Mapping

workflowr

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Last updated: 2022-02-19

Checks: 7 0

Knit directory: wildlife-ticks/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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Repository version: cf0cae8

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The results in this page were generated with repository version cf0cae8. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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Untracked files:
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Unstaged changes:
    Modified:   analysis/_site.yml
    Modified:   output/plots/combined-map1.pdf
    Modified:   output/plots/combined-map2.pdf
    Modified:   output/plots/combined-map3.pdf
    Modified:   output/plots/combined-map4.pdf
    Modified:   output/plots/map-ixhol1.pdf
    Modified:   output/plots/map-ixhol2.pdf
    Modified:   output/plots/map-ixtas1.pdf
    Modified:   output/plots/map-ixtas2.pdf

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/mapping.Rmd) and HTML (docs/mapping.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	4d29a72	Siobhon Egan	2022-02-19	re-build to consolidate related data
html	4d29a72	Siobhon Egan	2022-02-19	re-build to consolidate related data

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Map usingozmaps

Reference

Load libraries

library(ozmaps)
library(sf)

Linking to GEOS 3.8.1, GDAL 3.2.1, PROJ 7.2.1

library(sp)
library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

library(rgdal)

Please note that rgdal will be retired by the end of 2023,
plan transition to sf/stars/terra functions using GDAL and PROJ
at your earliest convenience.

rgdal: version: 1.5-28, (SVN revision 1158)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.2.1, released 2020/12/29
Path to GDAL shared files: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/gdal
GDAL binary built with GEOS: TRUE 
Loaded PROJ runtime: Rel. 7.2.1, January 1st, 2021, [PJ_VERSION: 721]
Path to PROJ shared files: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:1.4-6
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
Overwritten PROJ_LIB was /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/proj

library(raster)

Attaching package: 'raster'

The following object is masked from 'package:dplyr':

    select

library(ggplot2)
library(readr)

Warning: replacing previous import 'lifecycle::last_warnings' by
'rlang::last_warnings' when loading 'hms'

library(paletteer)
library(rmapshaper)

Registered S3 method overwritten by 'geojsonlint':
  method         from 
  print.location dplyr

library(ggrepel)
library(tidyverse)

── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──

✓ tibble  3.1.4     ✓ stringr 1.4.0
✓ tidyr   1.1.3     ✓ forcats 0.5.1
✓ purrr   0.3.4     

── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
x tidyr::extract() masks raster::extract()
x dplyr::filter()  masks stats::filter()
x dplyr::lag()     masks stats::lag()
x raster::select() masks dplyr::select()

# ozmaps data not on CRAN
#devtools::install_github("mdsumner/ozmaps.data")
#library(ozmaps.data)
library(readxl)
library(ggpubr)

Attaching package: 'ggpubr'

The following object is masked from 'package:raster':

    rotate

Configure base mapping of Australia

oz_states <- ozmaps::ozmap_states
ggplot(oz_states) + 
  geom_sf() + 
  coord_sf()

Past versions of unnamed-chunk-2-1.png

Version	Author	Date
4d29a72	Siobhon Egan	2022-02-19

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()

Past versions of unnamed-chunk-2-2.png

Version	Author	Date
4d29a72	Siobhon Egan	2022-02-19

Mapping Amblyomma triguttatum records

Load data

obs.data.atrig <- read_csv("data/tick_records/atrig/compiled_record_list.csv")

New names:
* Identifier -> Identifier...1
* Identifier -> Identifier...20

Rows: 926 Columns: 21
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (19): Identifier...1, Source, State, Locality_1, Locaity_2, Lat_lon, Col...
dbl  (2): Lat, Lon

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

obs.data.atrig$Subspecies <- obs.data.atrig$Tick_subspecies

**Make single map with point showing

Create a map showing different subspecies of Am. triguttatum

Make map with state and voting outlines, overlay with all observation data

Atrig1 = ggplot() + 
  geom_sf(data = oz_votes) + 
  geom_sf(data = oz_states, colour = "black", fill = "NA") + 
  geom_point(data = obs.data.atrig, mapping = aes(x = Lon, y = Lat, shape=Subspecies, color =Subspecies, stroke = 1)) + 
  coord_sf() + theme_bw() + 
  theme(axis.title.x = element_blank(), axis.title.y = element_blank())  +
  scale_color_manual(values=c("#252525", "#1b9e77", "#e7298a", "#66a61e", "#7570b3")) +
  scale_shape_manual(values=c(16, 17, 15, 3, 7)) + 
  xlim (111,155)
Atrig1

Warning: Removed 47 rows containing missing values (geom_point).

