0efbaebfdd03ff4540125a790" "site/built/07-r-help.md" "2024-04-04"
-"instructors/instructor-notes.md" "78f6fe6109a0eb19a16ec6663941da7f" "site/built/instructor-notes.md" "2024-04-04"
-"learners/discuss.md" "522bcb192adf6702a2e3cb2f0d1412b5" "site/built/discuss.md" "2024-04-04"
-"learners/reference.md" "4e0dcbc7892af6f9610d44d356e66617" "site/built/reference.md" "2024-04-04"
-"learners/setup.md" "8e109a52a3f92f4e454de0d71bf4df11" "site/built/setup.md" "2024-04-04"
-"profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2024-04-04"
-"renv/profiles/lesson-requirements/renv.lock" "86461e6541043e25d1bdc4062277e404" "site/built/renv.lock" "2024-04-04"
+"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2024-05-14"
+"LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2024-05-14"
+"config.yaml" "b91cd97fa3b408bd1ac0a00e67ab3219" "site/built/config.yaml" "2024-05-14"
+"index.md" "7f9c30e6487338a0c3f8ecc4018873ab" "site/built/index.md" "2024-05-14"
+"episodes/00-introduction.Rmd" "e1354ed92fb458179c8c00b00ee1cf55" "site/built/00-introduction.md" "2024-05-14"
+"episodes/01-r-basics.Rmd" "ba3faa27a6f2eb8087acf99679a7ac03" "site/built/01-r-basics.md" "2024-05-14"
+"episodes/02-data-prelude.Rmd" "ab2b1fd3cdaae919f9e409f713a0a8ad" "site/built/02-data-prelude.md" "2024-05-14"
+"episodes/03-basics-factors-dataframes.Rmd" "109ed19fade231fe8e1da43903b06539" "site/built/03-basics-factors-dataframes.md" "2024-05-14"
+"episodes/04-bioconductor-vcfr.Rmd" "10eb69b4697d7ecb9695d36c0d974208" "site/built/04-bioconductor-vcfr.md" "2024-05-14"
+"episodes/05-dplyr.Rmd" "f74055bd8677338a213e0a0c6c430119" "site/built/05-dplyr.md" "2024-05-14"
+"episodes/06-data-visualization.Rmd" "0b45534421bad05f040b24c40b6da71b" "site/built/06-data-visualization.md" "2024-05-14"
+"episodes/07-r-help.Rmd" "1a7610b0efbaebfdd03ff4540125a790" "site/built/07-r-help.md" "2024-05-14"
+"instructors/instructor-notes.md" "78f6fe6109a0eb19a16ec6663941da7f" "site/built/instructor-notes.md" "2024-05-14"
+"learners/discuss.md" "522bcb192adf6702a2e3cb2f0d1412b5" "site/built/discuss.md" "2024-05-14"
+"learners/reference.md" "4e0dcbc7892af6f9610d44d356e66617" "site/built/reference.md" "2024-05-14"
+"learners/setup.md" "8e109a52a3f92f4e454de0d71bf4df11" "site/built/setup.md" "2024-05-14"
+"profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2024-05-14"
+"renv/profiles/lesson-requirements/renv.lock" "c19d687abbfdec1be561034ab884c8fd" "site/built/renv.lock" "2024-05-14"
diff --git a/renv.lock b/renv.lock
deleted file mode 100644
index 6caa352b5..000000000
--- a/renv.lock
+++ /dev/null
@@ -1,974 +0,0 @@
-{
-  "R": {
-    "Version": "4.3.3",
-    "Repositories": [
-      {
-        "Name": "carpentries",
-        "URL": "https://carpentries.r-universe.dev"
-      },
-      {
-        "Name": "carpentries_archive",
-        "URL": "https://carpentries.github.io/drat"
-      },
-      {
-        "Name": "CRAN",
-        "URL": "https://cran.rstudio.com"
-      }
-    ]
-  },
-  "Packages": {
-    "MASS": {
-      "Package": "MASS",
-      "Version": "7.3-60.0.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "b765b28387acc8ec9e9c1530713cb19c"
-    },
-    "Matrix": {
-      "Package": "Matrix",
-      "Version": "1.6-5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "grid",
-        "lattice",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "8c7115cd3a0e048bda2a7cd110549f7a"
-    },
-    "R6": {
-      "Package": "R6",
-      "Version": "2.5.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
-    },
-    "RColorBrewer": {
-      "Package": "RColorBrewer",
-      "Version": "1.1-3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "45f0398006e83a5b10b72a90663d8d8c"
-    },
-    "base64enc": {
-      "Package": "base64enc",
-      "Version": "0.1-3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "543776ae6848fde2f48ff3816d0628bc"
-    },
-    "bit": {
-      "Package": "bit",
