Prepara matriz de datos ambientales
ajpelu
2022-01-18
Last updated: 2022-01-18
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Knit directory: ms_mariposas_biodiversity/
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Introduction
library(tidyverse)
library(readxl)
library(janitor)
library(here)
library(corrplot)
library(corrr)
library(factoextra)
library(kableExtra)- Prepare data
rawdata <- readxl::read_excel(here::here("data/Tabla_variables_2012_2020.xls")) %>% dplyr::select(-contains("LS_B"),
-contains("MT_"),
-LS_NDVI,
-FR_OLIVO, -FR_EUCAL,
-FR_URBAN, -FR_AGUA,
-FR_VIASC, -FR_CULTI,
-DS_VIASC, -DS_URBAN,
-DS_LAGIN, -DS_AGUA,
-DS_RIOS, -DS_CULTI) %>%
rename(Pp_oto = "Precipitación Otoños",
Pp_inv = "Precipitación Inviernos",
PP_pri = "Precipitación Primaveras",
Pp_ver = "Precipitación Veranos",
tmed_oto = "Temperatura media Otoños",
tmed_inv = "Temperatura media Inviernos",
tmed_pri = "Temperatura media Primaveras",
tmed_ver = "Temperatura media Veranos")
# Mean of Annual precipitation
pp_anu_year <- rawdata %>%
dplyr::select(Abreviatura, contains("Acumulado ANUAL")) %>%
rowwise() %>%
mutate(m = mean(c_across(where(is.numeric)))) %>%
dplyr::select(Abreviatura, Pp_anu = m)
# Average of Mean temperature
temp_anu_year <- rawdata %>%
dplyr::select(Abreviatura, contains("Temperatura media")) %>%
rowwise() %>%
mutate(m = mean(c_across(where(is.numeric)))) %>%
dplyr::select(Abreviatura, temp_anu = m)
env <- rawdata %>%
inner_join(temp_anu_year) %>%
inner_join(pp_anu_year) %>%
dplyr::select(-contains("Temperatura media")) %>%
dplyr::select(-contains("Acumulado ANUAL")) %>%
rename(elev = "Elevación")Correlation bewteen variables
# Escalamos las variables
env_selecccion <- env %>%
dplyr::select(-Transecto, -Id_transect, -Abreviatura, -Longitud)
env.scale <- scale(env_selecccion)
# correlaciones
env.correlations <- cor(env.scale) # res
symnum(env.correlations , abbr.colnames = FALSE) %>% kbl()| elev | TP_ES_OE | TP_EXPO | TP_PEND | TP_RSD_A | TP_RSD_I | TP_RSD_O | TP_RSD_P | TP_RSD_V | TP_RSH_I | TP_RSH_P | TP_RSH_V | TP_SU_NO | HIDRO_ACUM | HIDRO_ICT | HIDRO_ITH | DS_ARBOL | FR_ARBOL | FR_CONIF | FR_MATDE | FR_MATDI | FR_PASTO | FR_QUERC | Pp_oto | Pp_inv | PP_pri | Pp_ver | tmed_oto | tmed_inv | tmed_pri | tmed_ver | temp_anu | Pp_anu | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| elev | 1 | ||||||||||||||||||||||||||||||||
| TP_ES_OE | . | 1 | |||||||||||||||||||||||||||||||
| TP_EXPO | , | . | 1 | ||||||||||||||||||||||||||||||
| TP_PEND | . | 1 | |||||||||||||||||||||||||||||||
