mallaRd

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).

Installation and usage

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 package

Then load the package in your R session and check the main help page where we placed all analyses:

load("mallaRd")
?mallaRd

Raw data

You 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

Developer corner

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