Author(s): Galina M. Jönsson
This repository contains all the code and some data for:
Jönsson, G. M., Broad, G. R., Sumner, S. and Isaac, N. J. B. (in press.). A century of social wasp occupancy trends from natural history collections: spatiotemporal resolutions have little effect on model performance. Insect Conservation and Diversity. doi:10.1111/icad.12494.
We used two sources of data: specimen records from the Natural History Museum, London (NHM), and observational records from the Bees, Ants and Wasps Recording Society (BWARS). The BWARS data is available upon request from:
The National Biodiversity Network
Unit F, 14-18 St. Mary’s Gate
Lace Market
Nottingham, UK
Telephone: +44 (0)115 850 0177
Email: [email protected]
For reproducibility purposes, download this and place it into the data/rawdata/ folder to rerun our analyses.
The georeferenced NHM dataset is available via the NHM data portal. If you use it, please cite as folows:
Galina M. Jönsson (2020). Dataset: Georeferenced UK social wasps. Natural History Museum Data Portal (data.nhm.ac.uk). https://doi.org/10.5519/0082541
In this repository, we have uploaded the georeferenced NHM data for all Vespula vulgaris, Vespula germanica and Vespa crabro specimens in the folder /data/rawData, as well as the cleaned NHM data in the folder /data/cleanData, and auxiliary data in the folder /data/auxiliaryData.
We were unable to upload the formatted date files and the model output files to GitHub because the files are too large. For reproducibility purposes, format the raw data according to the code in /analyses/02-format-data.Rdm and place into the /output/formattedData. All model outputs are available via the NHM data portal. If you use it, please cite as folows:
Galina M. Jönsson (2020). Dataset: Historical wasp occupancies: model outputs. Natural History Museum Data Portal (data.nhm.ac.uk). https://doi.org/10.5519/0055095
For reproducibility purposes, download it and place it into the /output/modelOutput folder to rerun our analyses.
The analyses code is divided into .Rmd files that run the analyses for each section of the manuscript/supplementary materials, more detailed scripts for some functions used in analyses and called by the .Rmd files, and scripts for the figures found in the manuscript.
Note that throughout I've commented out write.csv and saveRDS commands in order to not clog up your machine. For code chunks that run the models, I've set eval to FALSE, again, to not clog up your macine as the analyses are computationally expensive and were run on high performance machines.
- 01-data-cleaning-Rdm cleans and standardises the georeferenced data.
- 02-format-model.Rdm formats the clean data and runs the models.
- 03-summaries.Rmd summarises the data used in models and model outputs.
- figure-record_numbers.R
- figure-spatial_cover.R
- figure-spatial_species.R
- figure-occupancy_estimates.R
- figure-detectionProbability_estimates.R
- figure-DIC.R
- figure-spatial_species.R
- figure-pD.R
- figure-deviance.R
- figure-NortherlySites.R
- figure-graphical_abstract.R
- function-readRDS_multi.R
- function-summarise_Rhat.R
- function-detProbChange.R
/figscontains the figures with file names matching those of the manuscript/outputcontains the empty subfolders/output/formattedDataand/output/modelOutputs, as well as the subfolder/output/summaryTablesthat contains tables summarising both the data used in models and model outputs. For reproducibility purposes, format the raw data according to the code in/analyses/02-format-data.Rdmand place into/output/formattedData, and download the model outputs and place into/output/modelOutputs. All model outputs are available via the NHM data portal.
For reproducibility purposes, here is the output of devtools::session_info() used to perform the analyses in the publication.
─ Session info ───────────────────────────────────────────────────────────────────────────────
setting value
version R version 3.5.2 (2018-12-20)
os macOS Mojave 10.14.3
system x86_64, darwin15.6.0
ui RStudio
language (EN)
collate en_GB.UTF-8
ctype en_GB.UTF-8
tz Europe/London
date 2020-01-27
─ Packages ───────────────────────────────────────────────────────────────────────────────────
package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 3.5.0)
AICcmodavg * 2.2-2 2019-05-29 [1] CRAN (R 3.5.2)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.5.2)
