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Commit a5aecc7b authored by Francesco Sabatini's avatar Francesco Sabatini
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00_Mesobromion_DataPreparation.R
+ 27
− 27
View file @ a5aecc7b
...@@ -140,7 +140,7 @@ species <- env %>% ...@@ -140,7 +140,7 @@ species <- env %>%
#dplyr::select(traits$species0) #dplyr::select(traits$species0)
dim(species) # [1] 5810 873 dim(species) # [1] 5810 873
### 3.1 Subset plots based on trait coverage ####
releve08trait <- species %>% releve08trait <- species %>%
rownames_to_column("RELEVE_NR") %>% rownames_to_column("RELEVE_NR") %>%
reshape2::melt(.id="RELEVE_NR") %>% reshape2::melt(.id="RELEVE_NR") %>%
...@@ -358,7 +358,7 @@ traits %>% ...@@ -358,7 +358,7 @@ traits %>%
source("01b_MesobromionCluster.R") source("01b_MesobromionCluster.R")
#### 1. Traits individually significant for COVER data#### na.exclude=T ######## #### 1. Traits individually significant for COVER data#### na.exclude=T ########
traits <- read_delim("_data/Mesobromion/traits.v2.10perc.txt", delim="\t") traits <- read_delim("_data/Mesobromion/traits.v2.10perc.txt", delim="\t")
myfilelist <- list.files(path="_derived/Mesobromion/Cover", pattern="HIDDENcov-nona2_[0-9]+_.RData", full.names = T) myfilelist <- list.files(path="_derived/Mesobromion/Cover/onebyone", pattern="HIDDENcov-nona2_[0-9]+_.RData", full.names = T)
dataFiles = purrr::map(myfilelist, function(x){get(load(x))}) dataFiles = purrr::map(myfilelist, function(x){get(load(x))})
corXY = bind_rows(dataFiles) %>% corXY = bind_rows(dataFiles) %>%
as_tibble() %>% as_tibble() %>%
...@@ -401,17 +401,17 @@ write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.cov.sign.txt", ...@@ -401,17 +401,17 @@ write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.cov.sign.txt",
8 35 0.241 0.128 0.217 0.289 0.970 999 TRUE FALSE 1 LeafP " 8 35 0.241 0.128 0.217 0.289 0.970 999 TRUE FALSE 1 LeafP "
### COV - NONA2 - modified Matrix.x to deal with NAs INSIDE the analysis ### COV - NONA2 - modified Matrix.x to deal with NAs INSIDE the analysis
"# A tibble: 53 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>
1 36 0.304 0.151 0.280 0.355 0.998 999 TRUE FALSE 1 PlantHeight 1 31 0.304 0.0805 0.280 0.357 0.994 999 TRUE FALSE 1 PlantHeight
2 50 0.292 0.0641 0.265 0.346 0.988 999 TRUE FALSE 1 BL_ANAT 2 45 0.292 0.205 0.263 0.344 0.990 999 TRUE FALSE 1 BL_ANAT
3 2 0.262 0.0633 0.223 0.312 0.989 999 TRUE FALSE 1 LEB_F_Nanophanerophyt 3 2 0.262 0.126 0.230 0.317 0.988 999 TRUE FALSE 1 LEB_F_Nanophanerophyt
4 30 0.259 0.145 0.230 0.307 0.976 999 TRUE FALSE 1 BL_DAU 4 25 0.259 0.125 0.227 0.307 0.974 999 TRUE FALSE 1 BL_DAU
5 20 0.251 0.109 0.205 0.324 0.984 999 TRUE FALSE 1 V_VER_Fragmentation 5 16 0.251 0.0718 0.204 0.326 0.983 999 TRUE FALSE 1 V_VER_Fragmentation
6 32 0.247 0.238 0.224 0.297 0.964 999 TRUE FALSE 1 SLA 6 27 0.247 0.0761 0.227 0.297 0.965 999 TRUE FALSE 1 SLA
7 35 0.241 0.200 0.221 0.287 0.965 999 TRUE FALSE 1 LeafP 7 30 0.241 0.207 0.213 0.286 0.951 999 TRUE FALSE 1 LeafP
8 49 0.238 0.0786 0.217 0.286 0.965 999 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 ### COV - without deleting NAs
"# A tibble: 53 x 11 "# A tibble: 53 x 11
