intra ecocode

R/analysis/lmer.run.R

@@ -54,6 +54,9 @@ model.files.lmer.Tf.intra.1 <- file.path(path.model,
 model.files.lmer.Tf.intra.2 <- file.path(path.model,
       c("model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.set.species.R",
         "model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.set.fixed.biomes.species.R"))
+model.files.lmer.Tf.intra.3 <- file.path(path.model,
+      c("model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.ecocode.species.R",
+        "model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.ecocode.fixed.biomes.species.R"))
 
 
 

R/analysis/model.lmer/model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.ecocode.fixed.biomes.species.R

+load.model <- function () {
+    list(name="lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.ecocode.fixed.biomes.species",
+         var.BLUP = 'ecocode.id',
+         lmer.formula.tree.id=formula("logG~1+biomes.id+MAT+MAP+Tf+Tf:biomes.id+logD+sumBn.inter+sumBn.inter:biomes.id+sumBn.intra+sumBn.intra:biomes.id+sumTfBn+sumTfBn:biomes.id+sumTnBn+sumTnBn:biomes.id+sumTnTfBn.abs+sumTnTfBn.abs:biomes.id +(1+logD+sumBn.inter+sumBn.intra||species.id)+(1|plot.id)+(1+Tf+sumBn.inter+sumBn.intra+sumTfBn+sumTnBn+sumTnTfBn.abs||ecocode.id)"))
+}
+

R/analysis/model.lmer/model.lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.ecocode.species.R

+load.model <- function () {
+    list(name="lmer.LOGLIN.ER.AD.Tf.MAT.MAP.intra.r.ecocode.species",
+         var.BLUP = 'ecocode.id',
+         lmer.formula.tree.id=formula("logG~1+Tf+logD+sumBn.inter+MAT+MAP+sumBn.intra+sumTfBn+sumTnBn+sumTnTfBn.abs +(1+logD+sumBn.inter+sumBn.intra||species.id)+(1|plot.id)+(1+Tf+sumBn.inter+sumBn.intra+sumTfBn+sumTnBn+sumTnTfBn.abs||ecocode.id)"))
+}
+
+
+

docs/paper/extended_data.R

@@ -100,7 +100,7 @@ pandoc.table(cor.mat,
 ## ![Variation of the four parameters linking the three studied traits with maximum growth and competition - maximum growth ($t_f \, m_1$), tolerance to competition ($t_f \, \alpha_t$), competitive effect ($t_c \, \alpha_e$) and limiting similarity ($|t_f - t_c| \, \alpha_l$ ($t_c$ was fixed at the lowest value and $t_f$ varying from quantile 5 to 95\%). The shaded area represents the 95% confidence interval of the prediction (including uncertainty associated with $\alpha_0$ or $m_0$).](../../figs/figres4b.pdf)
 
 
-## ![**Global trait effects and trait-independent effects on maximum growth and competition and their variation among biomes.** Standardized regression coefficients for growth models, fitted separately for each trait (points: mean estimates and lines: 95\% confidence intervals). Black points and lines represent global estimates and coloured points and lines represent the biome level estimates. The parameter estimates represent: effect of focal tree's trait value on maximum growth ($m_1$), the competitive effect independent of traits for intra- ($\\alpha_{0, intra}$) and inter-specific interaction ($\\alpha_{0, inter}$), the effect of competitor trait values on their competitive effect ($\\alpha_e$) (positive values indicate that higher trait values lead to a stronger reduction in growth of the focal tree), the effect of the focal tree's trait value on its tolerance of competition($\\alpha_t$) (positive values indicate that greater trait values result in greater tolerance of competition), and the effect on competition of trait similarity between the focal tree and its competitors ($\\alpha_s$) (negative values indicate that higher trait similarity leads to a stronger reduction of the growth of the focal tree). Tropical rainforest and tropical seasonal forest were merged together as tropical forest, tundra was merged with taiga, and desert was not included as too few plots were available (see Fig 1a. for biomes definitions).](../../figs/figres12_TP_intra.pdf)
+## ![**TODO**. BLABLA.](../../figs/rho_set_TP_intra.pdf)
 
 
 ##+ ComputeTable_Effectsize, echo = FALSE, results = 'hide', message=FALSE
@@ -109,7 +109,7 @@ list.all.results <-
 
 list.all.results.intra <-
     readRDS('output/list.lmer.out.all.NA.intra.set.rds')
-
+#TODO UPDATE FOR INTRA
 
 mat.param <- do.call('cbind', lapply(c('Wood.density', 'SLA', 'Max.height'),
                                      extract.param, list.res = list.all.results,

launch.cluster/launch_all_lmer.bash

@@ -54,13 +54,13 @@ samplesize=$1
 #   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[2], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/allTP2${trait}.sh
 # 	qsub Rscript_temp/allTP2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.TP2${trait}" -q opt32G -j oe
 
-# # INTRA 0
-  	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.0[1], run.lmer,$trait, data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA0${trait}.sh
-	qsub Rscript_temp/allINTRA0${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA0${trait}" -q opt32G -j oe
+# # # INTRA 0
+#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.0[1], run.lmer,$trait, data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA0${trait}.sh
+# 	qsub Rscript_temp/allINTRA0${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA0${trait}" -q opt32G -j oe
 
 
-  	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.0[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA02${trait}.sh
-	qsub Rscript_temp/allINTRA02${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA02${trait}" -q opt32G -j oe
+#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.0[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA02${trait}.sh
+# 	qsub Rscript_temp/allINTRA02${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA02${trait}" -q opt32G -j oe
 
 # # # INTRA 1
 #   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.1[1], run.lmer,$trait, data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA${trait}.sh
@@ -78,6 +78,14 @@ samplesize=$1
 #   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.2[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'intra');print('done')\"" > Rscript_temp/allINTRAB2${trait}.sh
 # 	qsub Rscript_temp/allINTRAB2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRAB2${trait}" -q opt32G -j oe
 
+# # INTRA 3
+  	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.3[1], run.lmer,$trait, data.type = 'intra');print('done')\"" > Rscript_temp/allINTRAE${trait}.sh
+	qsub Rscript_temp/allINTRAE${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRAE${trait}" -q opt32G -j oe
+
+
+  	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.3[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'intra');print('done')\"" > Rscript_temp/allINTRAE2${trait}.sh
+	qsub Rscript_temp/allINTRAE2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRAE2${trait}" -q opt32G -j oe
+
 
 # # # # # ecocode 3
 #   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.2[1], run.lmer,$trait, data.type = 'simple');print('done')\"" > Rscript_temp/allECO${trait}.sh