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The goal of mallaRd is to reproduces the analyses and results from the paper "Housing search in the concrete jungle – breeding site fidelity of urban mallards and implications for conservation management strategies" by Engler et al. (in prep).
You can install our package mallaRd from GitHub with:
install.packages("remotes") ## install the package remotes if you don't have it
remotes::install_github("courtiol/mallaRd") ## install our packageThen load the package in your R session and check the main help page where we placed all analyses:
load("mallaRd")
?mallaRdYou can access the raw data used for the paper here or via the R package:
head(data_raw) ## first 6 rows
#> ID year date species location_ID location_lat location_long habitat_type floor_level body_mass_g wing_length_mm hatch_date clutch_size brood_size ring_number
#> 1 1 2005 01.04.2005 mallard_duck 729 52.52495 13.30129 courtyard NA NA NA NA NA JC8002
#> 2 2 2005 04.04.2005 mallard_duck 1116 52.60742 13.23319 other NA NA NA NA 1
#> 3 3 2005 25.04.2005 mallard_duck 720 52.52412 13.34539 roof_terrace NA NA NA NA 8
#> 4 11 2005 26.04.2005 mallard_duck 555 52.51043 13.19960 balcony NA 750 257 26.04.2005 12 12 JC54565
#> 5 12 2005 27.04.2005 mallard_duck 991 52.56289 13.20875 courtyard NA NA NA NA 3
#> 6 13 2005 29.04.2005 mallard_duck 115 52.44341 13.58433 balcony NA 830 272 29.04.2005 NA 10 JC52194
#> release_site_lat release_site_long DNSW PSW1000 PSW2000 trafficvolume500 populationdensity500 trafficvolume1000 populationdensity1000 trafficvolume2000 populationdensity2000
#> 1 52.54819 13.31221 276.1204 1 1 1018.6459 143.70396 1679.24304 88.71829 1297.3898 93.85891
#> 2 NA NA 929.5084 1 1 158.7811 25.50148 72.82336 23.18329 131.7400 14.51628
#> 3 NA NA 127.3921 1 1 843.3160 127.61779 743.98803 147.67042 858.6173 78.80484
#> 4 52.51088 13.20227 162.9485 1 1 734.5966 23.64657 529.66019 21.79157 339.1518 26.49088
#> 5 NA NA 426.5027 1 1 0.0000 138.54895 117.49123 67.91985 111.4260 38.82886
#> 6 52.44400 13.62276 80.8951 1 1 108.0740 114.83922 172.58178 59.27967 208.3172 44.26453Our package relies on the following packages:
pkgs <- desc::desc_get_deps()
pkgs <- pkgs[pkgs$package != "R", ]
pkgs$version_used <- sapply(pkgs$package, \(pkg) paste(packageVersion(pkg), sep = "."))
pkgs
#> type package version version_used
#> 1 Imports cowplot * 1.1.3
#> 2 Imports dplyr * 1.1.4
#> 3 Imports furrr * 0.3.1
#> 4 Imports future * 1.34.0
#> 5 Imports ggplot2 * 3.5.1
#> 6 Imports sf * 1.0.17
#> 7 Imports showtext * 0.9.7
#> 8 Imports spaMM * 4.5.0
#> 9 Imports tibble * 3.2.1
#> 10 Imports tidyr * 1.3.1
#> 11 Imports tidyselect * 1.2.1
#> 12 Suggests desc * 1.4.3
#> 13 Suggests doSNOW * 1.0.20
#> 14 Suggests DHARMa * 0.4.6
#> 15 Suggests spelling * 2.3.0
#> 16 Suggests devtools * 2.4.5
#> 17 Suggests knitr * 1.48Here is the information of the R & RStudio environment used to run all the analyses:
sessionInfo()
#> R version 4.4.1 (2024-06-14)
#> Platform: x86_64-redhat-linux-gnu
#> Running under: Fedora Linux 40 (Forty)
#>
#> Matrix products: default
#> BLAS/LAPACK: FlexiBLAS OPENBLAS-OPENMP; LAPACK version 3.11.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: Europe/Berlin
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] mallaRd_0.1.0
#>
#> loaded via a namespace (and not attached):
#> [1] gtable_0.3.5 xfun_0.47 ggplot2_3.5.1 htmlwidgets_1.6.4 devtools_2.4.5 remotes_2.5.0.9000 processx_3.8.4 lattice_0.22-6
#> [9] numDeriv_2016.8-1.1 callr_3.7.6 vctrs_0.6.5 tools_4.4.1 ps_1.8.0 generics_0.1.3 parallel_4.4.1 curl_5.2.3
#> [17] proxy_0.4-27 tibble_3.2.1 crancache_0.0.0.9001 fansi_1.0.6 RSQLite_2.3.7 blob_1.2.4 pkgconfig_2.0.3 Matrix_1.7-0
#> [25] checkmate_2.3.2 desc_1.4.3 lifecycle_1.0.4 compiler_4.4.1 munsell_0.5.1 httpuv_1.6.15 htmltools_0.5.8.1 usethis_3.0.0
#> [33] later_1.3.2 pillar_1.9.0 crayon_1.5.3 urlchecker_1.0.1 MASS_7.3-61 ellipsis_0.3.2 cachem_1.1.0 sessioninfo_1.2.2
#> [41] boot_1.3-31 nlme_3.1-166 spaMM_4.5.0 mime_0.12 tidyselect_1.2.1 digest_0.6.37 slam_0.1-53 dplyr_1.1.4
#> [49] purrr_1.0.2 rematch2_2.1.2 fastmap_1.2.0 grid_4.4.1 colorspace_2.1-1 cranlike_1.0.3 cli_3.6.3 magrittr_2.0.3
#> [57] pkgbuild_1.4.4 utf8_1.2.4 backports_1.5.0 scales_1.3.0 promises_1.3.0 rappdirs_0.3.3 bit64_4.0.5 registry_0.5-1
#> [65] bit_4.5.0 ROI_1.0-1 pbapply_1.7-2 memoise_2.0.1 shiny_1.9.1 parsedate_1.3.1 evaluate_1.0.0 knitr_1.48
#> [73] miniUI_0.1.1.1 profvis_0.4.0 rlang_1.1.4 Rcpp_1.0.13 xtable_1.8-4 glue_1.7.0 DBI_1.2.3 pkgload_1.4.0
#> [81] minqa_1.2.8 debugme_1.2.0 jsonlite_1.8.9 R6_2.5.1 fs_1.6.4