-      "Version": "4.0.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "d242abec29412ce988848d0294b208fd"
-    },
-    "bit64": {
-      "Package": "bit64",
-      "Version": "4.0.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "bit",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "9fe98599ca456d6552421db0d6772d8f"
-    },
-    "bslib": {
-      "Package": "bslib",
-      "Version": "0.7.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "base64enc",
-        "cachem",
-        "fastmap",
-        "grDevices",
-        "htmltools",
-        "jquerylib",
-        "jsonlite",
-        "lifecycle",
-        "memoise",
-        "mime",
-        "rlang",
-        "sass"
-      ],
-      "Hash": "8644cc53f43828f19133548195d7e59e"
-    },
-    "cachem": {
-      "Package": "cachem",
-      "Version": "1.0.8",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "fastmap",
-        "rlang"
-      ],
-      "Hash": "c35768291560ce302c0a6589f92e837d"
-    },
-    "cellranger": {
-      "Package": "cellranger",
-      "Version": "1.1.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "rematch",
-        "tibble"
-      ],
-      "Hash": "f61dbaec772ccd2e17705c1e872e9e7c"
-    },
-    "cli": {
-      "Package": "cli",
-      "Version": "3.6.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
-    },
-    "clipr": {
-      "Package": "clipr",
-      "Version": "0.8.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
-    },
-    "colorspace": {
-      "Package": "colorspace",
-      "Version": "2.1-0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "methods",
-        "stats"
-      ],
-      "Hash": "f20c47fd52fae58b4e377c37bb8c335b"
-    },
-    "cpp11": {
-      "Package": "cpp11",
-      "Version": "0.4.7",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "5a295d7d963cc5035284dcdbaf334f4e"
-    },
-    "crayon": {
-      "Package": "crayon",
-      "Version": "1.5.2",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "grDevices",
-        "methods",
-        "utils"
-      ],
-      "Hash": "e8a1e41acf02548751f45c718d55aa6a"
-    },
-    "digest": {
-      "Package": "digest",
-      "Version": "0.6.35",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31"
-    },
-    "dplyr": {
-      "Package": "dplyr",
-      "Version": "1.1.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "cli",
-        "generics",
-        "glue",
-        "lifecycle",
-        "magrittr",
-        "methods",
-        "pillar",
-        "rlang",
-        "tibble",
-        "tidyselect",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "fedd9d00c2944ff00a0e2696ccf048ec"
-    },
-    "evaluate": {
-      "Package": "evaluate",
-      "Version": "0.23",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "daf4a1246be12c1fa8c7705a0935c1a0"
-    },
-    "fansi": {
-      "Package": "fansi",
-      "Version": "1.0.6",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "utils"
-      ],
-      "Hash": "962174cf2aeb5b9eea581522286a911f"
-    },
-    "farver": {
-      "Package": "farver",
-      "Version": "2.1.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "8106d78941f34855c440ddb946b8f7a5"
-    },
-    "fastmap": {
-      "Package": "fastmap",
-      "Version": "1.1.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "f7736a18de97dea803bde0a2daaafb27"
-    },
-    "fontawesome": {
-      "Package": "fontawesome",
-      "Version": "0.5.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "htmltools",
-        "rlang"
-      ],
-      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
-    },
-    "fs": {
-      "Package": "fs",
-      "Version": "1.6.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "47b5f30c720c23999b913a1a635cf0bb"
-    },
-    "generics": {
-      "Package": "generics",
-      "Version": "0.1.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "15e9634c0fcd294799e9b2e929ed1b86"
-    },
-    "ggplot2": {
-      "Package": "ggplot2",
