differences for PR #13

carpentries-incubator · Sep 19, 2022 · ed370f2 · ed370f2
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diff --git a/05-extra-challenges.md → extra-challenges.md b/05-extra-challenges.md → extra-challenges.md
diff --git a/fig/01-visualizing-ggplot-rendered-boxplot-jitter-1.png b/fig/01-visualizing-ggplot-rendered-boxplot-jitter-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-boxplot-outliers-1.png b/fig/01-visualizing-ggplot-rendered-boxplot-outliers-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-customizing-challenge-answer-1.png b/fig/01-visualizing-ggplot-rendered-customizing-challenge-answer-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-element-blank-1.png b/fig/01-visualizing-ggplot-rendered-element-blank-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-facet-wrap-1.png b/fig/01-visualizing-ggplot-rendered-facet-wrap-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-fill-na-1.png b/fig/01-visualizing-ggplot-rendered-fill-na-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-geom-color-1.png b/fig/01-visualizing-ggplot-rendered-geom-color-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-global-color-1.png b/fig/01-visualizing-ggplot-rendered-global-color-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-labels-1.png b/fig/01-visualizing-ggplot-rendered-labels-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-legend-remove-1.png b/fig/01-visualizing-ggplot-rendered-legend-remove-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-reverse-layers-1.png b/fig/01-visualizing-ggplot-rendered-reverse-layers-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-text-size-1.png b/fig/01-visualizing-ggplot-rendered-text-size-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-theme-bw-1.png b/fig/01-visualizing-ggplot-rendered-theme-bw-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-unnamed-chunk-1-1.png b/fig/01-visualizing-ggplot-rendered-unnamed-chunk-1-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-violin-challenge-answer-1.png b/fig/01-visualizing-ggplot-rendered-violin-challenge-answer-1.png
diff --git a/fig/01-visualizing-ggplot-rendered-violin-challenge-answer-2-1.png b/fig/01-visualizing-ggplot-rendered-violin-challenge-answer-2-1.png
diff --git a/fig/03-working-with-data-rendered-date-plot-challenge-answer-1.png b/fig/03-working-with-data-rendered-date-plot-challenge-answer-1.png
diff --git a/...sualizing-ggplot-rendered-bare-plot-1.png → ...sualizing-ggplot-rendered-bare-plot-1.png b/...sualizing-ggplot-rendered-bare-plot-1.png → ...sualizing-ggplot-rendered-bare-plot-1.png
diff --git a/...izing-ggplot-rendered-blank-boxplot-1.png → ...izing-ggplot-rendered-blank-boxplot-1.png b/...izing-ggplot-rendered-blank-boxplot-1.png → ...izing-ggplot-rendered-blank-boxplot-1.png
diff --git a/...visualizing-ggplot-rendered-boxplot-1.png → ...visualizing-ggplot-rendered-boxplot-1.png b/...visualizing-ggplot-rendered-boxplot-1.png → ...visualizing-ggplot-rendered-boxplot-1.png
diff --git a/...izing-ggplot-rendered-boxplot-color-1.png → ...izing-ggplot-rendered-boxplot-color-1.png b/...izing-ggplot-rendered-boxplot-color-1.png → ...izing-ggplot-rendered-boxplot-color-1.png
diff --git a/...lizing-ggplot-rendered-boxplot-fill-1.png → ...lizing-ggplot-rendered-boxplot-fill-1.png b/...lizing-ggplot-rendered-boxplot-fill-1.png → ...lizing-ggplot-rendered-boxplot-fill-1.png
diff --git a/fig/visualizing-ggplot-rendered-boxplot-jitter-1.png b/fig/visualizing-ggplot-rendered-boxplot-jitter-1.png
diff --git a/...-ggplot-rendered-boxplot-label-wrap-1.png → ...-ggplot-rendered-boxplot-label-wrap-1.png b/...-ggplot-rendered-boxplot-label-wrap-1.png → ...-ggplot-rendered-boxplot-label-wrap-1.png
diff --git a/fig/visualizing-ggplot-rendered-boxplot-outliers-1.png b/fig/visualizing-ggplot-rendered-boxplot-outliers-1.png
diff --git a/...zing-ggplot-rendered-boxplot-points-1.png → ...zing-ggplot-rendered-boxplot-points-1.png b/...zing-ggplot-rendered-boxplot-points-1.png → ...zing-ggplot-rendered-boxplot-points-1.png
diff --git a/...lizing-ggplot-rendered-change-alpha-1.png → ...lizing-ggplot-rendered-change-alpha-1.png b/...lizing-ggplot-rendered-change-alpha-1.png → ...lizing-ggplot-rendered-change-alpha-1.png
diff --git a/...lizing-ggplot-rendered-change-color-1.png → ...lizing-ggplot-rendered-change-color-1.png b/...lizing-ggplot-rendered-change-color-1.png → ...lizing-ggplot-rendered-change-color-1.png
