courtiol / mallard

Analysis for a paper on breeding site selection and breeding output of mallards living in Berlin, Germany

mallaRd

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).

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	4/1/2005	mallard_duck	729	52.52495	13.30129	courtyard	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	4/4/2005	mallard_duck	1116	52.60742	13.23319	other	NA	NA	NA			1		NA	NA	929.5084	1	1	158.7811	25.50148	72.82336	23.18329	131.7400	14.51628
3	2005	4/25/2005	mallard_duck	720	52.52412	13.34539	roof_terrace	NA	NA	NA			8		NA	NA	127.3921	1	1	843.3160	127.61779	743.98803	147.67042	858.6173	78.80484
11	2005	4/26/2005	mallard_duck	555	52.51043	13.19960	balcony	NA	750	257	4/26/2005	1/11/1900	12	JC54565	52.51088	13.20227	162.9485	1	1	734.5966	23.64657	529.66019	21.79157	339.1518	26.49088
12	2005	4/27/2005	mallard_duck	991	52.56289	13.20875	courtyard	NA	NA	NA			3		NA	NA	426.5027	1	1	0.0000	138.54895	117.49123	67.91985	111.4260	38.82886
13	2005	4/29/2005	mallard_duck	115	52.44341	13.58433	balcony	NA	830	272	4/29/2005		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	*	1.33.1
Imports	ggplot2	*	3.5.0
Imports	sf	*	1.0.15
Imports	showtext	*	0.9.7
Imports	spaMM	*	4.4.23.1
Imports	tibble	*	3.2.1
Imports	tidyr	*	1.3.1
Imports	tidyselect	*	1.2.1
Suggests	desc	*	1.4.3
Suggests	doSNOW	*	1.0.20
Suggests	DHARMa	*	0.4.6
Suggests	spelling	*	2.3.0
Suggests	devtools	*	2.4.5
Suggests	knitr	*	1.45

Here is the information of the R & RStudio environment used to run all the analyses:

sessionInfo()
#> R version 4.3.1 (2023-06-16)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Debian GNU/Linux 12 (bookworm)
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3;  LAPACK version 3.11.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
#>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
#>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_GB.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] Matrix_1.6-5        gtable_0.3.4        dplyr_1.1.4        
#>  [4] compiler_4.3.1      crayon_1.5.2        tidyselect_1.2.1   
#>  [7] Rcpp_1.0.12         slam_0.1-50         parallel_4.3.1     
#> [10] scales_1.3.0        boot_1.3-30         yaml_2.3.8         
#> [13] fastmap_1.1.1       lattice_0.22-5      spaMM_4.4.23.1     
#> [16] ggplot2_3.5.0       R6_2.5.1            generics_0.1.3     
#> [19] knitr_1.45          backports_1.4.1     MASS_7.3-60.0.1    
#> [22] checkmate_2.3.1     ROI_1.0-1           tibble_3.2.1       
#> [25] desc_1.4.3          munsell_0.5.0       minqa_1.2.6        
#> [28] pillar_1.9.0        rlang_1.1.3         utf8_1.2.4         
#> [31] xfun_0.42           registry_0.5-1      cli_3.6.2          
#> [34] magrittr_2.0.3      digest_0.6.35       grid_4.3.1         
#> [37] rstudioapi_0.15.0   pbapply_1.7-2       lifecycle_1.0.4    
#> [40] nlme_3.1-164        vctrs_0.6.5         proxy_0.4-27       
#> [43] evaluate_0.23       glue_1.7.0          numDeriv_2016.8-1.1
#> [46] fansi_1.0.6         colorspace_2.1-0    rmarkdown_2.26     
#> [49] tools_4.3.1         pkgconfig_2.0.3     htmltools_0.5.7