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Source  : 97a6310
Branch  : master
Author  : Craig Grosch <[email protected]>
Time    : 2026-01-07 23:02:18 +0000
Message : Merge pull request swcarpentry#938 from swcarpentry/update/packages

Update 16 packages

Author: actions-user

01-rstudio-intro.md

@@ -643,7 +643,7 @@ function (name, pos = -1L, envir = as.environment(pos), all.names = FALSE,
     }
     else all.names
 }
-<bytecode: 0x55cc871b9fd0>
+<bytecode: 0x559f3e4abf90>
 <environment: namespace:base>
 ```
 
@@ -695,7 +695,8 @@ rm(list <- ls())
 ```
 
 ``` error
-Error in rm(list <- ls()): ... must contain names or character strings
+Error in `rm()`:
+! ... must contain names or character strings
 ```
 
 :::::::::::::::::::::::::::::::::::::::::  callout

02-project-intro.md

@@ -190,7 +190,7 @@ ls -lh data/gapminder_data.csv
 ```
 
 ``` output
--rw-r--r-- 1 runner runner 80K Nov 11 01:04 data/gapminder_data.csv
+-rw-r--r-- 1 runner runner 80K Jan 20 01:02 data/gapminder_data.csv
 ```
 
 The file size is 80K.

03-seeking-help.md

@@ -186,8 +186,8 @@ attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 loaded via a namespace (and not attached):
-[1] compiler_4.5.2 tools_4.5.2    yaml_2.3.10    knitr_1.50     xfun_0.53     
-[6] renv_1.1.5     evaluate_1.0.5
+[1] compiler_4.5.2 cli_3.6.5      tools_4.5.2    yaml_2.3.12    knitr_1.51    
+[6] xfun_0.55      rlang_1.1.6    renv_1.1.6     evaluate_1.0.5
 ```
 
 Will print out your current version of R, as well as any packages you

04-data-structures-part1.md

@@ -168,7 +168,8 @@ cats$weight + cats$coat
 ```
 
 ``` error
-Error in cats$weight + cats$coat: non-numeric argument to binary operator
+Error in `cats$weight + cats$coat`:
+! non-numeric argument to binary operator
 ```
 
 Understanding what happened here is key to successfully analyzing data in R.
@@ -284,7 +285,8 @@ cats2$weight + 2
 ```
 
 ``` error
-Error in cats2$weight + 2: non-numeric argument to binary operator
+Error in `cats2$weight + 2`:
+! non-numeric argument to binary operator
 ```
 
 What happened?
@@ -975,7 +977,8 @@ pizza_price$pizzafresh
 ```
 
 ``` error
-Error in pizza_price$pizzafresh: $ operator is invalid for atomic vectors
+Error in `pizza_price$pizzafresh`:
+! $ operator is invalid for atomic vectors
 ```
 
 It will pay off if you remember this error message, you will meet it in your own

05-data-structures-part2.md

@@ -70,7 +70,8 @@ cbind(cats, age)
 ```
 
 ``` error
-Error in data.frame(..., check.names = FALSE): arguments imply differing number of rows: 3, 4
+Error in `data.frame()`:
+! arguments imply differing number of rows: 3, 4
 ```
 
 ``` r
@@ -79,7 +80,8 @@ cbind(cats, age)
 ```
 
 ``` error
-Error in data.frame(..., check.names = FALSE): arguments imply differing number of rows: 3, 2
+Error in `data.frame()`:
+! arguments imply differing number of rows: 3, 2
 ```
 
 Why didn't this work? Of course, R wants to see one element in our new column

06-data-subsetting.md

@@ -215,7 +215,8 @@ This gives a somewhat cryptic error:
 
 
 ``` error
-Error in x[-1:3]: only 0's may be mixed with negative subscripts
+Error in `x[-1:3]`:
+! only 0's may be mixed with negative subscripts
 ```
 
 But remember the order of operations. `:` is really a function.
@@ -522,7 +523,8 @@ x[-"a"]
 ```
 
