diff --git a/00-before-we-start.md b/00-before-we-start.md
index 76dafe3d..de89b2d1 100644
--- a/00-before-we-start.md
+++ b/00-before-we-start.md
@@ -432,7 +432,7 @@ and help others to pinpoint where the issue might be. Try to...
 sessionInfo()
 ```
 
-```{.output}
+```output
 #> R version 4.3.3 (2024-02-29)
 #> Platform: x86_64-pc-linux-gnu (64-bit)
 #> Running under: Ubuntu 22.04.4 LTS
@@ -454,20 +454,20 @@ sessionInfo()
 #> [1] stats     graphics  grDevices utils     datasets  methods   base     
 #> 
 #> other attached packages:
-#>  [1] RSQLite_2.3.4   lubridate_1.9.3 forcats_1.0.0   stringr_1.5.1  
-#>  [5] dplyr_1.1.4     purrr_1.0.2     readr_2.1.4     tidyr_1.3.0    
-#>  [9] tibble_3.2.1    ggplot2_3.4.4   tidyverse_2.0.0 knitr_1.45     
+#>  [1] RSQLite_2.3.6   lubridate_1.9.3 forcats_1.0.0   stringr_1.5.1  
+#>  [5] dplyr_1.1.4     purrr_1.0.2     readr_2.1.5     tidyr_1.3.1    
+#>  [9] tibble_3.2.1    ggplot2_3.5.1   tidyverse_2.0.0 knitr_1.46     
 #> 
 #> loaded via a namespace (and not attached):
-#>  [1] bit_4.0.5        gtable_0.3.4     compiler_4.3.3   renv_1.0.5      
-#>  [5] highr_0.10       tidyselect_1.2.0 blob_1.2.4       scales_1.3.0    
+#>  [1] bit_4.0.5        gtable_0.3.5     compiler_4.3.3   renv_1.0.7      
+#>  [5] highr_0.10       tidyselect_1.2.1 blob_1.2.4       scales_1.3.0    
 #>  [9] fastmap_1.1.1    yaml_2.3.8       R6_2.5.1         generics_0.1.3  
-#> [13] munsell_0.5.0    DBI_1.2.0        pillar_1.9.0     tzdb_0.4.0      
-#> [17] rlang_1.1.2      utf8_1.2.4       cachem_1.0.8     stringi_1.8.3   
-#> [21] xfun_0.41        bit64_4.0.5      memoise_2.0.1    timechange_0.2.0
-#> [25] cli_3.6.2        withr_2.5.2      magrittr_2.0.3   grid_4.3.3      
+#> [13] munsell_0.5.1    DBI_1.2.2        pillar_1.9.0     tzdb_0.4.0      
+#> [17] rlang_1.1.3      utf8_1.2.4       cachem_1.0.8     stringi_1.8.4   
+#> [21] xfun_0.43        bit64_4.0.5      memoise_2.0.1    timechange_0.3.0
+#> [25] cli_3.6.2        withr_3.0.0      magrittr_2.0.3   grid_4.3.3      
 #> [29] hms_1.1.3        lifecycle_1.0.4  vctrs_0.6.5      evaluate_0.23   
-#> [33] glue_1.6.2       fansi_1.0.6      colorspace_2.1-0 tools_4.3.3     
+#> [33] glue_1.7.0       fansi_1.0.6      colorspace_2.1-0 tools_4.3.3     
 #> [37] pkgconfig_2.0.3
 ```
 
diff --git a/01-intro-to-r.md b/01-intro-to-r.md
index deb2472a..923ce615 100644
--- a/01-intro-to-r.md
+++ b/01-intro-to-r.md
@@ -222,7 +222,7 @@ Let's try a function that can take multiple arguments: `round()`.
 round(3.14159)
 ```
 
-```{.output}
+```output
 #> [1] 3
 ```
 
@@ -238,7 +238,7 @@ help for this function using `?round`.
 args(round)
 ```
 
-```{.output}
+```output
 #> function (x, digits = 0) 
 #> NULL
 ```
@@ -256,7 +256,7 @@ type `digits = 2` or however many we want.
 round(3.14159, digits = 2)
 ```
 
-```{.output}
+```output
 #> [1] 3.14
 ```
 
@@ -268,7 +268,7 @@ don't have to name them:
 round(3.14159, 2)
 ```
 
-```{.output}
+```output
 #> [1] 3.14
 ```
 
@@ -279,7 +279,7 @@ And if you do name the arguments, you can switch their order:
 round(digits = 2, x = 3.14159)
 ```
 
-```{.output}
+```output
 #> [1] 3.14
 ```
 
