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Commit 0bc2be36 authored by Francesco Sabatini's avatar Francesco Sabatini
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00_Mesobromion_DataPreparation.R
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...@@ -412,19 +412,22 @@ traits.sign <- traits %>% ...@@ -412,19 +412,22 @@ traits.sign <- traits %>%
dplyr::select(species0, any_of(traits.sign.alone)) dplyr::select(species0, any_of(traits.sign.alone))
write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.cov.sign.txt", delim="\t") write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.cov.sign.txt", delim="\t")
### COV - NONAs - all species with at least 1 NAs in traits excluded BEFORE The analysis ### COV - NONAs - NEW DATASET
" Trait.comb Coef.obs Coef.perm q025 q975 greater.than.perm n sign_plus sign_minus ntraits trait.name "# A tibble: 49 x 11
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <lgl> <lgl> <int> <fct> Trait.comb Coef.obs Coef.perm q025 q975 greater.than.perm n sign_plus sign_minus ntraits trait.name
1 36 0.316 0.154 0.290 0.370 0.997 999 TRUE FALSE 1 PlantHeight <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <lgl> <lgl> <int> <fct>
2 50 0.286 0.154 0.257 0.339 0.977 999 TRUE FALSE 1 BL_ANAT 1 46 0.317 0.106 0.289 0.365 0.997 999 TRUE FALSE 1 Leaf_Scleroph
3 30 0.259 0.114 0.232 0.308 0.974 999 TRUE FALSE 1 BL_DAU 2 33 0.267 0.168 0.244 0.317 0.990 999 TRUE FALSE 1 Height
4 2 0.256 0.228 0.222 0.303 0.992 999 TRUE FALSE 1 LEB_F_Nanophanerophyt 3 29 0.251 0.206 0.231 0.300 0.976 999 TRUE FALSE 1 SLA
5 20 0.253 0.0703 0.205 0.324 0.992 999 TRUE FALSE 1 V_VER_Fragmentation 4 2 0.250 0.111 0.218 0.296 0.988 999 TRUE FALSE 1 GF_Nanophan
6 49 0.252 0.116 0.226 0.303 0.967 999 TRUE FALSE 1 STRAT_T 5 27 0.237 0.167 0.213 0.284 0.975 999 TRUE FALSE 1 FP_Dur
7 32 0.251 0.127 0.226 0.303 0.968 999 TRUE FALSE 1 SLA 6 30 0.212 0.125 0.192 0.260 0.953 999 TRUE FALSE 1 LeafCdrymass
8 35 0.241 0.128 0.217 0.289 0.970 999 TRUE FALSE 1 LeafP " 7 5 0.210 0.0489 0.176 0.267 0.977 999 TRUE FALSE 1 GF_Hemiphan
8 17 0.207 0.123 0.166 0.273 0.965 999 TRUE FALSE 1 VP_Fragm
### COV - NONA2 - modified Matrix.x to deal with NAs INSIDE the analysis 9 32 0.214 0.0827 0.195 0.262 0.939 999 FALSE FALSE 1 LeafP
10 31 0.195 0.133 0.176 0.241 0.919 999 FALSE FALSE 1 LeafN"
### COV - NONAs - old dataset - First selection of plots
"# A tibble: 48 x 11 "# A tibble: 48 x 11
Trait.comb Coef.obs Coef.perm q025 q975 greater.than.perm n sign_plus sign_minus ntraits trait.name Trait.comb Coef.obs Coef.perm q025 q975 greater.than.perm n sign_plus sign_minus ntraits trait.name
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <lgl> <lgl> <int> <fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <lgl> <lgl> <int> <fct>
...@@ -437,13 +440,6 @@ write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.cov.sign.txt", ...@@ -437,13 +440,6 @@ write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.cov.sign.txt",
7 30 0.241 0.207 0.213 0.286 0.951 999 TRUE FALSE 1 LeafP 7 30 0.241 0.207 0.213 0.286 0.951 999 TRUE FALSE 1 LeafP
8 44 0.238 0.187 0.213 0.285 0.971 999 TRUE FALSE 1 STRAT_T " 8 44 0.238 0.187 0.213 0.285 0.971 999 TRUE FALSE 1 STRAT_T "
### COV - without deleting NAs
"# A tibble: 53 x 11
Trait.comb Coef.obs Coef.perm q025 q975 greater.than.perm n sign_plus sign_minus ntraits trait.name
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <lgl> <lgl> <int> <fct>
1 36 0.304 0.117 0.280 0.356 0.995 999 TRUE FALSE 1 PlantHeight
2 32 0.247 0.127 0.221 0.299 0.976 999 TRUE FALSE 1 SLA
3 35 0.241 0.175 0.218 0.288 0.951 999 TRUE FALSE 1 LeafP "
#### 2. Traits individually significant for Presence|absence data#### #### 2. Traits individually significant for Presence|absence data####
traits <- read_delim("_data/Mesobromion/traits.v2.10perc.txt", delim="\t") traits <- read_delim("_data/Mesobromion/traits.v2.10perc.txt", delim="\t")
...@@ -470,26 +466,24 @@ traits.sign <- traits %>% ...@@ -470,26 +466,24 @@ traits.sign <- traits %>%
