custom3.css

Head:     rmd custom css added
Merge:    origin/rmd Working on Rmd vignette; almost there?
Tag:      2.3.12 (8)

Untracked files (6)
OncoSimulR/vignettes/OncoSimulR.md
OncoSimulR/vignettes/bioconductor.css
OncoSimulR/vignettes/bioconductor2.css
OncoSimulR/vignettes/custom2.css
OncoSimulR/vignettes/o1.Rmd
OncoSimulR/vignettes/or.html

Unstaged changes (2)
modified   OncoSimulR/vignettes/OncoSimulR.Rmd
@@ -13,16 +13,16 @@ author: "\\
 ##    <rdiaz02@gmail.com>, <http://ligarto.org/rdiaz>
 ## date: "`r Sys.Date()`"
 date: "`r paste0(Sys.Date(),'. ', pkg_ver('OncoSimulR'), '. Revision: ', system('git rev-parse --short HEAD', intern = TRUE))`"
-## With BiocStyle no floating toc as I want
-## But with default style, no package version
+
+## Bioc html_document no refs
+## Bioc html_document2 too wide margins
+## Simplest is to use bookdown and add BioC CSS
 output: 
-  BiocStyle::html_document2:
-    toc: true	
-##  BiocStyle::pdf_document:
-##    toc: true	
-##  html_document:
-##    toc: true 
-##    toc_float: true
+##  BiocStyle::html_document2:
+  bookdown::html_document2:  
+    toc: true
+    toc_float: true
+    css: custom2.css
 ## package: "`r paste0(pkg_ver('OncoSimulR'), '. Rev.: ', system('git rev-parse --short HEAD', intern = TRUE))`"
 bibliography: OncoSimulR.bib
 link-citations: true
@@ -171,7 +171,7 @@ different fitness specifications is also unique.
 
 
 
-## Steps in using OncoSimulR}
+## Steps in using OncoSimulR
 
 
 Using this package will often involve the following steps:
@@ -524,7 +524,7 @@ models) and also had a larger number of clones returned (5 to 16 vs. 1 to
 
 
 
-## Citing OncoSimulR and other documentation} {#citing}
+## Citing OncoSimulR and other documentation {#citing}
 
 In R, you can do
 ```{r}
@@ -532,6 +532,8 @@ citation("OncoSimulR")
 ``` 
 which will tell you how to cite the package.
 
+FIXME!!!
+
 % You can also take a look at the poster (presented at ECCB 2016), <zz>
 % and included under docs.
 
@@ -1012,7 +1014,7 @@ small positive ones (or for mildly deleterious effects, small negative
 numbers), while the values of `s` are much larger positive numbers.
 
 
-### Extended posets}
+### Extended posets
 
 In version 1 of this package we used posets in the sense of
 @Beerenwinkel2007; @Gerstung2009, as explained in section \@ref(poset)
@@ -5378,7 +5380,7 @@ that function is optimized for other uses. This might change in the future.
 
 
 
-# Generating fitness landscapes} {#gener-fit-land}
+# Generating fitness landscapes {#gener-fit-land}
 
 
 It is possible to generate mappings of genotype to fitness using the
@@ -5732,14 +5734,14 @@ computing fitness, however, should deal with all of this just fine.
 
 
 
-# Session info and packages used}
+# Session info and packages used
 
 This is the information about the version of R and packages used:
 ```{r}
 sessionInfo()
 ``` 
 
-# Funding}
+# Funding
 
 Supported by BFU2015-67302-R (MINECO/FEDER, EU).
 
modified   OncoSimulR/vignettes/custom.css
@@ -11,3 +11,11 @@ table, td, th {
 tbody tr:nth-child(odd) td {
   background-color: #F8F8F8;
 }
+
+@page :left {
+    margin: 2mm 2mm 2mm 2mm;
+}
+
+@page :right {
+    margin: 2mm 2mm 2mm 2mm;
+}

Unmerged into origin/rmd (1)
911c5dc rmd custom css added