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Petr,

Thanks for the template for manuscript writing. I found it very useful. Would you be able to help with one issue that I found? I have issue to control figure arrangement location within a document and margin.

The figures that I generated from ggplot2 seems to be arranged not directly under the section of discussion. Is there a way to place it right next to the discussion? The caption number is automated. However, how to keep same number within paragraph for proper citation?

Some figures I used grid package to embed into the document. However, the margin from this method is very wide in PDF file. Is there a way to control fig margin?
img <- readPNG("fig/reaction.png")
grid.raster(img)

Both questions are probably due to my unfamiliarity of LaTex format. Hope you could point to right direction. Thanks,

Rich

I use Chrome.

I see that on html file (yours, posted on your blog) :

Equations
The deterministic part of the model is defined by this in-line equation as [Math Processing Error], and the stochastic part by the centered equation:

[Math Processing Error]

Please add a note in the manuscript_template.Rmd on how to use in-text cross-ref for figures @

https://github.com/petrkeil/Blog/blob/master/2015_03_12_R_ms_template/manuscript_template.Rmd