@@ -459,7 +459,7 @@ animals <- c("mouse", "rat", "dog", "cat")
 animals[2]
 ```
 
-```{.output}
+```output
 #> [1] "rat"
 ```
 
@@ -467,7 +467,7 @@ animals[2]
 animals[c(3, 2)]
 ```
 
-```{.output}
+```output
 #> [1] "dog" "rat"
 ```
 
@@ -480,7 +480,7 @@ more_animals <- animals[c(1, 2, 3, 2, 1, 4)]
 more_animals
 ```
 
-```{.output}
+```output
 #> [1] "mouse" "rat"   "dog"   "rat"   "mouse" "cat"
 ```
 
@@ -500,7 +500,7 @@ weight_g <- c(21, 34, 39, 54, 55)
 weight_g[c(TRUE, FALSE, FALSE, TRUE, TRUE)]
 ```
 
-```{.output}
+```output
 #> [1] 21 54 55
 ```
 
@@ -513,7 +513,7 @@ values above 50:
 weight_g > 50    # will return logicals with TRUE for the indices that meet the condition
 ```
 
-```{.output}
+```output
 #> [1] FALSE FALSE FALSE  TRUE  TRUE
 ```
 
@@ -522,7 +522,7 @@ weight_g > 50    # will return logicals with TRUE for the indices that meet the
 weight_g[weight_g > 50]
 ```
 
-```{.output}
+```output
 #> [1] 54 55
 ```
 
@@ -534,7 +534,7 @@ You can combine multiple tests using `&` (both conditions are true, AND) or `|`
 weight_g[weight_g > 30 & weight_g < 50]
 ```
 
-```{.output}
+```output
 #> [1] 34 39
 ```
 
@@ -542,7 +542,7 @@ weight_g[weight_g > 30 & weight_g < 50]
 weight_g[weight_g <= 30 | weight_g == 55]
 ```
 
-```{.output}
+```output
 #> [1] 21 55
 ```
 
@@ -550,7 +550,7 @@ weight_g[weight_g <= 30 | weight_g == 55]
 weight_g[weight_g >= 30 & weight_g == 21]
 ```
 
-```{.output}
+```output
 #> numeric(0)
 ```
 
@@ -573,7 +573,7 @@ animals <- c("mouse", "rat", "dog", "cat", "cat")
 animals[animals == "cat" | animals == "rat"]
 ```
 
-```{.output}
+```output
 #> [1] "rat" "cat" "cat"
 ```
 
@@ -583,7 +583,7 @@ animals[animals == "cat" | animals == "rat"]
 animals %in% c("rat", "cat", "dog", "duck", "goat", "bird", "fish")
 ```
 
-```{.output}
+```output
 #> [1] FALSE  TRUE  TRUE  TRUE  TRUE
 ```
 
@@ -593,7 +593,7 @@ animals %in% c("rat", "cat", "dog", "duck", "goat", "bird", "fish")
 animals[animals %in% c("rat", "cat", "dog", "duck", "goat", "bird", "fish")]
 ```
 
-```{.output}
+```output
 #> [1] "rat" "dog" "cat" "cat"
 ```
 
diff --git a/02-starting-with-data.md b/02-starting-with-data.md
index fe59231b..282955cb 100644
--- a/02-starting-with-data.md
+++ b/02-starting-with-data.md
@@ -122,7 +122,7 @@ about data frames later):
 surveys <- read_csv("data_raw/portal_data_joined.csv")
 ```
 
-```{.output}
+```output
 #> Rows: 34786 Columns: 13
 #> ── Column specification ────────────────────────────────────────────────────────
 #> Delimiter: ","
@@ -175,7 +175,7 @@ We can also extract the first few lines of this data using the function
 head(surveys)
 ```
 
-```{.output}
+```output
 #> # A tibble: 6 × 13
 #>   record_id month   day  year plot_id species_id sex   hindfoot_length weight
 #>       <dbl> <dbl> <dbl> <dbl>   <dbl> <chr>      <chr>           <dbl>  <dbl>
@@ -290,7 +290,7 @@ questions?
 str(surveys)
 ```
 
-```{.output}
+```output
 #> spc_tbl_ [34,786 × 13] (S3: spec_tbl_df/tbl_df/tbl/data.frame)
 #>  $ record_id      : num [1:34786] 1 72 224 266 349 363 435 506 588 661 ...
 #>  $ month          : num [1:34786] 7 8 9 10 11 11 12 1 2 3 ...
@@ -532,7 +532,7 @@ the `sex` vector would be:
 sex # current order
 ```
 
