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admahood · Nov 29, 2022 · 354b4d0 · 354b4d0
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diff --git a/Appendix_S1.pdf b/Appendix_S1.pdf
diff --git a/Appendix_figures.Rmd b/Appendix_figures.Rmd
@@ -14,7 +14,7 @@ output:
 
 # Appendix S1 for: "Fuel connectivity, burn severity, and seedbank survivorship drive ecosystem transformation in a semi-arid shrubland." 
 
-<!-- -Submitted to *Ecology* -->
+-Submitted to *Ecology*
 
 Adam L. Mahood^1,2,3,`*`^, Michael J. Koontz^2^, Jennifer K. Balch^1,2,4^
 

diff --git a/Appendix_figures.pdf b/Appendix_figures.pdf
diff --git a/Appendix_figures.tex b/Appendix_figures.tex
@@ -53,6 +53,20 @@
   \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
 \setcounter{secnumdepth}{-\maxdimen} % remove section numbering
 \newcommand{\beginsupplement} {\renewcommand{\thetable}{S\arabic{table}}      \setcounter{table}{0} \renewcommand{\thefigure}{S\arabic{figure}}}
+\usepackage{booktabs}
+\usepackage{longtable}
+\usepackage{array}
+\usepackage{multirow}
+\usepackage{wrapfig}
+\usepackage{float}
+\usepackage{colortbl}
+\usepackage{pdflscape}
+\usepackage{tabu}
+\usepackage{threeparttable}
+\usepackage{threeparttablex}
+\usepackage[normalem]{ulem}
+\usepackage{makecell}
+\usepackage{xcolor}
 \ifLuaTeX
   \usepackage{selnolig}  % disable illegal ligatures
 \fi
@@ -75,6 +89,8 @@ \section{Appendix S1 for: ``Fuel connectivity, burn severity, and
 seedbank survivorship drive ecosystem transformation in a semi-arid
 shrubland.''}\label{appendix-s1-for-fuel-connectivity-burn-severity-and-seedbank-survivorship-drive-ecosystem-transformation-in-a-semi-arid-shrubland.}}
 
+-Submitted to \emph{Ecology}
+
 Adam L. Mahood\textsuperscript{1,2,3,\texttt{*}}, Michael J.
 Koontz\textsuperscript{2}, Jennifer K. Balch\textsuperscript{1,2,4}
 

diff --git a/R/conceptual_figure.R b/R/conceptual_figure.R
@@ -176,10 +176,13 @@ ph3 <- ggsem(pm_h3,
 
 
 p_final<- ggarrange(ph1, ph2, ph3, ph2a, ph2b, make_legend(), nrow=2, ncol=3)
-
+extrafont::loadfonts()
 ggsave(plot = p_final, 
          filename = "images/conceptual_figure.png", 
-         bg="white", height=11, width=17)
+         bg="white", height=11, width=17, dpi=600)
+ggsave(plot = p_final, 
+       filename = "images/conceptual_figure.jpg", 
+       bg="white", height=11, width=17, dpi=600)
 ggsave(plot = p_final, 
-       filename = "images/conceptual_figure.pdf", 
+       filename = "images/conceptual_figure.png", 
        bg="white", height=11, width=17)
diff --git a/R/ggplot_sem_sb.R b/R/ggplot_sem_sb.R
@@ -154,7 +154,8 @@ ggsem <- function(fit, filename, title="Path Model",layout_df = NA, rename_nodes
     theme(#plot.title = element_text(size = 30),
           legend.position = "none",
           plot.background = element_rect(color="black", fill="transparent")
-          )
+          )+
+    theme_graph(base_family = 'Helvetica')
   if(length(title) ==1)p1 <- p1 + ggtitle(title[1]) else p1 <- p1 + ggtitle(title[1], title[2])
   if(rename_nodes){ p1 <- p1 + geom_node_text(aes(label = new_node_names_df$new_names),
                                              fontface = "bold",

diff --git a/R/make_appendix.R b/R/make_appendix.R
@@ -11,7 +11,7 @@ rmarkdown::render("Appendix_tables.Rmd")
 x=date()
 x=strsplit(x," ")[[1]]
 
-system("pdftk Appendix_figures.pdf Appendix_tables.pdf cat output Appendix_S1_preprint.pdf")
+system("pdftk Appendix_figures.pdf Appendix_tables.pdf cat output Appendix_S1.pdf")
 