Past versions of unnamed-chunk-4-1.png

Version	Author	Date
4d29a72	Siobhon Egan	2022-02-19

# Map without legend
Atrig2 <- Atrig1 + theme(legend.position = "none")

# Save
ggsave("map-atrig-comb.pdf", plot = Atrig1, path = "output/plots", width = 30, height = 15, units = "cm")
ggsave("map-atrig-comb-nolegend.pdf", plot = Atrig2, path = "output/plots", width = 30, height = 15, units = "cm")

Facet by subspecies

# Filter out data where subspecies is not specified
obs.data.ssp = filter(obs.data.atrig, Subspecies != "Not specified")

# make master plot
Atrig3 = ggplot() + 
  geom_sf(data = oz_votes) + 
  geom_sf(data = oz_states, colour = "black", fill = "NA") + 
  geom_point(data = obs.data.ssp, mapping = aes(x = Lon, y = Lat, shape=Subspecies, color =Subspecies, stroke = 1)) + 
  coord_sf() + theme_bw() + 
  theme(legend.position = "none", axis.title.x = element_blank(), axis.title.y = element_blank()) + 
  scale_color_manual(values=c("#1b9e77", "#e7298a", "#66a61e", "#7570b3")) +
  scale_shape_manual(values=c(17, 15, 3, 7)) + xlim (111,155)
# Facet
Atrig3 = Atrig3 + facet_wrap(~ Subspecies)
Atrig3

Warning: Removed 30 rows containing missing values (geom_point).

Past versions of unnamed-chunk-6-1.png

Version	Author	Date
4d29a72	Siobhon Egan	2022-02-19

# Save
ggsave("map-atrig-facet.pdf", plot = Atrig3, path = "output/plots", width = 30, height = 20, units = "cm")

Simple map

Make simple map for summary slides

Atrig4 = ggplot() + 
  geom_sf(data = oz_votes) + 
  geom_sf(data = oz_states, colour = "black", fill = "NA") + 
  geom_point(data = obs.data.atrig, mapping = aes(x = Lon, y = Lat, color="#7570b3", stroke = 1))
# Customise scale
Atrig4 = Atrig4 + coord_sf() + theme_bw() + theme(legend.position = "none", axis.title.x = element_blank(), axis.title.y = element_blank())  + scale_color_manual(values=c("#7570b3"))
# Remove scale
Atrig5 = Atrig4 + coord_sf() + theme_void() + theme(legend.position = "none")  + scale_color_manual(values=c("#7570b3"))

Coordinate system already present. Adding new coordinate system, which will replace the existing one.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

Save maps

ggsave("map-atrig-simple1.pdf", plot = Atrig4, path = "output/plots", width = 30, height = 15, units = "cm")
ggsave("map-atrig-simple2.pdf", plot = Atrig5, path = "output/plots", width = 30, height = 15, units = "cm")

Map of Ixodes holocyclus records

Load data

# raw ala records
ixhol.ala <- read_csv(file = "data/tick_records/ixhol/Ixhol-records-2021-02-23/records-2021-02-23.csv")

Rows: 321 Columns: 57
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr  (40): Record ID, Catalogue Number, Taxon Concept GUID, Scientific Name ...
dbl   (8): Latitude - original, Longitude - original, Latitude, Longitude, C...
lgl   (8): Vernacular name, Subspecies, Coordinate Precision, IMCRA 4 Region...
date  (1): Event Date - parsed

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

# curated ala records - removed likely incorrect (or as a result of travel?) records from WA, SA and TAS. 
ixhol.alacur <- read_csv(file = "data/tick_records/ixhol/Ixhol-records-2021-02-23/records-2021-02-23-curated.csv")

Rows: 316 Columns: 57
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (39): Record ID, Catalogue Number, Taxon Concept GUID, Scientific Name -...
dbl (10): Latitude - original, Longitude - original, Latitude, Longitude, Co...
lgl  (8): Vernacular name, Subspecies, Coordinate Precision, IMCRA 4 Regions...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Make map with state and voting outlines, overlay with all observation data

Ixhol = ggplot() + 
  geom_sf(data = oz_votes) + 
  geom_sf(data = oz_states, colour = "black", fill = "NA") + 
  geom_point(data = ixhol.alacur, mapping = aes(x = Longitude, y = Latitude, color="#d95f02", stroke = 1))
# Customise scale
Ixhol1 = Ixhol + coord_sf() + theme_bw() + theme(legend.position = "none", axis.title.x = element_blank(), axis.title.y = element_blank())  + scale_color_manual(values=c("#d95f02"))
Ixhol1

Warning: Removed 56 rows containing missing values (geom_point).