-```{.output}
+```output
 #> [1] male   female female male  
 #> Levels: female male
 ```
@@ -542,7 +542,7 @@ sex <- factor(sex, levels = c("male", "female"))
 sex # after re-ordering
 ```
 
-```{.output}
+```output
 #> [1] male   female female male  
 #> Levels: male female
 ```
@@ -650,7 +650,7 @@ sex <- surveys$sex
 levels(sex)
 ```
 
-```{.output}
+```output
 #> [1] "F" "M"
 ```
 
@@ -659,7 +659,7 @@ sex <- addNA(sex)
 levels(sex)
 ```
 
-```{.output}
+```output
 #> [1] "F" "M" NA
 ```
 
@@ -667,7 +667,7 @@ levels(sex)
 head(sex)
 ```
 
-```{.output}
+```output
 #> [1] M    M    <NA> <NA> <NA> <NA>
 #> Levels: F M <NA>
 ```
@@ -677,7 +677,7 @@ levels(sex)[3] <- "undetermined"
 levels(sex)
 ```
 
-```{.output}
+```output
 #> [1] "F"            "M"            "undetermined"
 ```
 
@@ -685,7 +685,7 @@ levels(sex)
 head(sex)
 ```
 
-```{.output}
+```output
 #> [1] M            M            undetermined undetermined undetermined
 #> [6] undetermined
 #> Levels: F M undetermined
@@ -844,7 +844,7 @@ This character vector can be used as the argument for `ymd()`:
 ymd(paste(surveys$year, surveys$month, surveys$day, sep = "-"))
 ```
 
-```{.warning}
+```warning
 #> Warning: 129 failed to parse.
 ```
 
@@ -859,7 +859,7 @@ vector to the `surveys` data frame as a new column called `date`:
 surveys$date <- ymd(paste(surveys$year, surveys$month, surveys$day, sep = "-"))
 ```
 
-```{.warning}
+```warning
 #> Warning: 129 failed to parse.
 ```
 
@@ -875,7 +875,7 @@ column is to use `summary()`:
 summary(surveys$date)
 ```
 
-```{.output}
+```output
 #>         Min.      1st Qu.       Median         Mean      3rd Qu.         Max. 
 #> "1977-07-16" "1984-03-12" "1990-07-22" "1990-12-15" "1997-07-29" "2002-12-31" 
 #>         NA's 
@@ -898,7 +898,7 @@ missing_dates <- surveys[is.na(surveys$date), c("year", "month", "day")]
 head(missing_dates)
 ```
 
-```{.output}
+```output
 #> # A tibble: 6 × 3
 #>    year month   day
 #>   <dbl> <dbl> <dbl>
diff --git a/03-dplyr.md b/03-dplyr.md
index 0ffecfb1..1d6de21c 100644
--- a/03-dplyr.md
+++ b/03-dplyr.md
@@ -88,7 +88,7 @@ tidyverse package **`readr`**.
 surveys <- read_csv("data_raw/portal_data_joined.csv")
 ```
 
-```{.output}
+```output
 #> Rows: 34786 Columns: 13
 #> ── Column specification ────────────────────────────────────────────────────────
 #> Delimiter: ","
@@ -353,7 +353,7 @@ surveys %>%
   tail()
 ```
 
-```{.output}
+```output
 #> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
 #> argument.
 ```
@@ -376,7 +376,7 @@ surveys %>%
   summarize(mean_weight = mean(weight))
 ```
 
-```{.output}
+```output
 #> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
 #> argument.
 ```
@@ -395,7 +395,7 @@ surveys %>%
   print(n = 15)
 ```
 
-```{.output}
+```output
 #> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
 #> argument.
 ```
@@ -413,7 +413,7 @@ surveys %>%
             min_weight = min(weight))
 ```
 
-```{.output}
+```output
 #> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
 #> argument.
 ```
@@ -430,7 +430,7 @@ surveys %>%
   arrange(min_weight)
 ```
 
-```{.output}
+```output
 #> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
 #> argument.
 ```
@@ -447,7 +447,7 @@ surveys %>%
   arrange(desc(mean_weight))
 ```
 
-```{.output}
+```output
 #> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
 #> argument.
 ```
@@ -628,7 +628,7 @@ surveys_gw <- surveys %>%
   summarize(mean_weight = mean(weight))
 ```
 
-```{.output}
+```output
 #> `summarise()` has grouped output by 'plot_id'. You can override using the
 #> `.groups` argument.
 ```
@@ -730,7 +730,7 @@ surveys_wide_genera <- surveys %>%
   pivot_wider(names_from = year, values_from = n_genera)
 ```
 
