The goal of mallaRd is to reproduces the analyses and results from the paper “Breeding site fidelity in the concrete jungle: implications for the management of urban mallards.” by Engler et al. (accepted in Journal of Urban Ecology).
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 | release_site_lat | release_site_long | DNSW | PSW1000 | PSW2000 | trafficvolume500 | populationdensity500 | trafficvolume1000 | populationdensity1000 | trafficvolume2000 | populationdensity2000 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2005 | 01.04.2005 | mallard_duck | 729 | 52.52495 | 13.30129 | courtyard | NA | NA | NA | NA | NA | JC8002 | 52.54819 | 13.31221 | 276.1204 | 1 | 1 | 1018.6459 | 143.70396 | 1679.24304 | 88.71829 | 1297.3898 | 93.85891 | |
| 2 | 2005 | 04.04.2005 | mallard_duck | 1116 | 52.60742 | 13.23319 | other | NA | NA | NA | NA | 1 | NA | NA | 929.5084 | 1 | 1 | 158.7811 | 25.50148 | 72.82336 | 23.18329 | 131.7400 | 14.51628 | ||
| 3 | 2005 | 25.04.2005 | mallard_duck | 720 | 52.52412 | 13.34539 | roof_terrace | NA | NA | NA | NA | 8 | NA | NA | 127.3921 | 1 | 1 | 843.3160 | 127.61779 | 743.98803 | 147.67042 | 858.6173 | 78.80484 | ||
| 11 | 2005 | 26.04.2005 | mallard_duck | 555 | 52.51043 | 13.19960 | balcony | NA | 750 | 257 | 26.04.2005 | 12 | 12 | JC54565 | 52.51088 | 13.20227 | 162.9485 | 1 | 1 | 734.5966 | 23.64657 | 529.66019 | 21.79157 | 339.1518 | 26.49088 |
| 12 | 2005 | 27.04.2005 | mallard_duck | 991 | 52.56289 | 13.20875 | courtyard | NA | NA | NA | NA | 3 | NA | NA | 426.5027 | 1 | 1 | 0.0000 | 138.54895 | 117.49123 | 67.91985 | 111.4260 | 38.82886 | ||
| 13 | 2005 | 29.04.2005 | mallard_duck | 115 | 52.44341 | 13.58433 | balcony | NA | 830 | 272 | 29.04.2005 | NA | 10 | JC52194 | 52.44400 | 13.62276 | 80.8951 | 1 | 1 | 108.0740 | 114.83922 | 172.58178 | 59.27967 | 208.3172 | 44.26453 |
Our 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 |
|---|---|---|---|
| Imports | cowplot | * | 1.1.3 |
| Imports | dplyr | * | 1.1.4 |
| Imports | furrr | * | 0.3.1 |
| Imports | future | * | 1.34.0 |
| Imports | ggplot2 | * | 3.5.1 |
| Imports | sf | * | 1.0.19 |
| Imports | spaMM | * | 4.5.0 |
| Imports | tibble | * | 3.2.1 |
| Imports | tidyr | * | 1.3.1 |
| Imports | tidyselect | * | 1.2.1 |
| Suggests | desc | * | 1.4.3 |
| Suggests | devtools | * | 2.4.5 |
| Suggests | doSNOW | * | 1.0.20 |
| Suggests | DHARMa | * | 0.4.7 |
| Suggests | spelling | * | 2.3.1 |
| Suggests | showtext | * | 0.9.7 |
| Suggests | knitr | * | 1.49 |
Here is the information of the R & RStudio environment used to run all the analyses:
sessionInfo()
#> R version 4.4.2 (2024-10-31)
#> Platform: x86_64-redhat-linux-gnu
#> Running under: Fedora Linux 41 (KDE Plasma)
#>
#> Matrix products: default
#> BLAS/LAPACK: FlexiBLAS OPENBLAS-OPENMP; LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: Europe/Berlin
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices datasets utils methods base
#>
#> other attached packages:
#> [1] mallaRd_0.1.0
#>
#> loaded via a namespace (and not attached):
#> [1] Matrix_1.7-1 gtable_0.3.6 crayon_1.5.3
#> [4] dplyr_1.1.4 compiler_4.4.2 tidyselect_1.2.1
#> [7] Rcpp_1.0.13-1 slam_0.1-53 parallel_4.4.2
#> [10] scales_1.3.0 boot_1.3-31 yaml_2.3.10
#> [13] fastmap_1.2.0 lattice_0.22-6 spaMM_4.5.0
#> [16] ggplot2_3.5.1 R6_2.5.1 generics_0.1.3
#> [19] knitr_1.49 backports_1.5.0 MASS_7.3-61
#> [22] checkmate_2.3.2 ROI_1.0-1 tibble_3.2.1
#> [25] desc_1.4.3 munsell_0.5.1 minqa_1.2.8
#> [28] pillar_1.9.0 rlang_1.1.4 utf8_1.2.4
#> [31] xfun_0.49 registry_0.5-1 cli_3.6.3
#> [34] magrittr_2.0.3 digest_0.6.37 grid_4.4.2
#> [37] rstudioapi_0.17.1 pbapply_1.7-2 CoprManager_0.5.7
#> [40] lifecycle_1.0.4 nlme_3.1-166 vctrs_0.6.5
#> [43] proxy_0.4-27 evaluate_1.0.1 glue_1.8.0
#> [46] numDeriv_2016.8-1.1 fansi_1.0.6 colorspace_2.1-1
#> [49] rmarkdown_2.29 tools_4.4.2 pkgconfig_2.0.3
#> [52] htmltools_0.5.8.1