 ``` error
-Error in -"a": invalid argument to unary operator
+Error in `-"a"`:
+! invalid argument to unary operator
 ```
 
 However, we can use the `!=` (not-equals) operator to construct a logical vector that will do what we want:
@@ -795,7 +797,8 @@ m[, c(3,6)]
 ```
 
 ``` error
-Error in m[, c(3, 6)]: subscript out of bounds
+Error in `m[, c(3, 6)]`:
+! subscript out of bounds
 ```
 
 :::::::::::::::::::::::::::::::::::::::::  callout
@@ -954,7 +957,8 @@ xlist[[1:2]]
 ```
 
 ``` error
-Error in xlist[[1:2]]: subscript out of bounds
+Error in `xlist[[1:2]]`:
+! subscript out of bounds
 ```
 
 Nor use it to skip elements:
@@ -965,7 +969,8 @@ xlist[[-1]]
 ```
 
 ``` error
-Error in xlist[[-1]]: invalid negative subscript in get1index <real>
+Error in `xlist[[-1]]`:
+! invalid negative subscript in get1index <real>
 ```
 
 But you can use names to both subset and extract elements:

07-control-flow.md

@@ -187,7 +187,8 @@ Did anyone get a warning message like this?
 
 
 ``` error
-Error in if (gapminder$year == 2012) {: the condition has length > 1
+Error in `if (gapminder$year == 2012) ...`:
+! the condition has length > 1
 ```
 
 The `if()` function only accepts singular (of length 1) inputs, and therefore

08-plot-ggplot2.md

@@ -185,7 +185,7 @@ ggplot(data = gapminder, mapping = aes(x=year, y=lifeExp, color=continent)) +
   geom_line()
 ```
 
-<img src="fig/08-plot-ggplot2-rendered-lifeExp-line-1.png" style="display: block; margin: auto;" />
+<img src="fig/08-plot-ggplot2-rendered-lifeExp-line-1.png" alt="" style="display: block; margin: auto;" />
 
 Instead of adding a `geom_point` layer, we've added a `geom_line` layer.
 
@@ -197,7 +197,7 @@ ggplot(data = gapminder, mapping = aes(x=year, y=lifeExp, group=country, color=c
   geom_line()
 ```
 
-<img src="fig/08-plot-ggplot2-rendered-lifeExp-line-by-1.png" style="display: block; margin: auto;" />
+<img src="fig/08-plot-ggplot2-rendered-lifeExp-line-by-1.png" alt="" style="display: block; margin: auto;" />
 
 We've added the **group** *aesthetic*, which tells `ggplot` to draw a line for each
 country.
@@ -211,7 +211,7 @@ ggplot(data = gapminder, mapping = aes(x=year, y=lifeExp, group=country, color=c
   geom_line() + geom_point()
 ```
 
-<img src="fig/08-plot-ggplot2-rendered-lifeExp-line-point-1.png" style="display: block; margin: auto;" />
+<img src="fig/08-plot-ggplot2-rendered-lifeExp-line-point-1.png" alt="" style="display: block; margin: auto;" />
 
 It's important to note that each layer is drawn on top of the previous layer. In
 this example, the points have been drawn *on top of* the lines. Here's a
@@ -223,7 +223,7 @@ ggplot(data = gapminder, mapping = aes(x=year, y=lifeExp, group=country)) +
   geom_line(mapping = aes(color=continent)) + geom_point()
 ```
 
-<img src="fig/08-plot-ggplot2-rendered-lifeExp-layer-example-1-1.png" style="display: block; margin: auto;" />
+<img src="fig/08-plot-ggplot2-rendered-lifeExp-layer-example-1-1.png" alt="" style="display: block; margin: auto;" />
 
 In this example, the *aesthetic* mapping of **color** has been moved from the
 global plot options in `ggplot` to the `geom_line` layer so it no longer applies
@@ -275,7 +275,7 @@ ggplot(data = gapminder, mapping = aes(x = gdpPercap, y = lifeExp)) +
   geom_point()
 ```
 
-<img src="fig/08-plot-ggplot2-rendered-lifeExp-vs-gdpPercap-scatter3-1.png" style="display: block; margin: auto;" />
+<img src="fig/08-plot-ggplot2-rendered-lifeExp-vs-gdpPercap-scatter3-1.png" alt="" style="display: block; margin: auto;" />
 
 Currently it's hard to see the relationship between the points due to some strong
 outliers in GDP per capita. We can change the scale of units on the x axis using
@@ -404,7 +404,7 @@ ggplot(data = gapminder, mapping = aes(x = gdpPercap, y = lifeExp, color = conti
 `geom_smooth()` using formula = 'y ~ x'
 ```
 