-```{.output}
+```output
 #> `summarise()` has grouped output by 'plot_id'. You can override using the
 #> `.groups` argument.
 ```
@@ -793,7 +793,7 @@ surveys_long %>%
   pivot_wider(names_from = measurement, values_from = mean_value)
 ```
 
-```{.output}
+```output
 #> `summarise()` has grouped output by 'year', 'measurement'. You can override
 #> using the `.groups` argument.
 ```
diff --git a/04-visualization-ggplot2.md b/04-visualization-ggplot2.md
index 852dbaeb..9aef6a7d 100644
--- a/04-visualization-ggplot2.md
+++ b/04-visualization-ggplot2.md
@@ -567,7 +567,7 @@ yearly_weight <- surveys_complete %>%
                  summarize(avg_weight = mean(weight))
 ```
 
-```{.output}
+```output
 #> `summarise()` has grouped output by 'year'. You can override using the
 #> `.groups` argument.
 ```
diff --git a/05-r-and-databases.md b/05-r-and-databases.md
index cdd93e7b..537f2d9a 100644
--- a/05-r-and-databases.md
+++ b/05-r-and-databases.md
@@ -97,12 +97,12 @@ library(dplyr)
 library(dbplyr)
 ```
 
-```{.output}
+```output
 #> 
 #> Attaching package: 'dbplyr'
 ```
 
-```{.output}
+```output
 #> The following objects are masked from 'package:dplyr':
 #> 
 #>     ident, sql
@@ -131,8 +131,8 @@ Let's take a closer look at the `mammals` database we just connected to:
 src_dbi(mammals)
 ```
 
-```{.output}
-#> src:  sqlite 3.44.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data_raw/portal_mammals.sqlite]
+```output
+#> src:  sqlite 3.45.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data_raw/portal_mammals.sqlite]
 #> tbls: plots, species, surveys
 ```
 
@@ -186,9 +186,9 @@ rows of the table:
 head(surveys, n = 10)
 ```
 
-```{.output}
+```output
 #> # Source:   SQL [10 x 9]
-#> # Database: sqlite 3.44.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data_raw/portal_mammals.sqlite]
+#> # Database: sqlite 3.45.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data_raw/portal_mammals.sqlite]
 #>    record_id month   day  year plot_id species_id sex   hindfoot_length weight
 #>        <int> <int> <int> <int>   <int> <chr>      <chr>           <int>  <int>
 #>  1         1     7    16  1977       2 NL         M                  32     NA
@@ -217,7 +217,7 @@ how many rows there are in total using `nrow()`:
 nrow(surveys)
 ```
 
-```{.output}
+```output
 #> [1] NA
 ```
 
@@ -293,9 +293,9 @@ surveys %>%
   select(species_id, sex, weight)
 ```
 
-```{.output}
+```output
 #> # Source:   SQL [?? x 3]
-#> # Database: sqlite 3.44.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data_raw/portal_mammals.sqlite]
+#> # Database: sqlite 3.45.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data_raw/portal_mammals.sqlite]
 #>    species_id sex   weight
 #>    <chr>      <chr>  <int>
 #>  1 PF         M          4
@@ -357,9 +357,9 @@ data_subset %>%
   select(-sex)
 ```
 
-```{.output}
+```output
 #> # Source:   SQL [?? x 2]
-#> # Database: sqlite 3.44.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data_raw/portal_mammals.sqlite]
+#> # Database: sqlite 3.45.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data_raw/portal_mammals.sqlite]
 #>    species_id weight
 #>    <chr>       <int>
 #>  1 PF              4
@@ -426,9 +426,9 @@ plots <- tbl(mammals, "plots")
 plots
 ```
 
-```{.output}
-#> # Source:   table<plots> [?? x 2]
-#> # Database: sqlite 3.44.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data_raw/portal_mammals.sqlite]
+```output
+#> # Source:   table<`plots`> [?? x 2]
+#> # Database: sqlite 3.45.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data_raw/portal_mammals.sqlite]
 #>    plot_id plot_type                
 #>      <int> <chr>                    
 #>  1       1 Spectab exclosure        
@@ -451,9 +451,9 @@ The `plot_id` column also features in the `surveys` table:
 surveys
 ```
 
-```{.output}
-#> # Source:   table<surveys> [?? x 9]
-#> # Database: sqlite 3.44.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data_raw/portal_mammals.sqlite]
+```output
+#> # Source:   table<`surveys`> [?? x 9]
+#> # Database: sqlite 3.45.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data_raw/portal_mammals.sqlite]
 #>    record_id month   day  year plot_id species_id sex   hindfoot_length weight
 #>        <int> <int> <int> <int>   <int> <chr>      <chr>           <int>  <int>
 #>  1         1     7    16  1977       2 NL         M                  32     NA
@@ -495,11 +495,11 @@ plots %>%
   collect()
 ```
 
-```{.output}
+```output
 #> Joining with `by = join_by(plot_id)`
 ```
 
