Last updated: 2021-04-29
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Knit directory: booksn_dispersantes/
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| File | Version | Author | Date | Message |
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| Rmd | a6cd9dc | Antonio J Perez-Luque | 2021-04-29 | cleaning old censuses |
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| Rmd | 1ed7427 | Antonio J Perez-Luque | 2021-04-28 | Add my first analysis |
Data coming from two sources:
Old bird censuses provided by R. Zamora, consists in bird censuses in three locations: oak population (1700 masl); juniper-scrubland (2230 masl) and summit environments (3200 masl). Range temporal cover from 1981 to 1985.
Obsnev bird censuses provided by OBSNEV, realized in several transects distributed along Sierra Nevada. Temporal range from 2008 to 2020. The data were downloaded from new information system of OBSNEV (i.e. PostgreSQL db01.obsnev.es)
All data are stored in the folder /data_raw
File RObledal año 1981 RZAves_SN_10ha.xls:
File Enebral año 1985 RZAves_SN_10ha.xls
File Aves_SN_meses_reproduccion.xls
library("tidyverse")
library("here")
library("readxl")
library("DT")robledal1981 <- read_excel(here::here("data/data_raw/RObledal año 1981 RZAves_SN_10ha.xls")) %>%
pivot_longer(cols= mayo_1981:julio_1981, names_to="fecha") %>%
separate(fecha, into = c("mes", "year"), sep="_", remove = FALSE) %>%
rename("especie" = Aves, "den" = value) %>%
mutate(year = as.numeric(year),
habitat = "robledal",
cota = 1700,
mes = case_when(
mes == "mayo" ~ as.numeric(5),
mes == "junio" ~ as.numeric(6),
mes == "julio" ~ as.numeric(7)),
fecha = format(as.Date(paste(year, mes, "01", sep="-")), format="%Y-%m-%d"))
head(robledal1981)# A tibble: 6 x 7
especie fecha mes year den habitat cota
<chr> <chr> <dbl> <dbl> <dbl> <chr> <dbl>
1 Phylloscopus bonelli 1981-05-01 5 1981 8 robledal 1700
2 Phylloscopus bonelli 1981-06-01 6 1981 13.8 robledal 1700
3 Phylloscopus bonelli 1981-07-01 7 1981 14.6 robledal 1700
4 Sylvia atricapilla 1981-05-01 5 1981 4.4 robledal 1700
5 Sylvia atricapilla 1981-06-01 6 1981 4.6 robledal 1700
6 Sylvia atricapilla 1981-07-01 7 1981 6.8 robledal 1700enebral1985 <- read_excel(here::here("data/data_raw/Enebral año 1985 RZAves_SN_10ha.xls")) %>% pivot_longer(cols= mayo_1985:julio_1985, names_to="fecha") %>%
separate(fecha, into = c("mes", "year"), sep="_") %>%
rename("especie" = Aves, "den" = value) %>%
mutate(year = as.numeric(year),
habitat = "enebral",
cota = 2230,
mes = case_when(
mes == "mayo" ~ as.numeric(5),
mes == "junio" ~ as.numeric(6),
mes == "julio" ~ as.numeric(7)),
fecha = format(as.Date(paste(year, mes, "01", sep="-")), format="%Y-%m-%d"))
head(enebral1985)# A tibble: 6 x 7
especie mes year den habitat cota fecha
<chr> <dbl> <dbl> <dbl> <chr> <dbl> <chr>
1 Carduelis carduelis 5 1985 0 enebral 2230 1985-05-01
2 Carduelis carduelis 6 1985 0 enebral 2230 1985-06-01
3 Carduelis carduelis 7 1985 0.1 enebral 2230 1985-07-01
4 Alauda arvensis 5 1985 5.1 enebral 2230 1985-05-01