| TP_RSD_A | . | . | , | . | 1 | ||||||||||||||||||||||||||||
| TP_RSD_I | . | . | . |
|
1 | ||||||||||||||||||||||||||||
| TP_RSD_O | . |
|
. | . |
|
, | 1 | ||||||||||||||||||||||||||
| TP_RSD_P | . | . | . | . |
|
B | , | 1 | |||||||||||||||||||||||||
| TP_RSD_V | . | . | , | , |
|
, | , |
|
1 | ||||||||||||||||||||||||
| TP_RSH_I | , | , |
|
|
, |
|
|
1 | |||||||||||||||||||||||||
| TP_RSH_P | . | , | , | , | , | . | , |
|
|
1 | |||||||||||||||||||||||
| TP_RSH_V | . | , | . | . | , | 1 | |||||||||||||||||||||||||||
| TP_SU_NO | . | . |
|
B | . |
|
, | , | , | 1 | |||||||||||||||||||||||
| HIDRO_ACUM | . | . | . | . | 1 | ||||||||||||||||||||||||||||
| HIDRO_ICT | , | . | , | . | . | 1 | |||||||||||||||||||||||||||
| HIDRO_ITH | , | . | , | . |
|
1 | |||||||||||||||||||||||||||
| DS_ARBOL | , | . | . | . | . | . | . | . | 1 | ||||||||||||||||||||||||
| FR_ARBOL | . | . | . | . | . | . | , | . | . | . | . | . | 1 | ||||||||||||||||||||
| FR_CONIF | . | . | . | 1 | |||||||||||||||||||||||||||||
| FR_MATDE | . | . | . | . | . | . | . | . | 1 | ||||||||||||||||||||||||
| FR_MATDI | . | . | . | . | , | . | 1 | ||||||||||||||||||||||||||
| FR_PASTO | , | . | . | . |
|
. | . | . | , | 1 | |||||||||||||||||||||||
| FR_QUERC | . | , | . | . | . | . | . | , | . | . | . | . | . | . | . | 1 | |||||||||||||||||
| Pp_oto | . | . | . | . | . | . | . | . | . | . | . | 1 | |||||||||||||||||||||
| Pp_inv | . | . | , | 1 | |||||||||||||||||||||||||||||
| PP_pri | . | . | . | . | . | . | . | . | . | , | 1 | ||||||||||||||||||||||
| Pp_ver | . | . | . | . | . | . | . | , | . | . | . | . | , | . | . | . | . | . | 1 | ||||||||||||||
| tmed_oto | B | . | . | . | . | . | . | . | . | , | , | . | . | , | . | . | 1 | ||||||||||||||||
| tmed_inv | B | . | . | . | . | . | . | . | . | , | , | . | . | , | . | . | B | 1 | |||||||||||||||
| tmed_pri | B | . | . | . | . | . | . | . | . | , | , | . | . | , | . | . | B | B | 1 | ||||||||||||||
| tmed_ver | B | . | . | . | . | . | . | . | . | , | , | . | , | . | . | B | B | B | 1 | ||||||||||||||
| temp_anu | B | . | . | . | . | . | . | . | . | , | , | . | . | , | . | . | B | B | B | B | 1 | ||||||||||||
| Pp_anu | . | . | . | . |
|
B | , | . | . | . | 1 |
dfdis <- dist(env.correlations, method = "euclidean")- Generamos un plot de correlaciones
cor.mtest <- function(mat, ...) {
mat <- as.matrix(mat)
n <- ncol(mat)
p.mat<- matrix(NA, n, n)
diag(p.mat) <- 0
for (i in 1:(n - 1)) {
for (j in (i + 1):n) {
tmp <- cor.test(mat[, i], mat[, j], ...)
