add skeleton of the project

inst/rmarkdown/templates/beamer/skeleton/skeleton.Rmd

@@ -0,0 +1,100 @@
+---
+title: Template for using R 'xaringan' package in a 'rosr' project
+output: beamer_presentation
+always_allow_html: yes
+---
+
+```{r md-hint, include=FALSE}
+# Markdown Syntax
+
+# - *italic*, **bold**, `code`, ~subscript~, ^superscript^, > quote, ^[footnote]
+# - $inline equation$, $$display equation$$
+# - \begin{equation} (\#eq:eq-label)\end(equation), \@ref(eq:eq-label)
+# - [@bib-entry1; @bib-entry2]
+# - [](hyperlink)
+# - ![](image link), knitr::include_graphics(), \@ref(fig:fig1)
+# - knitr::kable(), \@ref(tab:tab1)
+```
+
+
+```{r, include=FALSE}
+options(htmltools.dir.version = FALSE)
+```
+
+# Introduction
+
+This template comes from the R 'xaringan' package and modified by Peng Zhao. It intends to show how to cross refer other files in a 'rosr' project, rather than to show how to use the original template.
+
+---
+
+# Methods
+
+## Set up
+
+Firstly, we switch off the codes and message display in a manuscript, and set the working directory to the rosr project.
+
+```{r setup}
+oldwd <- getwd()
+knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE) 
+knitr::opts_knit$set(root.dir = dirname(dirname(oldwd)))
+```
+
+---
+
+## Load data
+
+Now we can use the relative path. Let's sync the bib file and run an R script.
+
+```{r load, results='hide'}
+source('R/rosr.R')
+```
+
+---
+
+## Numbers
+
+As we just ran the `source()` command, we can use the results from the `R/rosr.R`. For example, the mean temperature is `r temperature` degree.
+
+---
+
+## Tables
+
+We could insert a table.
+
+
+```{r}
+aq$Month <- as.factor(aq$Month)
+DT::datatable(
+  aq, 
+  fillContainer = FALSE, options = list(pageLength = 4)
+)
+```
+
+---
+
+## Figures
+
+Plot the data in a diagram.
+
+```{r fig-lab, fig.cap='Air quality data.'}
+plot(aq)
+```
+
+---
+
+We could insert an image.
+
+```{r img-lab, fig.cap='Insert an image.'}
+knitr::include_graphics(paste0(getwd(), '/image/rosr_R.png'))
+```
+
+---
+
+## Equations
+
+Use the `rosr::eq()` function to insert an equation. See Eq. \@ref(eq:sd)
+
+```{r, results='asis'}
+eqs <- 'equation/rosr-eq.Rmd'
+rosr::eq(eqs, label = 'sd')
+```

inst/rmarkdown/templates/beamer/template.yaml

@@ -0,0 +1,4 @@
+name: beamer Presentation
+description: >
+  Create a beamer
+create_dir: false

inst/rmarkdown/templates/powerpoint/skeleton/skeleton.Rmd

@@ -0,0 +1,100 @@
+---
+title: Template for using R 'xaringan' package in a 'rosr' project
+output: powerpoint_presentation
+always_allow_html: yes
+---
+
+```{r md-hint, include=FALSE}
+# Markdown Syntax
+
+# - *italic*, **bold**, `code`, ~subscript~, ^superscript^, > quote, ^[footnote]
+# - $inline equation$, $$display equation$$
+# - \begin{equation} (\#eq:eq-label)\end(equation), \@ref(eq:eq-label)
+# - [@bib-entry1; @bib-entry2]
+# - [](hyperlink)
+# - ![](image link), knitr::include_graphics(), \@ref(fig:fig1)
+# - knitr::kable(), \@ref(tab:tab1)
+```
+
+
+```{r, include=FALSE}
+options(htmltools.dir.version = FALSE)
+```
+
+# Introduction
+
+This template comes from the R 'xaringan' package and modified by Peng Zhao. It intends to show how to cross refer other files in a 'rosr' project, rather than to show how to use the original template.
+
+---
+
+# Methods
+
+## Set up
+
+Firstly, we switch off the codes and message display in a manuscript, and set the working directory to the rosr project.
+
+```{r setup}
+oldwd <- getwd()
+knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE) 
+knitr::opts_knit$set(root.dir = dirname(dirname(oldwd)))
+```
+
+---
+
+## Load data
+
+Now we can use the relative path. Let's sync the bib file and run an R script.
+
+```{r load, results='hide'}
+source('R/rosr.R')
+```
+
+---
+
+## Numbers
+
+As we just ran the `source()` command, we can use the results from the `R/rosr.R`. For example, the mean temperature is `r temperature` degree.
+
+---
+
+## Tables
+
+We could insert a table.
+
+
+```{r}
+aq$Month <- as.factor(aq$Month)
+DT::datatable(
+  aq, 
+  fillContainer = FALSE, options = list(pageLength = 4)
+)
+```
+
+---
+
+## Figures
+
+Plot the data in a diagram.
+
+```{r fig-lab, fig.cap='Air quality data.'}
+plot(aq)
+```
+
+---
+
+We could insert an image.
+
+```{r img-lab, fig.cap='Insert an image.'}
+knitr::include_graphics(paste0(getwd(), '/image/rosr_R.png'))
+```
+
+---
+
+## Equations
+
+Use the `rosr::eq()` function to insert an equation. See Eq. \@ref(eq:sd)
+
+```{r, results='asis'}
+eqs <- 'equation/rosr-eq.Rmd'
+rosr::eq(eqs, label = 'sd')
+```