backports 1.1.5 2019-10-02 [1] CRAN (R 3.5.2)
boot * 1.3-23 2019-07-05 [1] CRAN (R 3.5.2)
BRCmap * 0.10.3.3 2017-11-13 [1] local
callr 3.3.2 2019-09-22 [1] CRAN (R 3.5.2)
cli 1.1.0 2019-03-19 [1] CRAN (R 3.5.2)
coda 0.19-3 2019-07-05 [1] CRAN (R 3.5.2)
codetools 0.2-16 2018-12-24 [1] CRAN (R 3.5.2)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.5.2)
cowplot * 1.0.0 2019-07-11 [1] CRAN (R 3.5.2)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.0)
devtools * 2.2.1 2019-09-24 [1] CRAN (R 3.5.2)
digest 0.6.22 2019-10-21 [1] CRAN (R 3.5.2)
dplyr * 0.8.3 2019-07-04 [1] CRAN (R 3.5.2)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.5.2)
evaluate 0.14 2019-05-28 [1] CRAN (R 3.5.2)
foreign 0.8-72 2019-08-02 [1] CRAN (R 3.5.2)
fs 1.3.1 2019-05-06 [1] CRAN (R 3.5.2)
gdata 2.18.0 2017-06-06 [1] CRAN (R 3.5.0)
ggplot2 * 3.2.1 2019-08-10 [1] CRAN (R 3.5.2)
ggthemes * 4.2.0 2019-05-13 [1] CRAN (R 3.5.2)
glue 1.3.1 2019-03-12 [1] CRAN (R 3.5.2)
gridExtra * 2.3 2017-09-09 [1] CRAN (R 3.5.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.5.2)
gtools 3.8.1 2018-06-26 [1] CRAN (R 3.5.0)
hms 0.5.2 2019-10-30 [1] CRAN (R 3.5.2)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.5.2)
httr 1.4.1 2019-08-05 [1] CRAN (R 3.5.2)
kableExtra * 1.1.0 2019-03-16 [1] CRAN (R 3.5.2)
knitr * 1.26 2019-11-12 [1] CRAN (R 3.5.2)
lattice 0.20-38 2018-11-04 [1] CRAN (R 3.5.2)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.5.2)
LearnBayes 2.15.1 2018-03-18 [1] CRAN (R 3.5.0)
lifecycle 0.1.0 2019-08-01 [1] CRAN (R 3.5.2)
lme4 * 1.1-21 2019-03-05 [1] CRAN (R 3.5.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.0)
maptools * 0.9-8 2019-10-05 [1] CRAN (R 3.5.2)
MASS 7.3-51.4 2019-03-31 [1] CRAN (R 3.5.2)
Matrix * 1.2-17 2019-03-22 [1] CRAN (R 3.5.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.0)
minqa 1.2.4 2014-10-09 [1] CRAN (R 3.5.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.0)
nlme 3.1-142 2019-11-07 [1] CRAN (R 3.5.2)
nloptr 1.2.1 2018-10-03 [1] CRAN (R 3.5.0)
pillar 1.4.2 2019-06-29 [1] CRAN (R 3.5.2)
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.5.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.5.2)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.0)
plyr * 1.8.4 2016-06-08 [1] CRAN (R 3.5.0)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.0)
processx 3.4.1 2019-07-18 [1] CRAN (R 3.5.2)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.5.0)
purrr 0.3.3 2019-10-18 [1] CRAN (R 3.5.2)
R2jags 0.5-7 2015-08-23 [1] CRAN (R 3.5.0)
R2WinBUGS 2.1-21 2015-07-30 [1] CRAN (R 3.5.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 3.5.2)
raster 3.0-7 2019-09-24 [1] CRAN (R 3.5.2)
Rcpp 1.0.3 2019-11-08 [1] CRAN (R 3.5.2)
readr 1.3.1 2018-12-21 [1] CRAN (R 3.5.0)
remotes 2.1.0 2019-06-24 [1] CRAN (R 3.5.2)
reshape2 * 1.4.3 2017-12-11 [1] CRAN (R 3.5.0)
rgdal * 1.4-7 2019-10-28 [1] CRAN (R 3.5.2)
rgeos * 0.5-2 2019-10-03 [1] CRAN (R 3.5.2)
rjags 4-10 2019-11-06 [1] CRAN (R 3.5.2)
rlang 0.4.1 2019-10-24 [1] CRAN (R 3.5.2)
rmarkdown 1.17 2019-11-13 [1] CRAN (R 3.5.2)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.0)
rstudioapi 0.10 2019-03-19 [1] CRAN (R 3.5.2)
rvest 0.3.5 2019-11-08 [1] CRAN (R 3.5.2)
scales 1.1.0 2019-11-18 [1] CRAN (R 3.5.2)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.0)
sp * 1.3-2 2019-11-07 [1] CRAN (R 3.5.2)
sparta * 0.2.07 2019-12-19 [1] Github (BiologicalRecordsCentre/sparta@9c4312f)
stringi 1.4.3 2019-03-12 [1] CRAN (R 3.5.2)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.5.2)
survival 3.1-7 2019-11-09 [1] CRAN (R 3.5.2)
testthat 2.3.0 2019-11-05 [1] CRAN (R 3.5.2)
tibble 2.1.3 2019-06-06 [1] CRAN (R 3.5.2)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.0)
unmarked 0.13-0 2019-11-12 [1] CRAN (R 3.5.2)
usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.5.2)
vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.5.2)
VGAM 1.1-1 2019-02-18 [1] CRAN (R 3.5.2)
viridis * 0.5.1 2018-03-29 [1] CRAN (R 3.5.0)
viridisLite * 0.3.0 2018-02-01 [1] CRAN (R 3.5.0)
webshot 0.5.1 2018-09-28 [1] CRAN (R 3.5.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.0)
xfun 0.11 2019-11-12 [1] CRAN (R 3.5.2)
xml2 1.2.2 2019-08-09 [1] CRAN (R 3.5.2)
xtable 1.8-4 2019-04-21 [1] CRAN (R 3.5.2)
yaml 2.2.0 2018-07-25 [1] CRAN (R 3.5.0)
zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.5.0)