Past versions of unnamed-chunk-11-1.png

Version	Author	Date
4d29a72	Siobhon Egan	2022-02-19

# Remove scale
Ixhol2 = Ixhol + coord_sf() + theme_void() + theme(legend.position = "none")  + scale_color_manual(values=c("#d95f02"))

Save maps

ggsave("map-ixhol1.pdf", plot = Ixhol1, path = "output/plots", width = 30, height = 15, units = "cm")

Warning: Removed 56 rows containing missing values (geom_point).

ggsave("map-ixhol2.pdf", plot = Ixhol2, path = "output/plots", width = 30, height = 15, units = "cm")

Warning: Removed 56 rows containing missing values (geom_point).

Map of Ixodes tasmani records

Load data

# curated records
obs.data.ixhol <- read_excel("data/tick_records/ixtas/curated.xlsx")

New names:
* Identifier -> Identifier...1
* Identifier -> Identifier...20

Make map with state and voting outlines, overlay with all observation data

Ixtas = ggplot() + 
  geom_sf(data = oz_votes) + 
  geom_sf(data = oz_states, colour = "black", fill = "NA") + 
  geom_point(data = obs.data.ixhol, mapping = aes(x = Lon, y = Lat, color="#a6761d", stroke = 1))
# Customise scale
Ixtas1 = Ixtas + coord_sf() + theme_bw() + theme(legend.position = "none", axis.title.x = element_blank(), axis.title.y = element_blank())  + scale_color_manual(values=c("#a6761d"))
Ixtas1

Warning: Removed 136 rows containing missing values (geom_point).

Past versions of unnamed-chunk-14-1.png

Version	Author	Date
4d29a72	Siobhon Egan	2022-02-19

# Remove scale
Ixtas2 = Ixtas1 + coord_sf() + theme_void() + theme(legend.position = "none")  + scale_color_manual(values=c("#a6761d"))

Coordinate system already present. Adding new coordinate system, which will replace the existing one.

Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

Save maps

ggsave("map-ixtas1.pdf", plot = Ixtas1, path = "output/plots", width = 30, height = 15, units = "cm")

Warning: Removed 136 rows containing missing values (geom_point).

ggsave("map-ixtas2.pdf", plot = Ixtas2, path = "output/plots", width = 30, height = 15, units = "cm")

Warning: Removed 136 rows containing missing values (geom_point).

Combined map

Make combine map of Am. trig, Ix. hol and Ix. tas.

figure1 <- ggarrange(Atrig2, Ixhol1, Ixtas1,
                    labels = c("A", "B", "C"),
                    ncol = 2, nrow = 2)

Warning: Removed 47 rows containing missing values (geom_point).

Warning: Removed 56 rows containing missing values (geom_point).

Warning: Removed 136 rows containing missing values (geom_point).

ggsave("combined-map1.pdf", plot = figure1, path = "output/plots", width = 30, height = 15, units = "cm")
figure1

Past versions of unnamed-chunk-16-1.png

Version	Author	Date
4d29a72	Siobhon Egan	2022-02-19

figure2 <- ggarrange(Atrig2, Ixhol1, Ixtas1,
                    labels = c("A", "B", "C"),
                    nrow = 3)

Warning: Removed 47 rows containing missing values (geom_point).

Warning: Removed 56 rows containing missing values (geom_point).

Warning: Removed 136 rows containing missing values (geom_point).

ggsave("combined-map2.pdf", plot = figure2, path = "output/plots", width = 30, height = 15, units = "cm")
figure2

Past versions of unnamed-chunk-16-2.png

Version	Author	Date
4d29a72	Siobhon Egan	2022-02-19

figure3 <- ggarrange(Atrig2, Ixhol1, Ixtas1,
                    labels = c("A", "B", "C"),
                    ncol = 3)

Warning: Removed 47 rows containing missing values (geom_point).

Warning: Removed 56 rows containing missing values (geom_point).

Warning: Removed 136 rows containing missing values (geom_point).

ggsave("combined-map3.pdf", plot = figure3, path = "output/plots", width = 30, height = 15, units = "cm")
figure3

Past versions of unnamed-chunk-16-3.png

Version	Author	Date
4d29a72	Siobhon Egan	2022-02-19

gp <- ggarrange(
  Atrig2,                # First row with line plot
  # Second row with box and dot plots
  ggarrange(Ixhol1, Ixtas1, ncol = 2, labels = c("B", "C")), 
  nrow = 2, 
  labels = "A"       # Label of the line plot
  ) 

Warning: Removed 56 rows containing missing values (geom_point).