dplyr::select(species0, any_of(traits.sign.alone)) dplyr::select(species0, any_of(traits.sign.alone))
write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.pa.sign.txt", delim="\t") write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.pa.sign.txt", delim="\t")
## Pres Abs No Nas ## NONAs - New data
"# A tibble: 13 x 11 "# A tibble: 49 x 11
Trait.comb Coef.obs Coef.perm q025 q975 greater.than.perm n sign_plus sign_minus ntraits trait.name Trait.comb Coef.obs Coef.perm q025 q975 greater.than.perm n sign_plus sign_minus ntraits trait.name
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <lgl> <lgl> <int> <fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <lgl> <lgl> <int> <fct>
1 36 0.313 0.0582 0.284 0.362 0.996 999 TRUE FALSE 1 PlantHeight 1 46 0.326 0.190 0.297 0.376 0.999 999 TRUE FALSE 1 Leaf_Scleroph
2 50 0.309 0.0598 0.279 0.361 0.992 999 TRUE FALSE 1 BL_ANAT 2 33 0.285 0.0765 0.256 0.334 0.997 999 TRUE FALSE 1 Height
3 2 0.284 0.0746 0.248 0.331 0.994 999 TRUE FALSE 1 LEB_F_Nanophanerophyt 3 2 0.281 0.0683 0.250 0.329 0.998 999 TRUE FALSE 1 GF_Nanophan
4 32 0.260 0.140 0.234 0.305 0.981 999 TRUE FALSE 1 SLA 4 29 0.265 0.0748 0.243 0.311 0.990 999 TRUE FALSE 1 SLA
5 30 0.256 0.215 0.223 0.311 0.980 999 TRUE FALSE 1 BL_DAU 5 30 0.254 0.105 0.227 0.306 0.988 999 TRUE FALSE 1 LeafCdrymass
6 35 0.254 0.0577 0.226 0.308 0.971 999 TRUE FALSE 1 LeafP 6 27 0.245 0.119 0.220 0.296 0.982 999 TRUE FALSE 1 FP_Dur
7 49 0.253 0.209 0.222 0.303 0.983 999 TRUE FALSE 1 STRAT_T 7 5 0.245 0.131 0.213 0.303 0.986 999 TRUE FALSE 1 GF_Hemiphan
8 33 0.251 0.272 0.223 0.307 0.979 999 TRUE FALSE 1 LeafC.perdrymass 8 31 0.235 0.0744 0.214 0.285 0.974 999 TRUE FALSE 1 LeafN
9 34 0.234 0.0945 0.209 0.283 0.968 999 TRUE FALSE 1 LeafN 9 32 0.231 0.189 0.204 0.283 0.976 999 TRUE FALSE 1 LeafP
10 5 0.233 0.115 0.196 0.291 0.981 999 TRUE FALSE 1 LEB_F_Hemiphanerophyt 10 35 0.207 0.0881 0.185 0.255 0.951 999 TRUE FALSE 1 SeedLength
11 38 0.222 0.152 0.198 0.274 0.966 999 TRUE FALSE 1 Seed.length 11 1 0.191 0.0483 0.161 0.239 0.961 999 TRUE FALSE 1 GF_Macrophan
12 9 0.217 0.110 0.179 0.272 0.968 999 TRUE FALSE 1 LEB_F_Chamaephyt 12 34 0.197 0.0669 0.179 0.244 0.948 999 FALSE FALSE 1 SeedMass "
13 31 0.211 0.0831 0.190 0.261 0.958 999 TRUE FALSE 1 LeafArea "
## NONAs - Old data
## Pres Abs NoNa2 -modified Matrix.x to deal with NAs INSIDE the analysis
## Data Filled up by HB used in this analysis
"# A tibble: 48 x 11 "# A tibble: 48 x 11
Trait.comb Coef.obs Coef.perm q025 q975 greater.than.perm n sign_plus sign_minus ntraits trait.name Trait.comb Coef.obs Coef.perm q025 q975 greater.than.perm n sign_plus sign_minus ntraits trait.name
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <lgl> <lgl> <int> <fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <lgl> <lgl> <int> <fct>
...@@ -508,14 +502,3 @@ write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.pa.sign.txt", ...@@ -508,14 +502,3 @@ write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.pa.sign.txt",
13 40 0.209 0.128 0.185 0.259 0.957 999 TRUE FALSE 1 Disp.unit.leng " 13 40 0.209 0.128 0.185 0.259 0.957 999 TRUE FALSE 1 Disp.unit.leng "
## Pres Abs - Without excluding species with NA in traits
"# A tibble: 7 x 11
Trait.comb Coef.obs Coef.perm q025 q975 greater.than.perm n sign_plus sign_minus ntraits trait.name
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <lgl> <lgl> <int> <fct>
1 36 0.307 0.109 0.279 0.358 0.999 999 TRUE FALSE 1 PlantHeight
2 32 0.260 0.122 0.235 0.308 0.987 999 TRUE FALSE 1 SLA
3 35 0.253 0.135 0.228 0.299 0.986 999 TRUE FALSE 1 LeafP
4 33 0.240 0.184 0.210 0.296 0.975 999 TRUE FALSE 1 LeafC.perdrymass
5 34 0.233 0.166 0.207 0.283 0.972 999 TRUE FALSE 1 LeafN
6 38 0.228 0.0792 0.205 0.278 0.975 999 TRUE FALSE 1 Seed.length
7 39 0.226 0.141 0.201 0.282 0.973 999 TRUE FALSE 1 LDMC "
02_Mesobromion_ExamineOutput.R
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− 154
View file @ 0bc2be36
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