-```{.output}
+```output
 #> # A tibble: 1,995 × 10
 #>    plot_id plot_type         record_id month   day  year species_id sex  
 #>      <int> <chr>                 <int> <int> <int> <int> <chr>      <chr>
@@ -557,7 +557,7 @@ left_join(surveys, species) %>%
   collect()
 ```
 
-```{.output}
+```output
 #> Joining with `by = join_by(species_id)`
 ```
 
@@ -628,7 +628,7 @@ unique_genera <- left_join(surveys, plots) %>%
     collect()
 ```
 
-```{.output}
+```output
 #> Joining with `by = join_by(plot_id)`
 #> Joining with `by = join_by(species_id)`
 ```
@@ -655,7 +655,7 @@ library(tidyverse)
 species <- read_csv("data_raw/species.csv")
 ```
 
-```{.output}
+```output
 #> Rows: 54 Columns: 4
 #> ── Column specification ────────────────────────────────────────────────────────
 #> Delimiter: ","
@@ -669,7 +669,7 @@ species <- read_csv("data_raw/species.csv")
 surveys <- read_csv("data_raw/surveys.csv")
 ```
 
-```{.output}
+```output
 #> Rows: 35549 Columns: 9
 #> ── Column specification ────────────────────────────────────────────────────────
 #> Delimiter: ","
@@ -684,7 +684,7 @@ surveys <- read_csv("data_raw/surveys.csv")
 plots <- read_csv("data_raw/plots.csv")
 ```
 
-```{.output}
+```output
 #> Rows: 24 Columns: 2
 #> ── Column specification ────────────────────────────────────────────────────────
 #> Delimiter: ","
@@ -708,7 +708,7 @@ my_db_file <- "data/portal-database-output.sqlite"
 my_db <- src_sqlite(my_db_file, create = TRUE)
 ```
 
-```{.warning}
+```warning
 #> Warning: `src_sqlite()` was deprecated in dplyr 1.0.0.
 #> ℹ Please use `tbl()` directly with a database connection
 #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
@@ -722,8 +722,8 @@ Currently, our new database is empty, it doesn't contain any tables:
 my_db
 ```
 
-```{.output}
-#> src:  sqlite 3.44.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data/portal-database-output.sqlite]
+```output
+#> src:  sqlite 3.45.2 [/home/runner/work/R-ecology-lesson/R-ecology-lesson/site/built/data/portal-database-output.sqlite]
 #> tbls:
 ```
 
diff --git a/CITATION.md b/CITATION.md
index 1ddd1ce9..9ad5b11d 100644
--- a/CITATION.md
+++ b/CITATION.md
@@ -1,7 +1,7 @@
 # CITATION
 
 
-```{.warning}
+```warning
 Warning in system("update-copyright.py"): error in running command
 ```
 
@@ -39,24 +39,24 @@ sponsored by the [ELIXIR project](https://elixir-europe.org/).
 You can cite this Data Carpentry lesson as follow:
 
 
-```{.warning}
+```warning
 Warning in file(con, "r"): cannot open file 'AUTHORS': No such file or
 directory
 ```
 
-```{.error}
+```error
 Error in file(con, "r"): cannot open the connection
 ```
 
 or as a BibTeX entry:
 
 
-```{.warning}
+```warning
 Warning in file(con, "r"): cannot open file 'AUTHORS': No such file or
 directory
 ```
 
-```{.error}
+```error
 Error in file(con, "r"): cannot open the connection
 ```
 
diff --git a/config.yaml b/config.yaml
deleted file mode 100644
index 506c7a11..00000000
--- a/config.yaml
+++ /dev/null
@@ -1,86 +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: 'Data Analysis and Visualisation in R for Ecologists'
-
-# Date the lesson was created (YYYY-MM-DD, this is empty by default)
-created: '2015-04-02'
-
-# 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: 'stable'
-
-# 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/R-ecology-lesson'
-
-# Default branch of your lesson
-branch: 'main'
-
-# Who to contact if there are any issues
-contact: 'curriculum@carpentries.org'
-
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-- 01-intro-to-r.Rmd
-- 02-starting-with-data.Rmd
-- 03-dplyr.Rmd
-- 04-visualization-ggplot2.Rmd
-- 05-r-and-databases.Rmd
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-- reference.md
-
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-- instructor-notes.md
-
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-
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