diff --git a/...ing-ggplot-rendered-color-plot-type-1.png → ...ing-ggplot-rendered-color-plot-type-1.png b/...ing-ggplot-rendered-color-plot-type-1.png → ...ing-ggplot-rendered-color-plot-type-1.png
diff --git a/fig/visualizing-ggplot-rendered-customizing-challenge-answer-1.png b/fig/visualizing-ggplot-rendered-customizing-challenge-answer-1.png
diff --git a/fig/visualizing-ggplot-rendered-element-blank-1.png b/fig/visualizing-ggplot-rendered-element-blank-1.png
diff --git a/fig/visualizing-ggplot-rendered-facet-wrap-1.png b/fig/visualizing-ggplot-rendered-facet-wrap-1.png
diff --git a/fig/visualizing-ggplot-rendered-fill-na-1.png b/fig/visualizing-ggplot-rendered-fill-na-1.png
diff --git a/fig/visualizing-ggplot-rendered-geom-color-1.png b/fig/visualizing-ggplot-rendered-geom-color-1.png
diff --git a/fig/visualizing-ggplot-rendered-global-color-1.png b/fig/visualizing-ggplot-rendered-global-color-1.png
diff --git a/fig/visualizing-ggplot-rendered-labels-1.png b/fig/visualizing-ggplot-rendered-labels-1.png
diff --git a/fig/visualizing-ggplot-rendered-legend-remove-1.png b/fig/visualizing-ggplot-rendered-legend-remove-1.png
diff --git a/...dered-modify-color-challenge-answer-1.png → ...dered-modify-color-challenge-answer-1.png b/...dered-modify-color-challenge-answer-1.png → ...dered-modify-color-challenge-answer-1.png
diff --git a/...ered-modify-points-challenge-answer-1.png → ...ered-modify-points-challenge-answer-1.png b/...ered-modify-points-challenge-answer-1.png → ...ered-modify-points-challenge-answer-1.png
diff --git a/...zing-ggplot-rendered-plot-with-axes-1.png → ...zing-ggplot-rendered-plot-with-axes-1.png b/...zing-ggplot-rendered-plot-with-axes-1.png → ...zing-ggplot-rendered-plot-with-axes-1.png
diff --git a/fig/visualizing-ggplot-rendered-reverse-layers-1.png b/fig/visualizing-ggplot-rendered-reverse-layers-1.png
diff --git a/...sualizing-ggplot-rendered-scale-log-1.png → ...sualizing-ggplot-rendered-scale-log-1.png b/...sualizing-ggplot-rendered-scale-log-1.png → ...sualizing-ggplot-rendered-scale-log-1.png
diff --git a/...izing-ggplot-rendered-scale-viridis-1.png → ...izing-ggplot-rendered-scale-viridis-1.png b/...izing-ggplot-rendered-scale-viridis-1.png → ...izing-ggplot-rendered-scale-viridis-1.png
diff --git a/...lizing-ggplot-rendered-scatter-plot-1.png → ...lizing-ggplot-rendered-scatter-plot-1.png b/...lizing-ggplot-rendered-scatter-plot-1.png → ...lizing-ggplot-rendered-scatter-plot-1.png
diff --git a/fig/visualizing-ggplot-rendered-text-size-1.png b/fig/visualizing-ggplot-rendered-text-size-1.png
diff --git a/fig/visualizing-ggplot-rendered-theme-bw-1.png b/fig/visualizing-ggplot-rendered-theme-bw-1.png
diff --git a/fig/visualizing-ggplot-rendered-unnamed-chunk-1-1.png b/fig/visualizing-ggplot-rendered-unnamed-chunk-1-1.png
diff --git a/fig/visualizing-ggplot-rendered-violin-challenge-answer-1.png b/fig/visualizing-ggplot-rendered-violin-challenge-answer-1.png
diff --git a/fig/visualizing-ggplot-rendered-violin-challenge-answer-2-1.png b/fig/visualizing-ggplot-rendered-violin-challenge-answer-2-1.png
diff --git a/fig/working-with-data-rendered-date-plot-challenge-answer-1.png b/fig/working-with-data-rendered-date-plot-challenge-answer-1.png
diff --git a/...ndered-time-series-challenge-answer-1.png → ...ndered-time-series-challenge-answer-1.png b/...ndered-time-series-challenge-answer-1.png → ...ndered-time-series-challenge-answer-1.png
diff --git a/02-how-r-thinks-about-data.md → how-r-thinks-about-data.md b/02-how-r-thinks-about-data.md → how-r-thinks-about-data.md
diff --git a/00-introduction-r-rstudio.md → introduction-r-rstudio.md b/00-introduction-r-rstudio.md → introduction-r-rstudio.md
diff --git a/md5sum.txt b/md5sum.txt
@@ -1,16 +1,15 @@
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-"index.md" "fe56dfea3c4269cceb361470e2ca1437" "site/built/index.md" "2022-09-13"
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-"update_plan.md" "cbffde7a61ae3ab0976a8515c420fce8" "site/built/update_plan.md" "2022-09-13"
-"episodes/00-introduction-r-rstudio.Rmd" "b85b48b9b947792088f13006797d2af2" "site/built/00-introduction-r-rstudio.md" "2022-09-13"
-"episodes/01-visualizing-ggplot.Rmd" "93d28ae2a77e0dd424cac595063051db" "site/built/01-visualizing-ggplot.md" "2022-09-13"
-"episodes/02-how-r-thinks-about-data.Rmd" "ccfcb3ce681291fb6a4d733ac1b5f444" "site/built/02-how-r-thinks-about-data.md" "2022-09-13"
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diff --git a/setup.md b/setup.md
@@ -89,7 +89,7 @@ During the course we will need a number of R packages. Packages contain useful R
 