inst/rmarkdown/templates/powerpoint/template.yaml

@@ -0,0 +1,4 @@
+name: Powerpoint Presentation
+description: >
+  Create a powerpoint presentation
+create_dir: false

inst/rstudio/addins.dcf

@@ -0,0 +1,4 @@
+Name: Create a rosr project
+Description: Create a interconnected R Markdown project for reproducible research
+Binding: create_ui
+Interactive: true

inst/skeleton/book/body.Rmd → inst/skeleton/book/bookdownplus/demo/body.Rmd

@@ -10,10 +10,10 @@ This template comes from the R 'bookdownplus' package and modified by Peng Zhao.
 
 Firstly, we switch off the codes and message display in a manuscript, and set the working directory to the rosr project.
 
-```{r setup}
+```{r set}
 oldwd <- getwd()
 knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE) 
-knitr::opts_knit$set(root.dir = dirname(oldwd))
+knitr::opts_knit$set(root.dir = dirname(dirname(oldwd)))
 ```
 
 ## Load data
@@ -49,7 +49,7 @@ knitr::kable(head(aq), booktabs = TRUE, caption = 'Air quality data.')
 
 Plot the data in a diagram as shown in Fig. \@ref(fig:fig-lab).
 
-```{r fig-lab, fig.cap='Air quality data.', out.width='100%'}
+```{r fig-lab, fig.cap='Air quality data.'}
 plot(aq)
 ```
 

inst/skeleton/poster/drposter/drposter.Rmd → inst/skeleton/poster/drposter/drposter/drposter.Rmd

@@ -24,7 +24,7 @@ output:
 
 ## Introduction
 
-This template comes from the R 'drposter' package and modified by Peng Zhao. It intends to show how to cross refer other files in a 'rosr' project, rather than to show how to use the 'drposter' template.
+This template comes from the R 'drposter' package and modified by Peng Zhao. It intends to show how to cross refer other files in a 'rosr' project, rather than to show how to use the original template.
 
 ## Set up
 

inst/skeleton/slide/xaringan/xaringan.Rmd → inst/skeleton/slide/xaringan/xaringan/xaringan.Rmd

@@ -31,7 +31,7 @@ options(htmltools.dir.version = FALSE)
 
 # Introduction
 
-This template comes from the R 'xaringan' package and modified by Peng Zhao. It intends to show how to cross refer other files in a 'rosr' project, rather than to show how to use the 'xaringan' template.
+This template comes from the R 'xaringan' package and modified by Peng Zhao. It intends to show how to cross refer other files in a 'rosr' project, rather than to show how to use the original template.
 
 ---
 

inst/skeleton/website/content/post/2019-01-15-rosr.Rmd → inst/skeleton/website/yihui_hugo-lithium/content/post/2019-01-15-rosr.Rmd

@@ -33,7 +33,7 @@ Firstly, we set the codes and message display, and set the working directory to
 ```{r setup}
 oldwd <- getwd()
 knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE) 
-knitr::opts_knit$set(root.dir = dirname(dirname(dirname(oldwd))))
+knitr::opts_knit$set(root.dir = dirname(dirname(dirname(dirname(oldwd)))))
 ```
 
 ## Load data
@@ -80,7 +80,7 @@ plot(aq)
 We could insert an image like Fig \@ref(fig:img-lab).
 
 ```{r}
-file.copy(dir('image/', full.names = TRUE), 'website/static/image/', recursive = TRUE, overwrite = TRUE)
+file.copy(dir('image/', full.names = TRUE), file.path(dirname(dirname(oldwd)), 'static', 'image'), recursive = TRUE, overwrite = TRUE)
 ```
 
 ```{r img-lab, fig.cap='Insert an image.'}