p.mat[i, j] <- p.mat[j, i] <- tmp$p.value
}
}
colnames(p.mat) <- rownames(p.mat) <- colnames(mat)
p.mat
}
p.mat <- cor.mtest(env.scale)
corrplot::corrplot(env.correlations, type = "upper", tl.col = "black", tl.srt = 90, tl.cex = 0.4,
p.mat = p.mat, sig.level = 0.05,
insig = "blank",
diag = FALSE)
pdf(here::here("figs/correlation_env_variables_numbers.pdf"))
corrplot::corrplot(env.correlations, method = "number",
type = "upper", tl.col = "black",
col= "black", tl.srt = 90, tl.cex = 0.35,
number.cex = .3, number.digits = 2,
diag = FALSE)
dev.off()quartz_off_screen
2 pdf(here::here("figs/correlation_env_variables.pdf"))
corrplot::corrplot(env.correlations, type = "upper",
tl.col = "black", tl.srt = 90, tl.cex = 0.4,
p.mat = p.mat, sig.level = 0.05,
insig = "blank",
diag = FALSE)
dev.off()quartz_off_screen
2 - Table of correlations
dfscale_corrr <- correlate(env.scale)
dfscale_corrr %>% shave(upper = FALSE) %>%
fashion() %>% kbl()| term | elev | TP_ES_OE | TP_EXPO | TP_PEND | TP_RSD_A | TP_RSD_I | TP_RSD_O | TP_RSD_P | TP_RSD_V | TP_RSH_I | TP_RSH_P | TP_RSH_V | TP_SU_NO | HIDRO_ACUM | HIDRO_ICT | HIDRO_ITH | DS_ARBOL | FR_ARBOL | FR_CONIF | FR_MATDE | FR_MATDI | FR_PASTO | FR_QUERC | Pp_oto | Pp_inv | PP_pri | Pp_ver | tmed_oto | tmed_inv | tmed_pri | tmed_ver | temp_anu | Pp_anu |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| elev | .42 | .61 | .34 | .45 | .37 | .44 | .41 | .51 | .25 | .24 | -.20 | -.28 | -.46 | -.69 | -.66 | .60 | -.38 | .02 | -.10 | -.01 | .70 | -.36 | .32 | .16 | -.07 | .17 | -.99 | -.99 | -.99 | -.98 | -.99 | .20 | |
| TP_ES_OE | .37 | -.08 | .58 | .29 | .82 | .32 | .40 | .28 | .32 | .01 | -.20 | -.04 | -.30 | -.18 | .26 | -.45 | -.11 | .23 | .03 | .23 | -.19 | -.14 | .04 | -.16 | .03 | -.41 | -.42 | -.43 | -.42 | -.42 | -.09 | ||
| TP_EXPO | -.23 | .63 | .54 | .50 | .59 | .74 | .62 | .71 | .39 | -.45 | -.30 | -.64 | -.37 | .35 | -.51 | .04 | -.29 | .31 | .33 | -.61 | .09 | .10 | .11 | .37 | -.57 | -.58 | -.56 | -.53 | -.56 | .15 | |||
| TP_PEND | -.52 | -.44 | -.38 | -.49 | -.60 | -.74 | -.68 | -.67 | .38 | -.40 | -.44 | -.72 | .03 | .39 | -.08 | .30 | .02 | .17 | .44 | .47 | .41 | .37 | -.58 | -.43 | -.41 | -.41 | -.45 | -.42 | .44 | ||||
| TP_RSD_A | .91 | .86 | .94 | .86 | .88 | .74 | .20 | -.84 | -.03 | -.23 | .04 | .37 | -.57 | .04 | -.21 | .10 | .26 | -.45 | -.15 | -.19 | -.35 | .56 | -.37 | -.39 | -.39 | -.36 | -.38 | -.20 | |||||
| TP_RSD_I | .60 | .99 | .75 | .88 | .69 | .12 | -.97 | -.04 | -.17 | .04 | .35 | -.36 | .04 | -.32 | .05 | .21 | -.31 | .02 | -.18 | -.32 | .56 | -.27 | -.30 | -.30 | -.26 | -.29 | -.12 | ||||||
| TP_RSD_O | .65 | .66 | .60 | .51 | .07 | -.51 | .01 | -.23 | .02 | .36 | -.68 | -.05 | .01 | .09 | .27 | -.41 | -.32 | -.14 | -.28 | .43 | -.40 | -.42 | -.42 | -.39 | -.41 | -.24 | |||||||