5 Alauda arvensis 6 1985 5.4 enebral 2230 1985-06-01
6 Alauda arvensis 7 1985 5.7 enebral 2230 1985-07-01enebral1984 <- read_excel(here::here("data/data_raw/Aves_SN_meses_reproduccion.xlsx"),
sheet = "2230") %>%
rename("especie" = Ave, "den" = `Número`) %>%
mutate(den = round(den*(10/10.2),2),
habitat = "enebral",
cota = 2230,
mes = lubridate::month(Fecha),
year = lubridate::year(Fecha),
Fecha = strftime(Fecha, format="%Y-%m-%d")) %>%
rename(fecha = Fecha)
head(enebral1984) # A tibble: 6 x 7
especie fecha den habitat cota mes year
<chr> <chr> <dbl> <chr> <dbl> <dbl> <dbl>
1 Oenanthe oenanthe 1984-05-05 15.7 enebral 2230 5 1984
2 Alauda arvensis 1984-05-05 3.92 enebral 2230 5 1984
3 Emberiza cia 1984-05-05 15.7 enebral 2230 5 1984
4 Phoenicurus ochuros 1984-05-05 0.98 enebral 2230 5 1984
5 Anthus campestris 1984-05-05 0.98 enebral 2230 5 1984
6 Alectoris rufa 1984-05-05 0.98 enebral 2230 5 1984cumbres1982 <- read_excel(here::here("data/data_raw/Aves_SN_meses_reproduccion.xlsx"),
sheet = "3200") %>%
rename("especie" = Ave, "den" = `Número`) %>%
mutate(den = round(den*(10/20),2),
habitat = "altas cumbres",
cota = 3200,
mes = lubridate::month(Fecha),
year = lubridate::year(Fecha),
Fecha = strftime(Fecha, format="%Y-%m-%d")) %>%
rename(fecha = Fecha)
head(cumbres1982)# A tibble: 6 x 7
especie fecha den habitat cota mes year
<chr> <chr> <dbl> <chr> <dbl> <dbl> <dbl>
1 Oenanthe oenanthe 1982-06-06 0.5 altas cumbres 3200 6 1982
2 Phoenicurus ochuros 1982-06-06 3 altas cumbres 3200 6 1982
3 Prunella collaris 1982-06-06 2.5 altas cumbres 3200 6 1982
4 Oenanthe oenanthe 1982-06-07 0.5 altas cumbres 3200 6 1982
5 Phoenicurus ochuros 1982-06-07 1 altas cumbres 3200 6 1982
6 Prunella collaris 1982-06-07 4 altas cumbres 3200 6 1982Bind old data
old_census <- bind_rows(cumbres1982, enebral1984, enebral1985, robledal1981)
datatable(old_census)
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] DT_0.17 readxl_1.3.1 here_1.0.1 forcats_0.5.1
[5] stringr_1.4.0 dplyr_1.0.4 purrr_0.3.4 readr_1.4.0
[9] tidyr_1.1.2 tibble_3.0.6 ggplot2_3.3.3 tidyverse_1.3.0
[13] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 lubridate_1.7.10 assertthat_0.2.1 rprojroot_2.0.2
[5] digest_0.6.27 utf8_1.1.4 R6_2.5.0 cellranger_1.1.0
[9] backports_1.2.1 reprex_1.0.0 evaluate_0.14 httr_1.4.2
[13] pillar_1.4.7 rlang_0.4.10 rstudioapi_0.13 whisker_0.4
[17] jquerylib_0.1.3 rmarkdown_2.6.6 htmlwidgets_1.5.3 munsell_0.5.0
[21] broom_0.7.4 compiler_4.0.2 httpuv_1.5.5 modelr_0.1.8
[25] xfun_0.20 pkgconfig_2.0.3 htmltools_0.5.1.1 tidyselect_1.1.0
[29] fansi_0.4.2 crayon_1.4.1 dbplyr_2.1.0 withr_2.4.1
[33] later_1.1.0.1 grid_4.0.2 jsonlite_1.7.2 gtable_0.3.0
[37] lifecycle_1.0.0 DBI_1.1.1 git2r_0.28.0 magrittr_2.0.1
[41] scales_1.1.1 cli_2.3.0 stringi_1.5.3 fs_1.5.0
[45] promises_1.2.0.1 xml2_1.3.2 bslib_0.2.4 ellipsis_0.3.1
[49] generics_0.1.0 vctrs_0.3.6 tools_4.0.2 glue_1.4.2
[53] hms_1.0.0 crosstalk_1.1.1 yaml_2.2.1 colorspace_2.0-0
[57] rvest_0.3.6 knitr_1.31 haven_2.3.1 sass_0.3.1