accepted version

docs/paper/ED_Table1.tex

+\documentclass{standalone}
+\usepackage{booktabs}
+\usepackage{fontspec}
+\setmainfont{Arial}
+\renewcommand{\arraystretch}{1.4}
+\setlength{\tabcolsep}{6pt}
+\begin{document}
+
+\begin{tabular}{@{\hskip 0.3cm}l@{\hskip 1cm}rrrrr@{\hskip 0.3cm}}
+  \toprule
+set & \# of trees & \# of species & \# of plots/quadrats & \% of angiosperm & \% of evergreen \\
+  \midrule
+Sweden & 202480 &  26 & 22552 & 27.0 & 73.0 \\
+New Zealand & 53775 & 117 & 1415 & 94.0 & 99.1 \\
+US & 1370541 & 492 & 59840 & 63.3 & 37.2 \\
+Canada & 495008 &  75 & 14983 & 34.4 & 64.8 \\
+Australia & 906 & 101 &  63 & 99.9 & 92.4 \\
+France & 184316 & 127 & 17611 & 74.1 & 28.5 \\
+Switzerland & 28286 &  60 & 2597 & 36.4 & 55.2 \\
+Spain & 418805 & 122 & 36462 & 34.7 & 81.6 \\
+Panama & 27089 & 237 & 2033 & 99.8 & 77.7 \\
+French Guiana & 46360 & 712 & 2157 & 100.0 & 83.5 \\
+Japan & 4658 & 139 & 318 & 72.8 & 70.0 \\
+Taiwan & 14701 &  72 & 623 & 92.0 & 75.3 \\
+Puerto Rico & 14011 &  82 & 399 & 100.0 & 99.0 \\
+Central African Republic & 17638 & 204 & 989 & 99.5 & 72.4 \\
+   \bottomrule
+\end{tabular}
+
+\end{document}

docs/paper/ED_Table2.tex

+\documentclass{standalone}
+\usepackage{booktabs}
+\usepackage{fontspec}
+\setmainfont{Arial}
+\renewcommand{\arraystretch}{1.4}
+\setlength{\tabcolsep}{6pt}
+\begin{document}
+
+\begin{tabular}{@{\hskip 0.3cm}l@{\hskip 1cm}rrr@{\hskip 0.3cm}}
+  \toprule
+set & \% cover SLA & \% cover Wood density & \% cover Max height \\
+  \midrule
+Sweden & 99.7 & 99.6 & 97.9 \\
+New Zealand & 99.8 & 99.5 & 99.9 \\
+US & 91.3 & 94.4 & 100.0 \\
+Canada & 99.4 & 99.4 & 99.9 \\
+Australia & 0.0 & 99.2 & 100.0 \\
+France & 99.2 & 98.9 & 99.9 \\
+Switzerland & 96.7 & 95.1 & 99.7 \\
+Spain & 97.3 & 98.9 & 100.0 \\
+Panama & 93.0 & 93.1 & 95.4 \\
+French Guiana & 73.3 & 73.5 & 63.5 \\
+Japan & 99.7 & 99.7 & 100.0 \\
+Taiwan & 99.9 & 99.3 & 95.8 \\
+Puerto Rico & 99.3 & 99.3 & 99.3 \\
+Central African Republic & 40.3 & 47.1 & 0.0 \\
+   \bottomrule
+\end{tabular}
+
+\end{document}

docs/paper/ED_Table3.tex

+\documentclass{standalone}
+\usepackage{booktabs}
+\usepackage{fontspec}
+\setmainfont{Arial}
+\renewcommand{\arraystretch}{1.4}
+\setlength{\tabcolsep}{6pt}
+\begin{document}
+
+\begin{tabular}{@{\hskip 0.3cm}l@{\hskip 1cm}rrr@{\hskip 0.3cm}}
+  \toprule
+ & Wood density & SLA & Max height \\
+  \midrule
+Wood density & 1 & 0.18 & -0.04 \\
+  SLA &  & 1 & 0.24 \\
+  Max height &  &  & 1.00 \\
+   \bottomrule
+\end{tabular}
+
+\end{document}

docs/paper/ED_Table4.tex

+
+\documentclass{standalone}
+\usepackage{booktabs}
+\usepackage{fontspec}
+\setmainfont{Arial}
+\renewcommand{\arraystretch}{1.4}
+\setlength{\tabcolsep}{6pt}
+\begin{document}
+\begin{tabular}{@{\hskip 0.3cm}l@{\hskip 1.3cm}rrr@{\hskip 0.3cm}}
+  \toprule
+ & Wood density & SLA & Maximum height \\
+  \midrule
+$m_0$ & 0.016 (0.127) & -0.087 (0.132) & 0.084 (0.089) \\
+  $\gamma$ & \textbf{0.418 (0.011)} & \textbf{0.401 (0.012)} & \textbf{0.42 (0.01)} \\
+  $m_1$ & \textbf{-0.149 (0.036)} & \textbf{0.119 (0.057)} & 0.063 (0.04) \\
+  $m_2$ & \textbf{0.111 (0.003)} & \textbf{0.093 (0.003)} & \textbf{0.081 (0.002)} \\
+  $m_3$ & \textbf{0.053 (0.002)} & \textbf{0.056 (0.003)} & \textbf{0.048 (0.002)} \\
+  $\alpha_{0 \, \rm intra}$ & \textbf{0.24 (0.037)} & \textbf{0.213 (0.052)} & \textbf{0.194 (0.046)} \\
+  $\alpha_{0 \, \rm inter}$ & \textbf{0.086 (0.022)} & \textbf{0.071 (0.025)} & \textbf{0.094 (0.024)} \\
+  $\alpha_e$ & \textbf{0.034 (0.016)} & \textbf{-0.083 (0.023)} & 0.017 (0.026) \\
+  $\alpha_t$ & \textbf{0.069 (0.021)} & -0.009 (0.033) & \textbf{-0.071 (0.032)} \\
+  $\alpha_d$ & 0 (0.009) & -0.018 (0.015) & \textbf{-0.017 (0.008)} \\
+  $R^2_m$* & 0.1393 & 0.1637 & 0.1429 \\
+  $R^2_c$* & 0.7297 & 0.7593 & 0.7166 \\
+  $\Delta$ AIC & 0 & 0 & 0 \\
+  $\Delta$ AIC no trait & 2469 & 1651 & 2748 \\
+   \bottomrule
+\end{tabular}
+\end{document}