-      "Version": "3.5.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "MASS",
-        "R",
-        "cli",
-        "glue",
-        "grDevices",
-        "grid",
-        "gtable",
-        "isoband",
-        "lifecycle",
-        "mgcv",
-        "rlang",
-        "scales",
-        "stats",
-        "tibble",
-        "vctrs",
-        "withr"
-      ],
-      "Hash": "52ef83f93f74833007f193b2d4c159a2"
-    },
-    "glue": {
-      "Package": "glue",
-      "Version": "1.7.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "e0b3a53876554bd45879e596cdb10a52"
-    },
-    "gtable": {
-      "Package": "gtable",
-      "Version": "0.3.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "grid",
-        "lifecycle",
-        "rlang"
-      ],
-      "Hash": "b29cf3031f49b04ab9c852c912547eef"
-    },
-    "highr": {
-      "Package": "highr",
-      "Version": "0.10",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "xfun"
-      ],
-      "Hash": "06230136b2d2b9ba5805e1963fa6e890"
-    },
-    "hms": {
-      "Package": "hms",
-      "Version": "1.1.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "lifecycle",
-        "methods",
-        "pkgconfig",
-        "rlang",
-        "vctrs"
-      ],
-      "Hash": "b59377caa7ed00fa41808342002138f9"
-    },
-    "htmltools": {
-      "Package": "htmltools",
-      "Version": "0.5.8",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "base64enc",
-        "digest",
-        "fastmap",
-        "grDevices",
-        "rlang",
-        "utils"
-      ],
-      "Hash": "149431ee39aba5bdc264112c8ff94444"
-    },
-    "isoband": {
-      "Package": "isoband",
-      "Version": "0.2.7",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "grid",
-        "utils"
-      ],
-      "Hash": "0080607b4a1a7b28979aecef976d8bc2"
-    },
-    "jquerylib": {
-      "Package": "jquerylib",
-      "Version": "0.1.4",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "htmltools"
-      ],
-      "Hash": "5aab57a3bd297eee1c1d862735972182"
-    },
-    "jsonlite": {
-      "Package": "jsonlite",
-      "Version": "1.8.8",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "methods"
-      ],
-      "Hash": "e1b9c55281c5adc4dd113652d9e26768"
-    },
-    "knitr": {
-      "Package": "knitr",
-      "Version": "1.45",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "evaluate",
-        "highr",
-        "methods",
-        "tools",
-        "xfun",
-        "yaml"
-      ],
-      "Hash": "1ec462871063897135c1bcbe0fc8f07d"
-    },
-    "labeling": {
-      "Package": "labeling",
-      "Version": "0.4.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "graphics",
-        "stats"
-      ],
-      "Hash": "b64ec208ac5bc1852b285f665d6368b3"
-    },
-    "lattice": {
-      "Package": "lattice",
-      "Version": "0.22-6",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "grid",
-        "stats",
-        "utils"
-      ],
-      "Hash": "cc5ac1ba4c238c7ca9fa6a87ca11a7e2"
-    },
-    "lifecycle": {
-      "Package": "lifecycle",
-      "Version": "1.0.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "rlang"
-      ],
-      "Hash": "b8552d117e1b808b09a832f589b79035"
-    },
-    "magrittr": {
-      "Package": "magrittr",
-      "Version": "2.0.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "7ce2733a9826b3aeb1775d56fd305472"
-    },
-    "memoise": {
-      "Package": "memoise",
-      "Version": "2.0.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "cachem",
-        "rlang"
-      ],
-      "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c"
-    },
-    "mgcv": {
-      "Package": "mgcv",
-      "Version": "1.9-1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "Matrix",
-        "R",
-        "graphics",
-        "methods",
-        "nlme",
-        "splines",
-        "stats",
-        "utils"
-      ],
-      "Hash": "110ee9d83b496279960e162ac97764ce"
-    },
-    "mime": {
-      "Package": "mime",