| TP_RSD_P | .83 | .92 | .74 | .19 | -.95 | -.05 | -.19 | .04 | .36 | -.41 | .05 | -.32 | .06 | .24 | -.39 | .00 | -.19 | -.35 | .58 | -.31 | -.34 | -.34 | -.30 | -.32 | -.13 | ||||||||
| TP_RSD_V | .91 | .85 | .51 | -.63 | -.06 | -.23 | .02 | .35 | -.55 | .17 | -.30 | .09 | .32 | -.67 | -.09 | -.21 | -.36 | .53 | -.42 | -.44 | -.43 | -.40 | -.42 | -.19 | |||||||||
| TP_RSH_I | .86 | .46 | -.79 | .07 | -.03 | .24 | .30 | -.48 | .08 | -.39 | .02 | .19 | -.54 | -.11 | -.28 | -.40 | .60 | -.14 | -.17 | -.17 | -.12 | -.15 | -.24 | ||||||||||
| TP_RSH_P | .70 | -.63 | -.06 | -.18 | .11 | .09 | -.34 | .26 | -.40 | .19 | .05 | -.56 | -.13 | -.23 | -.26 | .47 | -.14 | -.17 | -.15 | -.12 | -.15 | -.20 | |||||||||||
| TP_RSH_V | -.06 | .31 | .10 | .25 | -.26 | -.09 | .36 | -.31 | .32 | -.28 | -.47 | -.28 | -.19 | -.04 | .18 | .24 | .23 | .26 | .27 | .25 | -.19 | ||||||||||||
| TP_SU_NO | .09 | .17 | -.02 | -.21 | .21 | -.09 | .30 | -.09 | -.09 | .14 | -.03 | .20 | .32 | -.53 | .18 | .21 | .21 | .18 | .20 | .13 | |||||||||||||
| HIDRO_ACUM | .60 | .50 | .04 | -.20 | -.24 | -.00 | -.15 | -.18 | .09 | -.36 | -.21 | -.22 | .29 | .48 | .47 | .47 | .47 | .47 | -.28 | ||||||||||||||
| HIDRO_ICT | .90 | -.19 | .16 | -.04 | .07 | -.35 | -.30 | .24 | -.30 | -.21 | -.28 | .11 | .70 | .70 | .68 | .68 | .69 | -.30 | |||||||||||||||
| HIDRO_ITH | -.12 | -.05 | -.03 | -.10 | -.31 | -.25 | .00 | -.42 | -.27 | -.30 | .35 | .69 | .69 | .68 | .69 | .69 | -.35 | ||||||||||||||||
| DS_ARBOL | -.58 | -.53 | -.40 | -.61 | .92 | -.37 | .32 | .15 | -.15 | .53 | -.58 | -.59 | -.59 | -.58 | -.59 | .21 | |||||||||||||||||
| FR_ARBOL | .37 | .07 | .09 | -.48 | .54 | .39 | .27 | .28 | -.62 | .32 | .34 | .33 | .29 | .32 | .31 | ||||||||||||||||||
| FR_CONIF | -.11 | .58 | -.44 | -.18 | -.36 | -.34 | -.10 | -.24 | .01 | .00 | .01 | .02 | .01 | -.36 | |||||||||||||||||||
| FR_MATDE | .25 | -.38 | .48 | -.12 | .07 | -.04 | -.46 | .06 | .07 | .05 | .03 | .05 | -.08 | ||||||||||||||||||||
| FR_MATDI | -.61 | -.13 | -.36 | -.04 | .33 | -.31 | -.01 | -.00 | .03 | .02 | .01 | -.09 | |||||||||||||||||||||
| FR_PASTO | -.32 | .42 | .21 | -.11 | .37 | -.69 | -.69 | -.70 | -.69 | -.70 | .27 | ||||||||||||||||||||||
| FR_QUERC | .22 | .09 | -.07 | -.36 | .34 | .35 | .32 | .29 | .33 | .07 | |||||||||||||||||||||||
| Pp_oto | .71 | .37 | -.24 | -.38 | -.36 | -.38 | -.40 | -.38 | .83 | ||||||||||||||||||||||||
| Pp_inv | .79 | -.30 | -.29 | -.26 | -.26 | -.31 | -.28 | .97 | |||||||||||||||||||||||||
| PP_pri | -.38 | -.07 | -.04 | -.01 | -.05 | -.04 | .79 | ||||||||||||||||||||||||||
| Pp_ver | -.07 | -.09 | -.09 | -.06 | -.08 | -.25 | |||||||||||||||||||||||||||
| tmed_oto | 1.00 | 1.00 | 1.00 | 1.00 | -.32 | ||||||||||||||||||||||||||||