 # make full paper
 

diff --git a/data/blm_aim/BLM_Natl_AIM_TerrADat_Hub_2022.csv b/data/blm_aim/BLM_Natl_AIM_TerrADat_Hub_2022.csv
diff --git a/data/blm_aim/BLM_Natl_AIM_TerrADat_Hub_2022.zip b/data/blm_aim/BLM_Natl_AIM_TerrADat_Hub_2022.zip
diff --git a/images/conceptual_figure.jpg b/images/conceptual_figure.jpg
diff --git a/images/conceptual_figure.pdf b/images/conceptual_figure.pdf
diff --git a/images/conceptual_figure.png b/images/conceptual_figure.png
diff --git a/images/burnsev_fig.pdf → images/figure_1_burnsev_fig.pdf b/images/burnsev_fig.pdf → images/figure_1_burnsev_fig.pdf
diff --git a/images/fig2_seed_bank.pdf → images/figure_2_seed_bank.pdf b/images/fig2_seed_bank.pdf → images/figure_2_seed_bank.pdf
diff --git a/images/fig2_seed_bank.png → images/figure_2_seed_bank.png b/images/fig2_seed_bank.png → images/figure_2_seed_bank.png
diff --git a/images/figure_3_conceptual_figure.pdf b/images/figure_3_conceptual_figure.pdf
diff --git a/images/figure_3_conceptual_figure.png b/images/figure_3_conceptual_figure.png
diff --git a/images/big_plot_v2.pdf → images/figure_4_big_plot_v2.pdf b/images/big_plot_v2.pdf → images/figure_4_big_plot_v2.pdf
diff --git a/images/big_plot_v2.png → images/figure_4_big_plot_v2.png b/images/big_plot_v2.png → images/figure_4_big_plot_v2.png
diff --git a/sb_manuscript.Rmd b/sb_manuscript.Rmd
diff --git a/sb_manuscript.pdf b/sb_manuscript.pdf
diff --git a/sb_manuscript.tex b/sb_manuscript.tex
@@ -126,8 +126,11 @@
 
 \normalsize
 
-Open Research Statement: Data and code to recreate the analysis are
-freely available at \url{https://doi.org/10.5281/zenodo.5293996}.
+Open Research Statement: All data and code used in the analysis are
+freely available at \url{https://doi.org/10.5281/zenodo.5293996}. The
+Bureau of Land Management's Assessment, Inventory and Monitoring
+TerrADat dataset is available at version is available at:
+\url{https://blm-gbp-hub-blm-egis.hub.arcgis.com/}
 
 \newpage
 
@@ -423,7 +426,7 @@ \subsection{2. Methods}\label{methods}}
 \emph{2.1 Study Area}
 
 The study was conducted in north-central Nevada the day after a large
-fire (the Hot Pot Fire) was extinguished (Appendix S1, Fig. S1). The Hot
+fire (the Hot Pot Fire) was extinguished (Appendix S1: Fig. S1). The Hot
 Pot Fire burned just over 50,000 hectares in less than a week. The
 pre-fire landcover was predominantly \emph{B. tectorum} and Wyoming big
 sagebrush plant communities. The fire occurred after the early season
@@ -626,7 +629,7 @@ \subsection{3. Results}\label{results}}
 
 We found support for each hypothesized component of the positive
 feedback loop independently and when combined in the path model
-(\(\chi^2\) = 3.17, p = 0.39, Figure 4a, Appendix S1, Tables S4 \& S5).
+(\(\chi^2\) = 3.17, p = 0.39, Figure 4a, Appendix S1: Tables S4 \& S5).
 For H1, TVC had a weak positive relationship with burn severity
 (\(\beta\) = 2.4, p = 0.083, R\(^2\) = 0.27, Figure 4b, Appendix S1:
 Table S2). For our remotely sensed analysis, Green NDVI, NDSVI and their
@@ -731,10 +734,10 @@ \subsection{4. Discussion}\label{discussion}}
 provide enough niche compartmentalization to allow native plants to
 persist in spite of the invasion prior to fire occurrence. Three years
 after fire, almost all of the sites were dominated by introduced
-annuals, and lacked any structural heterogeneity (Appendix S1, Fig.
+annuals, and lacked any structural heterogeneity (Appendix S1: Fig.
 S6c). Thus native plants may have been able to persist via niche
 compartmentalization after the initial invasion, but fire burned away
-most of the seeds (Appendix S1, Fig. S3, S7) and removed all of the
+most of the seeds (Appendix S1: Fig. S3, S7) and removed all of the
 structural benefits, and microclimatic refugia that shrub cover
 provides. In this clean slate post-fire environment, the altered species
 composition of the seedbank and superior post-fire dispersal of \emph{B.
@@ -817,7 +820,7 @@ \subsection{4. Discussion}\label{discussion}}
 this system is controlled by measurable fire properties and ecosystem
 structural components. We found that annual grass cover was not the
 single variable that explained burn severity and fuel connectivity
-(Appendix S1, Fig S5). Rather, it was the contribution of annual grass
+(Appendix S1: Fig S5). Rather, it was the contribution of annual grass
 cover to the total connectivity of the system (Figure 2). The most
 important areas to prioritize for management interventions could
 paradoxically be areas with relatively low levels of annual grass cover
@@ -1682,36 +1685,4 @@ \subsection{Figure Captions}\label{figure-captions}}
 depth, aspect, elevation and pre-fire diversity. Black line is the mean
 prediction, each colored line represents one posterior sample.
 
-\newpage
-
-\begin{figure}
-\centering
-\includegraphics[width=0.75\textwidth,height=\textheight]{images/burnsev_fig.pdf}
-\caption{.}
-\end{figure}
-
-\newpage
-
-\begin{figure}
-\centering
-\includegraphics{images/fig2_seed_bank.pdf}
-\caption{.}
-\end{figure}
-
-\newpage
-
-\begin{figure}
-\centering
-\includegraphics{images/conceptual_figure.png}
-\caption{.}
-\end{figure}
-
-\newpage
-
-\begin{figure}
-\centering
-\includegraphics{images/big_plot_v2.pdf}
-\caption{.}
-\end{figure}
-
 \end{document}
diff --git a/sb_manuscript.zip b/sb_manuscript.zip