-      "Version": "0.12",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "tools"
-      ],
-      "Hash": "18e9c28c1d3ca1560ce30658b22ce104"
-    },
-    "munsell": {
-      "Package": "munsell",
-      "Version": "0.5.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "colorspace",
-        "methods"
-      ],
-      "Hash": "6dfe8bf774944bd5595785e3229d8771"
-    },
-    "nlme": {
-      "Package": "nlme",
-      "Version": "3.1-164",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "graphics",
-        "lattice",
-        "stats",
-        "utils"
-      ],
-      "Hash": "a623a2239e642806158bc4dc3f51565d"
-    },
-    "pillar": {
-      "Package": "pillar",
-      "Version": "1.9.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "cli",
-        "fansi",
-        "glue",
-        "lifecycle",
-        "rlang",
-        "utf8",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "15da5a8412f317beeee6175fbc76f4bb"
-    },
-    "pkgconfig": {
-      "Package": "pkgconfig",
-      "Version": "2.0.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "01f28d4278f15c76cddbea05899c5d6f"
-    },
-    "prettyunits": {
-      "Package": "prettyunits",
-      "Version": "1.2.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7"
-    },
-    "printr": {
-      "Package": "printr",
-      "Version": "0.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "knitr"
-      ],
-      "Hash": "03e0d4cc8152eed9515f517a8153c085"
-    },
-    "progress": {
-      "Package": "progress",
-      "Version": "1.2.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "crayon",
-        "hms",
-        "prettyunits"
-      ],
-      "Hash": "f4625e061cb2865f111b47ff163a5ca6"
-    },
-    "purrr": {
-      "Package": "purrr",
-      "Version": "1.0.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "lifecycle",
-        "magrittr",
-        "rlang",
-        "vctrs"
-      ],
-      "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc"
-    },
-    "rappdirs": {
-      "Package": "rappdirs",
-      "Version": "0.3.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
-    },
-    "readr": {
-      "Package": "readr",
-      "Version": "2.1.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "cli",
-        "clipr",
-        "cpp11",
-        "crayon",
-        "hms",
-        "lifecycle",
-        "methods",
-        "rlang",
-        "tibble",
-        "tzdb",
-        "utils",
-        "vroom"
-      ],
-      "Hash": "9de96463d2117f6ac49980577939dfb3"
-    },
-    "readxl": {
-      "Package": "readxl",
-      "Version": "1.4.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cellranger",
-        "cpp11",
-        "progress",
-        "tibble",
-        "utils"
-      ],
-      "Hash": "8cf9c239b96df1bbb133b74aef77ad0a"
-    },
-    "rematch": {
-      "Package": "rematch",
-      "Version": "2.0.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Hash": "cbff1b666c6fa6d21202f07e2318d4f1"
-    },
-    "renv": {
-      "Package": "renv",
-      "Version": "1.0.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "32c3f93e8360f667ca5863272ec8ba6a"
-    },
-    "rlang": {
-      "Package": "rlang",
-      "Version": "1.1.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "42548638fae05fd9a9b5f3f437fbbbe2"
-    },
-    "rmarkdown": {
-      "Package": "rmarkdown",
-      "Version": "2.26",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "bslib",
-        "evaluate",
-        "fontawesome",
-        "htmltools",
-        "jquerylib",
-        "jsonlite",
-        "knitr",
-        "methods",
-        "tinytex",
-        "tools",
-        "utils",
-        "xfun",
-        "yaml"
-      ],
-      "Hash": "9b148e7f95d33aac01f31282d49e4f44"
-    },
-    "sass": {
-      "Package": "sass",
-      "Version": "0.4.9",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R6",
-        "fs",
-        "htmltools",
-        "rappdirs",
-        "rlang"
-      ],