docs/paper/Makefile

@@ -5,9 +5,9 @@ tables: ED_Table1.eps ED_Table2.eps ED_Table3.eps ED_Table4.eps
 paper_all.pdf: paper_ED._NFpdf tables FigDef/*.pdf
 	gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=$@ paper_ED_NF.pdf FigDef/Fig1.pdf FigDef/Fig2.pdf FigDef/Fig3.pdf FigDef/ED_Fig1.pdf ED_Table1.pdf ED_Table2.pdf ED_Table3.pdf FigDef/ED_Fig2.pdf FigDef/ED_Fig3.pdf FigDef/ED_Fig4 .pdf ED_Table4.pdf 
 
-paper_ED.pdf: paper_ED.tex ms.sty references.bib
+paper_ED_FIG.pdf: paper_ED_FIG.tex ms.sty references.bib
 	xelatex $<
-	xelatex paper_ED.tex
+	xelatex paper_ED_FIG.tex
 
 paper_ED_NF.pdf: paper_ED_NF.tex ms.sty references.bib
 	xelatex $<

scripts/analysis/Table_param.R

+## export param estimates plus their CIs
+source("R/analysis/lmer.output-fun.R")
+source("R/analysis/lmer.run.R")
+
+list.all.results <-
+    readRDS('output/list.lmer.out.all.NA.intra.set.rds')
+
+mat.param <- do.call('cbind',
+               lapply(c('Wood.density', 'SLA', 'Max.height'),
+                   extract.param, list.res = list.all.results,
+                   model = 'lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.set.species',
+                   param.vec = c("Tf",
+                                 "sumBn.intra","sumBn.inter",
+                                 "sumTnBn","sumTfBn", "sumTnTfBn.abs"),
+                   data.type = 'intra'))
+
+mat.param[!row.names(mat.param) %in% c("(Intercept)", "logD",
+                                       "Tf", 'MAT', 'MAP', "sumTfBn"),] <-
+    -mat.param[!row.names(mat.param) %in% c("(Intercept)", "logD", "Tf",
+                                            'MAT', 'MAP',
+                                             "sumTfBn"),]
+
+mat.param.sd <- do.call('cbind',
+                lapply(c('Wood.density', 'SLA', 'Max.height'),
+                    extract.param.sd, list.res = list.all.results,
+                    model = 'lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.set.species',
+                    param.vec = c("Tf",
+                                  "sumBn.intra","sumBn.inter",
+                                  "sumTnBn","sumTfBn", "sumTnTfBn.abs"),
+                    data.type = 'intra'))
+colnames(mat.param.sd) <- c('Wood.density', 'SLA', 'Max.height')
+colnames(mat.param) <- c('Wood.density', 'SLA', 'Max.height')
+
+library(reshape2)
+df.param <- data.frame(param=rownames(mat.param), mat.param)
+df.param.sd <- data.frame(param=rownames(mat.param), mat.param.sd)
+
+df.param.melt <- melt(df.param, id.vars = 'param')
+df.param.sd.melt <- melt(df.param.sd, id.vars = 'param')
+names(df.param.melt) <- c('param', 'trait', 'value')
+
+df.param.melt$ci.l <- df.param.melt$value - 1.96 * df.param.sd.melt$value
+df.param.melt$ci.h <- df.param.melt$value + 1.96 * df.param.sd.melt$value
+
+df.param.melt$variable <- 'global'
+## FOR BIOMES
+list.param.b <- lapply(c('Wood.density', 'SLA', 'Max.height'),
+                   extract.param.b, list.res = list.all.results,
+       model = 'lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.set.fixed.biomes.species',
+                   param.vec = c("Tf",
+                                 "sumBn.intra","sumBn.inter",
+                                 "sumTnBn","sumTfBn", "sumTnTfBn.abs"),
+                   data.type = 'intra')
+names(list.param.b) <- c('Wood.density', 'SLA', 'Max.height')
+
+df.mean.b <- do.call("rbind",
+                     lapply(c('Wood.density', 'SLA', 'Max.height'),
+                   function(x,l) data.frame(trait = rep(x, nrow(l[[x]][[2]])),
+                                            l[[x]][[1]]),
+                   list.param.b))
+
+df.sd.b <- do.call("rbind",
+                     lapply(c('Wood.density', 'SLA', 'Max.height'),
+                   function(x,l) data.frame(trait = rep(x, nrow(l[[x]][[2]])),
+                                            l[[x]][[2]]),
+                   list.param.b))
+
+
+df.mean.b$ci.l <- df.mean.b$value - 1.96*df.sd.b$value
+df.mean.b$ci.h <- df.mean.b$value + 1.96*df.sd.b$value
+
+
+######
+df.m <- df.param.melt[ , names(df.mean.b)]
+df.tot <- rbind(df.m, df.mean.b)
+names(df.tot) <- c('param', 'trait', 'value', 'mean', 'ci.l', 'ci.h')
+
+write.csv(df.tot, 'data.param.csv', row.names = FALSE)