Author(s): Galina M. Jönsson
This repository contains all the code for:
Jönsson, G. M. (2020). Phenology change of British Lepioptera since 1900. Unpublished manucript.
I used specimen records from the Natural History Museum, London (NHM). The georeferenced NHM dataset is available via the NHM's iCollections. If you use it, please cite as folows:
Gordon L J Paterson; Sara Albuquerque; Vladimir Blagoderov; Steve Brooks et al. (2016). Dataset: iCollections. Natural History Museum Data Portal (data.nhm.ac.uk). https://doi.org/10.5519/0038559
I used the Met Office's HadUK-Grid dataset at 12 km resolution is derived from the associated 1km x 1km resolution, which spans the period from 1862 to 2017, and is avialable via CEDA archives (full citation below). I used the following climatic varibales:
- Mean monthly temperature (tas)
- Maximum monthly temperature (tasmax)
- Minimum monthly temperature (tasmin)
- Mean monthly precipitation (rainfall)
Met Office; Hollis, D.; McCarthy, M.; Kendon, M.; Legg, T.; Simpson, I. (2019): HadUK-Grid Gridded Climate Observations on a 12km grid over the UK, v1.0.0.0 (1862-2017). Centre for Environmental Data Analysis, 14 November 2019. doi:10.5285/dc2ef1e4f10144f29591c21051d99d39.
For reproducibility purposes, download all data and place it into the relevant data/-subfolder 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 machine as the analyses are computationally expensive and were run on high performance machines.
- 01-SpecimenData.Rdm summarises the NHM specimen data for eleven univoltine British butterfly species. For each speies used in analyses, I summarise the annual 10th and 19th percentile of julian record days, the range of annual records days and the first annual record day Julian day.
- 02-ClimateData.Rdm summarises the HadUK-Grid dataset's relevant climatic variables and WILL SUMMARISE RELEVANT CLIMATIC VARIABLES PER RECORD FOR ALL ELEVEN SPECIES
- 03-Analyses.Rdm WILL ANALYSE PHENOLOGY CHNAGE AND EFFECTS OF CLIMATIC VARIABLES ON PHENOLOGY AMONG THE ELEVEN SPECIES
- function-summarise_nc_tas.R
- function-summarise_nc_mintas.R
/figscontains the figures with file names matching those of the manuscript NONE YET*/outputcontains the empty subfolders/output/climate. For reproducibility purposes, format the raw HadUK-Grid datasets according to the code in/analyses/02-ClimateData.Rdmand place into/output/climate.
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)