-<img src="fig/08-plot-ggplot2-rendered-ch4b-sol-1.png" style="display: block; margin: auto;" />
+<img src="fig/08-plot-ggplot2-rendered-ch4b-sol-1.png" alt="" style="display: block; margin: auto;" />
 
 :::::::::::::::::::::::::
 
@@ -438,7 +438,7 @@ ggplot(data = americas, mapping = aes(x = year, y = lifeExp)) +
   theme(axis.text.x = element_text(angle = 45))
 ```
 
-<img src="fig/08-plot-ggplot2-rendered-facet-1.png" style="display: block; margin: auto;" />
+<img src="fig/08-plot-ggplot2-rendered-facet-1.png" alt="" style="display: block; margin: auto;" />
 
 The `facet_wrap` layer took a "formula" as its argument, denoted by the tilde
 (~). This tells R to draw a panel for each unique value in the country column
@@ -470,7 +470,7 @@ ggplot(data = americas, mapping = aes(x = year, y = lifeExp, color=continent)) +
   theme(axis.text.x = element_text(angle = 90, hjust = 1))
 ```
 
-<img src="fig/08-plot-ggplot2-rendered-theme-1.png" style="display: block; margin: auto;" />
+<img src="fig/08-plot-ggplot2-rendered-theme-1.png" alt="" style="display: block; margin: auto;" />
 
 ## Exporting the plot
 
@@ -531,7 +531,7 @@ ggplot(data = gapminder, mapping = aes(x = continent, y = lifeExp, fill = contin
        axis.ticks.x = element_blank())
 ```
 
-<img src="fig/08-plot-ggplot2-rendered-ch5-sol-1.png" style="display: block; margin: auto;" />
+<img src="fig/08-plot-ggplot2-rendered-ch5-sol-1.png" alt="" style="display: block; margin: auto;" />
 
 :::::::::::::::::::::::::
 

10-functions.md

@@ -291,7 +291,8 @@ fahr_to_kelvin(temp = as.factor(32))
 ```
 
 ``` error
-Error in fahr_to_kelvin(temp = as.factor(32)): is.numeric(temp) is not TRUE
+Error in `fahr_to_kelvin()`:
+! is.numeric(temp) is not TRUE
 ```
 
 :::::::::::::::::::::::::::::::::::::::  challenge

12-dplyr.md

@@ -582,7 +582,7 @@ ggplot(data = americas, mapping = aes(x = year, y = lifeExp)) +
   theme(axis.text.x = element_text(angle = 45))
 ```
 
-<img src="fig/12-dplyr-rendered-unnamed-chunk-27-1.png" style="display: block; margin: auto;" />
+<img src="fig/12-dplyr-rendered-unnamed-chunk-27-1.png" alt="" style="display: block; margin: auto;" />
 
 This code makes the right plot but it also creates an intermediate variable
 (`americas`) that we might not have any other uses for. Just as we used
@@ -604,7 +604,7 @@ gapminder %>%
   theme(axis.text.x = element_text(angle = 45))
 ```
 
-<img src="fig/12-dplyr-rendered-unnamed-chunk-28-1.png" style="display: block; margin: auto;" />
+<img src="fig/12-dplyr-rendered-unnamed-chunk-28-1.png" alt="" style="display: block; margin: auto;" />
 
 More examples of using the function `mutate()` and the `ggplot2` package.
 
@@ -622,7 +622,7 @@ gapminder %>%
   theme_minimal()
 ```
 
-<img src="fig/12-dplyr-rendered-unnamed-chunk-29-1.png" style="display: block; margin: auto;" />
+<img src="fig/12-dplyr-rendered-unnamed-chunk-29-1.png" alt="" style="display: block; margin: auto;" />
 
 :::::::::::::::::::::::::::::::::::::::  challenge