| tmed_inv | 1.00 | 1.00 | 1.00 | -.29 | |||||||||||||||||||||||||||||
| tmed_pri | 1.00 | 1.00 | -.28 | ||||||||||||||||||||||||||||||
| tmed_ver | 1.00 | -.32 | |||||||||||||||||||||||||||||||
| temp_anu | -.30 | ||||||||||||||||||||||||||||||||
| Pp_anu |
- Hierarchical cluster
# library("pvclust")
# fit <- hclust(dfdis, method="ward")
# plot(fit, cex = .6)
# 33 Variables
# Vamos a probar a reducir a 10
h <- hcut(dfdis, k=14)
dendro <- fviz_dend(h, rect = TRUE, horiz = TRUE, lwd = 0.5, cex = .5)Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
"none")` instead.dendro
ggsave(here::here("figs/dendrograma_env.pdf"),
height = 7, width = 5, device = "pdf")Selección final de variables
variables_sel <- c("Pp_anu", "TP_PEND", "FR_MATDE",
"TP_SU_NO", "FR_QUERC", "FR_CONIF",
"TP_RSH_V", "HIDRO_ITH", "temp_anu",
"TP_RSD_P", "Pp_ver", "TP_ES_OE", "TP_EXPO",
"DS_ARBOL", "elev")
env_seleccionadas <- env %>% dplyr::select(Transecto,Id_transect,Abreviatura, matches(variables_sel))
write_csv(env_seleccionadas, here::here("data/matrix_env_variables_selected.csv"))
sessionInfo()R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.3
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] kableExtra_1.3.1 factoextra_1.0.7 corrr_0.4.3 corrplot_0.84
[5] here_1.0.1 janitor_2.1.0 readxl_1.3.1 forcats_0.5.1
[9] stringr_1.4.0 dplyr_1.0.6 purrr_0.3.4 readr_1.4.0
[13] tidyr_1.1.3 tibble_3.1.2 ggplot2_3.3.5 tidyverse_1.3.1
[17] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] fs_1.5.0 lubridate_1.7.10 webshot_0.5.2 httr_1.4.2
[5] rprojroot_2.0.2 tools_4.0.2 backports_1.2.1 bslib_0.2.4
[9] utf8_1.1.4 R6_2.5.1 DBI_1.1.1 colorspace_2.0-2
[13] withr_2.4.1 tidyselect_1.1.1 gridExtra_2.3 processx_3.5.1
[17] curl_4.3 compiler_4.0.2 git2r_0.28.0 textshaping_0.3.2
[21] cli_2.5.0 rvest_1.0.0 xml2_1.3.2 labeling_0.4.2
[25] sass_0.3.1 scales_1.1.1.9000 callr_3.7.0 systemfonts_1.0.0
[29] digest_0.6.27 foreign_0.8-81 rmarkdown_2.8 rio_0.5.16
[33] pkgconfig_2.0.3 htmltools_0.5.2 dbplyr_2.1.1 fastmap_1.1.0
[37] highr_0.8 rlang_0.4.12 rstudioapi_0.13 farver_2.1.0
[41] jquerylib_0.1.3 generics_0.1.0 jsonlite_1.7.2 zip_2.1.1
[45] car_3.0-10 dendextend_1.14.0 magrittr_2.0.1 Rcpp_1.0.7
[49] munsell_0.5.0 fansi_0.4.2 abind_1.4-5 viridis_0.5.1
[53] lifecycle_1.0.1 stringi_1.7.4 whisker_0.4 yaml_2.2.1
[57] carData_3.0-4 snakecase_0.11.0 grid_4.0.2 promises_1.2.0.1
[61] ggrepel_0.9.1 crayon_1.4.1 haven_2.3.1 hms_1.0.0
[65] knitr_1.31 ps_1.5.0 pillar_1.6.1 ggpubr_0.4.0
[69] ggsignif_0.6.0 reprex_2.0.0 glue_1.4.2 evaluate_0.14
[73] getPass_0.2-2 data.table_1.14.0 modelr_0.1.8 vctrs_0.3.8
[77] httpuv_1.5.5 cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1
[81] openxlsx_4.2.3 xfun_0.23 broom_0.7.9 rstatix_0.6.0
[85] later_1.1.0.1 ragg_1.1.1 viridisLite_0.4.0 cluster_2.1.0
[89] ellipsis_0.3.2