 To try to install these packages, open RStudio and copy and paste the following command into the console window (look for a blinking cursor on the bottom left), then press the <kbd>Enter</kbd> (Windows and Linux) or <kbd>Return</kbd> (MacOS) to execute the command.
 
-```{r}
+```r
 install.packages(c("tidyverse", "lubridate", "patchwork", "ratdat"))
 ```
 
@@ -99,7 +99,7 @@ R tries to download and install the packages on your machine.
 
 When the installation has finished, you can try to load the packages by pasting the following code into the console:
 
-```{r}
+```r
 library(tidyverse)
 library(lubridate)
 library(patchwork)
@@ -120,4 +120,7 @@ Sometimes, package updates introduce changes that break your old code, which can
 
 We will download the data directly from R during the lessons. However, if you are expecting problems with the network, it may be better to download the data beforehand and store it on your machine.
 
-The data files for the lesson can be downloaded manually here: <https://www.michaelc-m.com/Rewrite-R-ecology-lesson/data/cleaned/surveys_complete_77_89.csv> and <https://www.michaelc-m.com/Rewrite-R-ecology-lesson/data/new_data.zip>.
+The data files for the lesson can be downloaded manually:
+
+ - [cleaned data](../episodes/data/cleaned/surveys_complete_77_89.csv) and 
+ - [zip file of raw data](../episodes//data/new_data.zip).
diff --git a/01-visualizing-ggplot.md → visualizing-ggplot.md b/01-visualizing-ggplot.md → visualizing-ggplot.md
diff --git a/03-working-with-data.md → working-with-data.md b/03-working-with-data.md → working-with-data.md
@@ -750,7 +750,7 @@ surveys %>%
 Warning: Removed 1692 rows containing missing values (geom_point).
 ```
 
-<img src="fig/03-working-with-data-rendered-date-plot-challenge-answer-1.png" width="600" height="600" style="display: block; margin: auto;" />
+<img src="fig/working-with-data-rendered-date-plot-challenge-answer-1.png" width="600" height="600" style="display: block; margin: auto;" />
 
 This isn't necessarily the most useful plot, but we will learn some techniques that will help produce nice time series plots
 
@@ -1111,7 +1111,7 @@ surveys_daily_counts %>%
   geom_line()
 ```
 
-<img src="fig/03-working-with-data-rendered-time-series-challenge-answer-1.png" width="600" height="600" style="display: block; margin: auto;" />
+<img src="fig/working-with-data-rendered-time-series-challenge-answer-1.png" width="600" height="600" style="display: block; margin: auto;" />
 
 ::::::::::::::::::::::::