...@@ -423,7 +423,7 @@ write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.cov.sign.txt", ...@@ -423,7 +423,7 @@ write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.cov.sign.txt",
#### 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")
myfilelist <- list.files(path="_derived/Mesobromion/PresAbs", pattern="HIDDENpa-nona2_[0-9]+_.RData", full.names = T) myfilelist <- list.files(path="_derived/Mesobromion/PresAbs/onebyone", pattern="HIDDENpa-nona2_[0-9]+_.RData", full.names = T)
dataFiles = purrr::map(myfilelist, function(x){get(load(x))}) dataFiles = purrr::map(myfilelist, function(x){get(load(x))})
corXY = bind_rows(dataFiles) %>% corXY = bind_rows(dataFiles) %>%
as_tibble() as_tibble()
...@@ -466,22 +466,22 @@ write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.pa.sign.txt", ...@@ -466,22 +466,22 @@ write_delim(traits.sign, path="_data/Mesobromion/traits.v2.10perc.pa.sign.txt",
## Pres Abs NoNa2 -modified Matrix.x to deal with NAs INSIDE the analysis ## Pres Abs NoNa2 -modified Matrix.x to deal with NAs INSIDE the analysis
## Data Filled up by HB used in this analysis ## Data Filled up by HB used in this analysis
" Trait.comb Coef.obs Coef.perm q025 q975 greater.than.perm n sign_plus sign_minus ntraits trait.name "# A tibble: 48 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> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <lgl> <lgl> <int> <fct>
1 50 0.311 0.0624 0.284 0.362 0.996 999 TRUE FALSE 1 BL_ANAT 1 45 0.311 0.139 0.282 0.364 0.999 999 TRUE FALSE 1 BL_ANAT
2 36 0.307 0.190 0.279 0.359 0.995 999 TRUE FALSE 1 PlantHeight 2 31 0.307 0.160 0.279 0.358 0.999 999 TRUE FALSE 1 PlantHeight
3 2 0.295 0.105 0.254 0.346 0.997 999 TRUE FALSE 1 LEB_F_Nanophanerophyt 3 2 0.295 0.123 0.256 0.347 0.994 999 TRUE FALSE 1 LEB_F_Nanophanerophyt
4 30 0.260 0.124 0.229 0.312 0.991 999 TRUE FALSE 1 BL_DAU 4 25 0.260 0.0982 0.231 0.307 0.983 999 TRUE FALSE 1 BL_DAU
5 32 0.260 0.243 0.237 0.305 0.987 999 TRUE FALSE 1 SLA 5 27 0.260 0.0963 0.237 0.305 0.984 999 TRUE FALSE 1 SLA
6 35 0.253 0.131 0.230 0.299 0.983 999 TRUE FALSE 1 LeafP 6 30 0.253 0.158 0.229 0.300 0.987 999 TRUE FALSE 1 LeafP
7 33 0.240 0.0910 0.211 0.296 0.979 999 TRUE FALSE 1 LeafC.perdrymass 7 28 0.240 0.0705 0.212 0.295 0.980 999 TRUE FALSE 1 LeafC.perdrymass
8 49 0.240 0.0954 0.212 0.287 0.975 999 TRUE FALSE 1 STRAT_T 8 44 0.240 0.0618 0.213 0.293 0.981 999 TRUE FALSE 1 STRAT_T
9 34 0.233 0.294 0.210 0.281 0.963 999 TRUE FALSE 1 LeafN 9 29 0.233 0.0978 0.210 0.285 0.966 999 TRUE FALSE 1 LeafN
10 38 0.228 0.0907 0.203 0.278 0.958 999 TRUE FALSE 1 Seed.length 10 33 0.228 0.183 0.205 0.275 0.968 999 TRUE FALSE 1 Seed.length
11 39 0.226 0.106 0.198 0.282 0.963 999 TRUE FALSE 1 LDMC 11 34 0.226 0.0736 0.196 0.281 0.965 999 TRUE FALSE 1 LDMC
12 5 0.226 0.103 0.192 0.281 0.975 999 TRUE FALSE 1 LEB_F_Hemiphanerophyt 12 5 0.226 0.113 0.190 0.283 0.975 999 TRUE FALSE 1 LEB_F_Hemiphanerophyt
13 1 0.202 0.0560 0.170 0.248 0.953 999 TRUE FALSE 1 LEB_F_Makrophanerophyt 13 40 0.209 0.128 0.185 0.259 0.957 999 TRUE FALSE 1 Disp.unit.leng "
14 9 0.196 0.127 0.162 0.249 0.954 999 TRUE FALSE 1 LEB_F_Chamaephyt "
## Pres Abs - Without excluding species with NA in traits ## Pres Abs - Without excluding species with NA in traits
......
02_Mesobromion_ExamineOutput.R
+ 170
− 58
View file @ a5aecc7b
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