Site map
Last updated: 2021-07-03
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Knit directory: wildlife-bacteria/
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Map usingozmaps
Create map of study sites using ozmaps package and associated data package for subdivision of regions.
Link to useful tutorial in the ggplot2 book here.
Load packages
#ozmaps data not on CRAN
#devtools::install_github("mdsumner/ozmaps.data")
pkgs <- c("ozmaps", "sf", "sp", "dplyr", "rgdal",
"raster", "ggplot2", "viridis", "readr",
"paletteer", "rmapshaper", "ggrepel",
"tidyverse", "ozmaps.data", "readxl")
lapply(pkgs, require, character.only = TRUE)Import data
site_map <- read_excel("data/site_map.xlsx")
site_map_lab = column_to_rownames(site_map, var = "Site name")Create large base map for Australia with study sites
oz_states <- ozmaps::ozmap_states
ggplot(oz_states) +
geom_sf() +
coord_sf()
oz_states <- ozmaps::ozmap_states %>% filter(NAME != "Other Territories")
oz_votes <- rmapshaper::ms_simplify(ozmaps::abs_ced)
ggplot() +
geom_sf(data = oz_states, mapping = aes(fill = NAME), show.legend = FALSE) +
geom_sf(data = oz_votes, fill = NA) +
coord_sf()
# large map
map1 = ggplot() +
geom_sf(data = oz_votes) +
geom_sf(data = oz_states, colour = "black", fill = "NA") +
geom_point(data = site_map_lab, mapping = aes(x = lon, y = lat, color = Site, shape=Site, size= 3)) +
coord_sf() + theme_classic() + theme(legend.position = "none", axis.title.x = element_blank(), axis.title.y = element_blank()) + xlim (114,155)
map1
Create insert maps for Perth and Sydney regions
# base map for inserts
map2 = ggplot() +
geom_sf(data = oz_votes) +
geom_sf(data = oz_states, colour = "black", fill = "NA") +
geom_point(data = site_map_lab, mapping = aes(x = lon, y = lat, color = Site, shape=Site, size= Size)) +
coord_sf() + theme_classic() + theme(legend.position = "none", axis.title.x = element_blank(), axis.title.y = element_blank())
# Sydney region
map3 = map2 + coord_sf(xlim = c(150, 152), ylim = c(-35, -33.0)) + theme(legend.position = "none") + theme(axis.title.x = element_blank(), axis.title.y = element_blank())Coordinate system already present. Adding new coordinate system, which will replace the existing one.map3
# Perth region
map4 = map2 + coord_sf(xlim = c(115, 117), ylim = c(-32.5, -31)) + theme(legend.position = "none") + theme(axis.title.x = element_blank(), axis.title.y = element_blank())Coordinate system already present. Adding new coordinate system, which will replace the existing one.map4
Save maps
ggsave("map_base.pdf", plot = map1, path = "output/plots", width = 30, height = 15, units = "cm")
ggsave("map_NSW.pdf", plot = map3, path = "output/plots", width = 10, height = 10, units = "cm")
ggsave("map_WA.pdf", plot = map4, path = "output/plots", width = 10, height = 10, units = "cm")Capital cities for reference
oz_capitals <- tibble::tribble(
~city, ~lat, ~lon,
"Sydney", -33.8688, 151.2093,
"Melbourne", -37.8136, 144.9631,
"Brisbane", -27.4698, 153.0251,
"Adelaide", -34.9285, 138.6007,
"Perth", -31.9505, 115.8605,
"Hobart", -42.8821, 147.3272,
"Canberra", -35.2809, 149.1300,
"Darwin", -12.4634, 130.8456,
)
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.3.1 ozmaps.data_0.0.1 forcats_0.5.1 stringr_1.4.0
[5] purrr_0.3.4 tidyr_1.1.2 tibble_3.1.0 tidyverse_1.3.0
[9] ggrepel_0.9.1 rmapshaper_0.4.4 paletteer_1.3.0 readr_1.4.0
[13] viridis_0.5.1 viridisLite_0.3.0 ggplot2_3.3.3 raster_3.4-5
[17] rgdal_1.5-23 dplyr_1.0.5 sp_1.4-5 sf_0.9-7
[21] ozmaps_0.3.6 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] fs_1.5.0 lubridate_1.7.10 httr_1.4.2 rprojroot_2.0.2
[5] tools_4.0.3 backports_1.2.1 bslib_0.2.4.9001 utf8_1.2.1
[9] R6_2.5.0 KernSmooth_2.23-18 lazyeval_0.2.2 rgeos_0.5-5
[13] DBI_1.1.1 colorspace_2.0-0 withr_2.4.1 tidyselect_1.1.0
[17] gridExtra_2.3 curl_4.3 compiler_4.0.3 git2r_0.28.0
[21] cli_2.3.1 rvest_0.3.6 geojsonsf_2.0.1 xml2_1.3.2
[25] sass_0.3.1 scales_1.1.1 classInt_0.4-3 digest_0.6.27
[29] foreign_0.8-81 rmarkdown_2.7.2 pkgconfig_2.0.3 htmltools_0.5.1.1
[33] highr_0.8 dbplyr_2.1.0 jsonvalidate_1.1.0 rlang_0.4.10
[37] rstudioapi_0.13 httpcode_0.3.0 jquerylib_0.1.3 generics_0.1.0
[41] farver_2.0.3 jsonlite_1.7.2 magrittr_2.0.1 Rcpp_1.0.6
[45] munsell_0.5.0 fansi_0.4.2 lifecycle_1.0.0 stringi_1.5.3
[49] whisker_0.4 yaml_2.2.1 jqr_1.2.0 oz_1.0-21
[53] maptools_1.0-2 grid_4.0.3 promises_1.2.0.1 geojsonio_0.9.4
[57] crayon_1.4.1 lattice_0.20-41 haven_2.3.1 geojson_0.3.4
[61] hms_1.0.0 knitr_1.31 pillar_1.5.1 geojsonlint_0.4.0
[65] codetools_0.2-18 crul_1.1.0 reprex_1.0.0 glue_1.4.2
[69] evaluate_0.14 V8_3.4.0 modelr_0.1.8 vctrs_0.3.7
[73] httpuv_1.5.5 cellranger_1.1.0 gtable_0.3.0 rematch2_2.1.2
[77] assertthat_0.2.1 xfun_0.21 broom_0.7.5 e1071_1.7-4
[81] later_1.1.0.1 class_7.3-18 units_0.7-0 ellipsis_0.3.1