Warning: Removed 136 rows containing missing values (geom_point).

Warning: Removed 47 rows containing missing values (geom_point).

gp

Past versions of unnamed-chunk-17-1.png

Version	Author	Date
4d29a72	Siobhon Egan	2022-02-19

ggsave("combined-map4.pdf", plot = gp, path = "output/plots", width = 30, height = 15, units = "cm")

Session information

sessionInfo()

R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] ggpubr_0.4.0     readxl_1.3.1     forcats_0.5.1    stringr_1.4.0   
 [5] purrr_0.3.4      tidyr_1.1.3      tibble_3.1.4     tidyverse_1.3.1 
 [9] ggrepel_0.9.1    rmapshaper_0.4.5 paletteer_1.4.0  readr_2.0.0     
[13] ggplot2_3.3.5    raster_3.4-13    rgdal_1.5-28     dplyr_1.0.7     
[17] sp_1.4-5         sf_1.0-2         ozmaps_0.4.5     workflowr_1.7.0 

loaded via a namespace (and not attached):
  [1] colorspace_2.0-2   ggsignif_0.6.2     ellipsis_0.3.2    
  [4] class_7.3-19       rio_0.5.27         rprojroot_2.0.2   
  [7] fs_1.5.0           httpcode_0.3.0     rstudioapi_0.13   
 [10] proxy_0.4-26       farver_2.1.0       bit64_4.0.5       
 [13] fansi_0.5.0        lubridate_1.7.10   xml2_1.3.2        
 [16] codetools_0.2-18   knitr_1.37         geojsonlint_0.4.0 
 [19] jsonlite_1.7.2     broom_0.7.9        dbplyr_2.1.1      
 [22] rgeos_0.5-9        compiler_4.1.2     httr_1.4.2        
 [25] backports_1.4.0    lazyeval_0.2.2     assertthat_0.2.1  
 [28] fastmap_1.1.0      cli_3.0.1          later_1.3.0       
 [31] s2_1.0.6           htmltools_0.5.2    tools_4.1.2       
 [34] gtable_0.3.0       glue_1.5.1         geojson_0.3.4     
 [37] wk_0.5.0           V8_4.1.0           Rcpp_1.0.8        
 [40] carData_3.0-4      cellranger_1.1.0   oz_1.0-21         
 [43] jquerylib_0.1.4    vctrs_0.3.8        crul_1.2.0        
 [46] xfun_0.28          ps_1.6.0           openxlsx_4.2.4    
 [49] rvest_1.0.1        lifecycle_1.0.0    rstatix_0.7.0     
 [52] jqr_1.2.2          getPass_0.2-2      scales_1.1.1      
 [55] vroom_1.5.7        hms_1.1.0          promises_1.2.0.1  
 [58] parallel_4.1.2     rematch2_2.1.2     yaml_2.2.1        
 [61] curl_4.3.2         sass_0.4.0         stringi_1.7.6     
 [64] jsonvalidate_1.3.2 highr_0.9          maptools_1.1-1    
 [67] e1071_1.7-8        zip_2.2.0          rlang_1.0.0       
 [70] pkgconfig_2.0.3    evaluate_0.14      lattice_0.20-45   
 [73] labeling_0.4.2     cowplot_1.1.1      bit_4.0.4         
 [76] processx_3.5.2     tidyselect_1.1.1   geojsonsf_2.0.1   
 [79] magrittr_2.0.2     R6_2.5.1           geojsonio_0.9.4   
 [82] generics_0.1.0     DBI_1.1.1          pillar_1.6.2      
 [85] haven_2.4.3        whisker_0.4        foreign_0.8-81    
 [88] withr_2.4.2        units_0.7-2        abind_1.4-5       
 [91] modelr_0.1.8       crayon_1.4.2       car_3.0-11        
 [94] KernSmooth_2.23-20 utf8_1.2.2         tzdb_0.1.2        
 [97] rmarkdown_2.11     grid_4.1.2         data.table_1.14.0 
[100] callr_3.7.0        git2r_0.28.0       reprex_2.0.1      
[103] digest_0.6.29      classInt_0.4-3     httpuv_1.6.1      
[106] munsell_0.5.0      bslib_0.2.5.1     

Project website by Siobhon L. Egan, 2022. This site was created in R Markdown with workflowr