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+The page you requested cannot be found (perhaps it was moved or renamed).
+You may want to try searching to find the page's new location, or use +the table of contents to find the page you are looking for.
+diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..160951a --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +.Rproj.user +.Rhistory +.RData +.Ruserdata +.DS_Store +*.Rproj diff --git a/01-introduction.Rmd b/01-introduction.Rmd new file mode 100644 index 0000000..330dc5b --- /dev/null +++ b/01-introduction.Rmd @@ -0,0 +1,19 @@ +# Introduction {#intro} + +You can label chapter and section titles using `{#label}` after them, e.g., we can reference Chapter \@ref(intro). If you do not manually label them, there will be automatic labels anyway, e.g., Chapter \@ref(methods). + +Figures and tables with captions will be placed in `figure` and `table` environments, respectively. + +```{r nice-fig, fig.cap='Here is a nice figure!', out.width='80%', fig.asp=.75, fig.align='center'} +par(mar = c(4, 4, .1, .1)) +plot(pressure, type = 'b', pch = 19) +``` + +Reference a figure by its code chunk label with the `fig:` prefix, e.g., see Figure \@ref(fig:nice-fig). Similarly, you can reference tables generated from `knitr::kable()`, e.g., see Table \@ref(tab:nice-tab). + +```{r nice-tab, tidy=FALSE} +knitr::kable( + head(iris, 20), caption = 'Here is a nice table!', + booktabs = TRUE +) +``` diff --git a/_bookdown.yml b/_bookdown.yml new file mode 100644 index 0000000..7313cb9 --- /dev/null +++ b/_bookdown.yml @@ -0,0 +1,6 @@ +output_dir: "docs" +book_filename: "a_new_instrument_for_microbial_epidemiology" +language: + ui: + chapter_name: "Chapter " +delete_merged_file: true diff --git a/_bookdown_files/a_new_instrument_for_microbial_epidemiology_files/figure-html/nice-fig-1.png b/_bookdown_files/a_new_instrument_for_microbial_epidemiology_files/figure-html/nice-fig-1.png new file mode 100644 index 0000000..04cb1da Binary files /dev/null and b/_bookdown_files/a_new_instrument_for_microbial_epidemiology_files/figure-html/nice-fig-1.png differ diff --git a/_output.yml b/_output.yml new file mode 100644 index 0000000..d2c1a5f --- /dev/null +++ b/_output.yml @@ -0,0 +1,22 @@ +bookdown::gitbook: + css: style.css + config: + toc: + before: | +
The page you requested cannot be found (perhaps it was moved or renamed).
+You may want to try searching to find the page's new location, or use +the table of contents to find the page you are looking for.
+You can label chapter and section titles using {#label}
after them, e.g., we can reference Chapter 1. If you do not manually label them, there will be automatic labels anyway, e.g., Chapter ??.
Figures and tables with captions will be placed in figure
and table
environments, respectively.
par(mar = c(4, 4, .1, .1))
+plot(pressure, type = 'b', pch = 19)
Reference a figure by its code chunk label with the fig:
prefix, e.g., see Figure 1.1. Similarly, you can reference tables generated from knitr::kable()
, e.g., see Table 1.1.
::kable(
+ knitrhead(iris, 20), caption = 'Here is a nice table!',
+ booktabs = TRUE
+ )
Sepal.Length | +Sepal.Width | +Petal.Length | +Petal.Width | +Species | +
---|---|---|---|---|
5.1 | +3.5 | +1.4 | +0.2 | +setosa | +
4.9 | +3.0 | +1.4 | +0.2 | +setosa | +
4.7 | +3.2 | +1.3 | +0.2 | +setosa | +
4.6 | +3.1 | +1.5 | +0.2 | +setosa | +
5.0 | +3.6 | +1.4 | +0.2 | +setosa | +
5.4 | +3.9 | +1.7 | +0.4 | +setosa | +
4.6 | +3.4 | +1.4 | +0.3 | +setosa | +
5.0 | +3.4 | +1.5 | +0.2 | +setosa | +
4.4 | +2.9 | +1.4 | +0.2 | +setosa | +
4.9 | +3.1 | +1.5 | +0.1 | +setosa | +
5.4 | +3.7 | +1.5 | +0.2 | +setosa | +
4.8 | +3.4 | +1.6 | +0.2 | +setosa | +
4.8 | +3.0 | +1.4 | +0.1 | +setosa | +
4.3 | +3.0 | +1.1 | +0.1 | +setosa | +
5.8 | +4.0 | +1.2 | +0.2 | +setosa | +
5.7 | +4.4 | +1.5 | +0.4 | +setosa | +
5.4 | +3.9 | +1.3 | +0.4 | +setosa | +
5.1 | +3.5 | +1.4 | +0.3 | +setosa | +
5.7 | +3.8 | +1.7 | +0.3 | +setosa | +
5.1 | +3.8 | +1.5 | +0.3 | +setosa | +