-      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
-    },
-    "scales": {
-      "Package": "scales",
-      "Version": "1.3.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "RColorBrewer",
-        "cli",
-        "farver",
-        "glue",
-        "labeling",
-        "lifecycle",
-        "munsell",
-        "rlang",
-        "viridisLite"
-      ],
-      "Hash": "c19df082ba346b0ffa6f833e92de34d1"
-    },
-    "stringi": {
-      "Package": "stringi",
-      "Version": "1.8.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "stats",
-        "tools",
-        "utils"
-      ],
-      "Hash": "058aebddea264f4c99401515182e656a"
-    },
-    "stringr": {
-      "Package": "stringr",
-      "Version": "1.5.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "lifecycle",
-        "magrittr",
-        "rlang",
-        "stringi",
-        "vctrs"
-      ],
-      "Hash": "960e2ae9e09656611e0b8214ad543207"
-    },
-    "tibble": {
-      "Package": "tibble",
-      "Version": "3.2.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "fansi",
-        "lifecycle",
-        "magrittr",
-        "methods",
-        "pillar",
-        "pkgconfig",
-        "rlang",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
-    },
-    "tidyr": {
-      "Package": "tidyr",
-      "Version": "1.3.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "cpp11",
-        "dplyr",
-        "glue",
-        "lifecycle",
-        "magrittr",
-        "purrr",
-        "rlang",
-        "stringr",
-        "tibble",
-        "tidyselect",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "915fb7ce036c22a6a33b5a8adb712eb1"
-    },
-    "tidyselect": {
-      "Package": "tidyselect",
-      "Version": "1.2.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "lifecycle",
-        "rlang",
-        "vctrs",
-        "withr"
-      ],
-      "Hash": "829f27b9c4919c16b593794a6344d6c0"
-    },
-    "tinytex": {
-      "Package": "tinytex",
-      "Version": "0.50",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "xfun"
-      ],
-      "Hash": "be7a76845222ad20adb761f462eed3ea"
-    },
-    "tzdb": {
-      "Package": "tzdb",
-      "Version": "0.4.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cpp11"
-      ],
-      "Hash": "f561504ec2897f4d46f0c7657e488ae1"
-    },
-    "utf8": {
-      "Package": "utf8",
-      "Version": "1.2.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "62b65c52671e6665f803ff02954446e9"
-    },
-    "vctrs": {
-      "Package": "vctrs",
-      "Version": "0.6.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "lifecycle",
-        "rlang"
-      ],
-      "Hash": "c03fa420630029418f7e6da3667aac4a"
-    },
-    "viridisLite": {
-      "Package": "viridisLite",
-      "Version": "0.4.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
-    },
-    "vroom": {
-      "Package": "vroom",
-      "Version": "1.6.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "bit64",
-        "cli",
-        "cpp11",
-        "crayon",
-        "glue",
-        "hms",
-        "lifecycle",
-        "methods",
-        "progress",
-        "rlang",
-        "stats",
-        "tibble",
-        "tidyselect",
-        "tzdb",
-        "vctrs",
-        "withr"
-      ],
-      "Hash": "390f9315bc0025be03012054103d227c"
-    },
-    "withr": {
-      "Package": "withr",
-      "Version": "3.0.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics"
-      ],
-      "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35"
-    },
-    "xfun": {
-      "Package": "xfun",
-      "Version": "0.43",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "grDevices",
-        "stats",
-        "tools"
-      ],
-      "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e"
-    },
-    "yaml": {
-      "Package": "yaml",
-      "Version": "2.3.8",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "29240487a071f535f5e5d5a323b7afbd"
-    }
-  }
-}