From 09c1a8ab29a28029bce5290b00a8a1aabc219a96 Mon Sep 17 00:00:00 2001
From: Nick Golding <goldingn35@gmail.com>
Date: Tue, 31 Jan 2017 19:07:38 +1100
Subject: [PATCH 1/3] add link to user panel to cover letter
---
zoon_app_cover.Rmd | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/zoon_app_cover.Rmd b/zoon_app_cover.Rmd
index 45d8168..ffec0ea 100644
--- a/zoon_app_cover.Rmd
+++ b/zoon_app_cover.Rmd
@@ -6,7 +6,7 @@ The Zoon Project was set up to improve reproducibility in the ecological sub dis
Like the many other SDM R packages, zoon enables users to fit of SDMs with a variety of methods. However the aim and novel contribution of zoon is quite different - to facilitate the SDM community in sharing methods (modules) and experiments (workflows) as standardised, repeatable and reusable artefacts. This aligns with the journal's recent efforts to improve archiving of analytical code and has the same end goal - improving the ecological community's ability to build on each others' work. We therefore believe that our manuscript would be well suited for publication as an Application paper.
-Note that two of the authors are MEE associate editors and that both Bob O'Hara and Rich FitzJohn have been involved in the development of Zoon, so one of the three remaining Applications AEs would be best placed to handle the manuscript.
+Note that two of the authors are MEE associate editors and that both Bob O'Hara and Rich FitzJohn have been involved in the development of Zoon, so one of the three remaining Applications AEs would be best placed to handle the manuscript. A list of researchers who have been involved in the development of zoon, and may therefore not be able to review the manuscript, is available at: https://zoonproject.wordpress.com/user-panel
Yours Sincerely,
Nick Golding, on behalf of the authors
From 9fca4813e4212f46a7ad8a36e6175cb379e71a21 Mon Sep 17 00:00:00 2001
From: Nick Golding <goldingn35@gmail.com>
Date: Wed, 1 Feb 2017 10:05:29 +1100
Subject: [PATCH 2/3] remove extraneous newpage commands
---
ms.Rmd | 2 --
1 file changed, 2 deletions(-)
diff --git a/ms.Rmd b/ms.Rmd
index 744106c..f1626f2 100644
--- a/ms.Rmd
+++ b/ms.Rmd
@@ -329,13 +329,11 @@ mtext(text = 'C',
adj = 0)
```
-\newpage
\blandscape
```{r feng_papes_plots, cache = FALSE, echo = FALSE, out.width = "450px", fig.cap = "Outputs of the workflow objects `FengPapes' and `FengPapesUpdate'. A) Map of the MaxEnt predicted distribution, with a 5\\% omission rate threshold, by the `PrintMap' module in the workflow `FengPapes' which encodes the core of a published analysis. B) A response curve produced by the `ResponseCurve' module for the first covariate, bio1 in the workflow `FengPapesUpdate', which modifies the original analysis workflow. C) A screenshot of the interactive map produced by the `InteractiveMap' modules in the workflow `FengPapesUpdate', displaying raw occurrence data and predicted distribution over a global map, allowing users to interactively explore their results. White areas are masked due to being in the MESS mask. Any SDM analysis distributed as a zoon workflow can be easily be explored and scrutinized by modifying its output modules using the function `ChangeWorkflow'."}
knitr::include_graphics("figs/combinefengupdate-1.png")
```
\elandscape
-\newpage
#### Example 2. Building a spatial thinning module
From a1ce9f2b399fed701bedffd6ade6c2a592c4d8f7 Mon Sep 17 00:00:00 2001
From: Nick Golding <goldingn35@gmail.com>
Date: Wed, 1 Feb 2017 10:05:40 +1100
Subject: [PATCH 3/3] add line numbers and double spacing
---
latex_preamble.tex | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/latex_preamble.tex b/latex_preamble.tex
index 94b3813..c1fe181 100644
--- a/latex_preamble.tex
+++ b/latex_preamble.tex
@@ -14,3 +14,9 @@
\usepackage{lscape}
\newcommand{\blandscape}{\begin{landscape}}
\newcommand{\elandscape}{\end{landscape}}
+
+\usepackage{lineno}
+\linenumbers
+
+\usepackage{setspace}
+\doublespacing