This template and example include:

• Common order for scientific papers (i.e., main text, references, tables and figures).
• Page breaks for both word and pdf documents
• Table and figure captions for main text and supporting information.

r page_break() will add page break for word and pdf documents. r page_break("Figures") will add page break and a new page starts with section "Figures".

References:

• https://gist.github.com/benmarwick/f3e0cafe668f3d6ff6e5

• https://daijiang.name/en/2017/04/05/writing-academic-papers-with-rmarkdown/

• http://svmiller.com/blog/2016/02/svm-r-markdown-manuscript/

• https://github.com/svmiller/svm-r-markdown-templates

# rendering to PDF
render("main_text.rmd", "bookdown::pdf_document2")

# rendering to docx
render("main_text.rmd", "bookdown::word_document2")

library(methods)
library(knitr)
library(kableExtra)
library(png)
library(grid)
library(pander)
source("rmd_func.r")

Title: Title of your manuscript

$$ $$

First Author^1,2^ Second Author^2^, and Third Author^3^

$$ $$

^1^ First Affiliation

^2^ Second Affiliation

^3^ Third Affiliation

r page_break("Abstract")

Your abstract.

Your introduction [@Wright2004a]. Some more text [@Kraft2008]. More text [@Hubbell2001].

Your Material and Methods. We fitted XXXX:

\begin{equation} N_{ij} \sim NB(\mu_{ij}, \phi) (#eq:NB) \end{equation}

where $\mu_{ij}$ is xxxxxx, xxxxxxxx,

\begin{equation} \mu_{ij} \times v_i = exp(\Sigma \beta_{jk} z_{ik}) (#eq:mu) \end{equation}

where $\beta_{jk}$ is xxxxxx. Prior for $\phi$ in Eq. @ref(eq:NB) was specified as xxxxx.

We found XXX (Fig. @ref(fig:scatplt) and Table @ref(tab:tblm)). We also found xxx (Fig. @ref(fig:boxplt)) yay!

Some texts.

r page_break()

Table: (#tab:tblm). Summary of the regression model.

fit <- lm(mpg ~ wt * cyl, data = mtcars)
tb1 <- pander(fit, caption = "")
tb1

r page_break()

tb2 <- head(mtcars)
kable(tb2, caption = "Some datasets.")

r page_break("Figures")

img <- readPNG("scat.png", native = TRUE, info = TRUE)
grid.raster(img, interpolate=F)

r page_break()

img <- readPNG("boxp.png", native = TRUE, info = TRUE)
grid.raster(img, interpolate=F)

knitr::kable(mtcars)

r page_break()

grid.raster(img, interpolate=F)