Commit 8c493678 authored by kunstler's avatar kunstler
Browse files

bugs fixed in launch two census type

parent c038a867
......@@ -146,24 +146,7 @@ analytical approach, wrote the computer code and performed analyses.
![**Figure 1 Assessing competitive interactions at global scale.** **a,** Precipitation-temperature space occupied by the natural forest communities studied. Biomes follow the definition of Whittaker [@ricklefs_economy_2001]:
1, tundra; 2, taiga; 3, woodland/shrubland; 4, temperate forest; 5,
temperate rainforest; 6, desert; 7, tropical seasonal forest; 8,
tropical rainforest. **b,** Sampled patches vary in the density of
competitors from species $c$ around individuals from a focal species
$f$. For each tree we record the stem diameter $D_i$ across multiple
censuses, and link this with records for the traits of the focal and
competitor species, $t_f$ and $t_c$ respectively. **c,** We use a
neighbourhood modelling framework to model the effects of the traits
and the total basal area ($B_c$) and traits of competitor species on
growth of the focal tree. These effects can be broken down into those
influencing potential growth rate (maximum growth red) and reductions in growth per unit basal area of competitor (blue), $\alpha_{c,f}$. Trait value of focal tree ($t_f$) can influences the tree growth without competition (maximum growth, $m_1$). The trait value of the focal tree can influences its tolerance to competition ($t_f \, \alpha_r$) and the trait values of the competitors can influence their competitive impact ($t_c \, \alpha_i$). Finally, the trait similarity between the focal tree and its competitors can influences competitive interactions ($\alpha_s \, \vert t_c-t_f \vert$) (see extended methods). The parameters $m_1, \alpha_0, \alpha_i, \alpha_r$ and $\alpha_s$ are fitted from data. \label{ilustr}](image/fig1eb.pdf)
\newpage
**OR**
![**Figure 1 Assessing competitive interactions at global scale.** **a,** Precipitation-temperature space occupied by the natural forest communities studied. Biomes follow the definition of Whittaker [@ricklefs_economy_2001]:
![**Assessing competitive interactions at global scale.** **a,** Precipitation-temperature space occupied by the natural forest communities studied (NFI data : national forest Inventories, LPP data : large permanent plots) . Biomes follow the definition of Whittaker [@ricklefs_economy_2001]:
1, tundra; 2, taiga; 3, woodland/shrubland; 4, temperate forest; 5,
temperate rainforest; 6, desert; 7, tropical seasonal forest; 8,
tropical rainforest. **b,** Sampled patches vary in the density of
......@@ -174,13 +157,9 @@ analytical approach, wrote the computer code and performed analyses.
neighbourhood modelling framework to model the effects of the traits
and size of the focal tree, and the total basal area ($B_c$) and
traits of competitor species on growth of the focal tree. These
effects can be broken down into those influencing potential growth
rate (maximum growth red) and reductions in growth per unit basal area of competitor (blue), $\alpha_{c,f}$. Trait value of focal tree ($t_f$) can influences the tree growth without competition (maximum growth, $m_1$). The trait value of the focal tree can influences its tolerance to competition ($t_f \, \alpha_r$) and the trait values of the competitors can influence their competitive impact ($t_c \, \alpha_i$). Finally, the trait similarity between the focal tree and its competitors can influences competitive interactions ($\alpha_s \, \vert t_c-t_f \vert$) (see extended methods). The parameters $m_0, m_1, \gamma, \alpha_0, \alpha_i, \alpha_r$ and $\alpha_s$ are fitted from data. \label{ilustr2}](image/fig1e.pdf)
\newpage
effects can be broken down into those influencing maximum growth
rate (red) and those influencing reduction in growth per unit basal area of competitor (blue), $\alpha_{c,f}$. Trait value of focal tree ($t_f$) can influences the tree growth without competition (maximum growth, $m_1$). The trait value of the focal tree can influences its tolerance to competition ($t_f \, \alpha_r$) and the trait values of the competitors can influence their competitive impact ($t_c \, \alpha_i$). Finally, the trait similarity between the focal tree and its competitors can influences competitive interactions ($\alpha_s \, \vert t_c-t_f \vert$) (see extended methods). The parameters $m_1, \gamma, \alpha_0, \alpha_i, \alpha_r$ and $\alpha_s$ are fitted from data. \label{ilustr2}](image/fig1e.pdf)
**COMMENT: NOT SURE THE BLACK ELLIPSE ARE THE BEST WAY TO REPRESENT THE DATA. May be have different colors per ellipse per data set?? such as the one in the follwing figure**
![**Data set in colors](../../figs/biomesnumbercol.pdf)
\newpage
......
......@@ -20,7 +20,7 @@ fi
samplesize=$1
# "'Seed.mass'" "'Leaf.N'"
# for trait in "'SLA'" "'Wood.density'" "'Max.height'" ; do
for trait in "'SLA'" "'Wood.density'" "'Max.height'" ; do
# ALL data
......@@ -50,8 +50,8 @@ done
# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.Multi[1]), run.lmer,'Multi', data.type ='Multi');print('done')\"" > Rscript_temp/Multi1.sh
# qsub Rscript_temp/Multi1.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "Multi1" -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(c(model.files.lmer.Tf.Multi[2]), run.lmer,'Multi', data.type ='Multi');print('done')\"" > Rscript_temp/Multi2.sh
qsub Rscript_temp/Multi2.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "Multi2" -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(c(model.files.lmer.Tf.Multi[2]), run.lmer,'Multi', data.type ='Multi');print('done')\"" > Rscript_temp/Multi2.sh
# qsub Rscript_temp/Multi2.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "Multi2" -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(c(model.files.lmer.Tf.Multi[3]), run.lmer,'Multi', data.type ='Multi');print('done')\"" > Rscript_temp/Multi3.sh
# qsub Rscript_temp/Multi3.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "Multi3" -q opt32G -j oe
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment