Field Sites

1.0 Overview

Site map templates to help field teams navigate a site, illustrating settlements, boundaries, and access routs, and locator maps showing geographic locations within local and national contexts.

1.1 Site Maps

Import AOI

crs_master = sf::st_crs('epsg:4326')
aoi_site   = sf::read_sf("../assets/inputs/chilwa_watershed_4326.shp") |>
  sf::st_cast() |> sf::st_transform(crs_master)
bbox_site  = terrainr::add_bbox_buffer(aoi_site, 20000, "meters")
vbox_site = terra::vect(bbox_site)

tmap::tmap_mode("view")
tmap::tm_shape(aoi_site) +
  tmap::tm_borders(col = "red") +
  tmap::tm_basemap("Esri.WorldImagery")

Figure 1a: Interactive map showing project boundary and ESRI’s basemap

Import Basemap

# zoom = 12 sources basemap at scale of 1:150,000
basemap_150k = maptiles::get_tiles(
  bbox_site, 
  zoom      = 10, 
  crop      = T,
  provider  = "OpenTopoMap"
)

tmap::tmap_mode("view")
tmap::tm_shape(basemap_150k) + tmap::tm_rgb() + 
  tmap::tm_shape(aoi_site) +
  tmap::tm_borders(col="red")

Figure 1b: Site map showing project boundary and downloaded basemap OpenTopoMap

Build Map

tmap::tmap_mode("plot")
site_map = tmap::tm_shape(basemap_150k) + tmap::tm_rgb() + 
  tmap::tm_shape(aoi_site) +
  tmap::tm_borders(lwd = 1, col = "red") +
  tmap::tm_graticules(lines=T,labels.rot=c(0,90),lwd=0.2) +
  tmap::tm_credits("EPSG:4326", position = c("left", "bottom")) +
  tmap::tm_scale_bar(
    c(0, 10, 20, 40), 
    position = c("RIGHT", "BOTTOM"), 
    text.size = .5
    ) +
  tmap::tm_compass(
    type = "4star", size = 1.5,
    color.dark = "gray60", text.color = "gray60",
    position = c("left", "top")
    )

Save output

# `width` & `height` controls output resolution 
# `dpi` controls size of map attributes relative to output resolution
tmap::tmap_save(site_map, width=15120, height=15120, asp=0, dpi=600,
  "/Users/seamus/Repos/map-templates/assets/outputs/01-site-draft.png"
  )
site_map

Figure 1c: Site Map rendered with customized attributes and resolution (15120x15120)

1.2 Locator Maps

Import AOI

aoi_country = giscoR::gisco_get_countries(country = "Malawi", resolution = "3") |>
  st_cast() |> st_transform(crs_master)
aoi_region = giscoR::gisco_get_countries(
  country = c("Malawi", "Zambia", "Tanzania", "Mozambique"), resolution = "3") |>
  st_cast() |> st_transform(crs_master)

bbox_site  = terrainr::add_bbox_buffer(aoi_site, 20000, "meters")
bbox_country = terrainr::add_bbox_buffer(aoi_country, 40000, "meters")
bbox_region = terrainr::add_bbox_buffer(aoi_region, 80000, "meters")

vbox_site = vect(bbox_site)
vbox_region = vect(bbox_region)
vbox_country = terra::vect(terra::ext(vect(aoi_country)) * 1.3) |> sf::st_as_sf()
sf::st_crs(vbox_country) <- "epsg:4326" 

# Interactive map mode: "view" 
tmap::tmap_mode("view")
tmap::tm_shape(vbox_country) +
  tmap::tm_borders(lwd = 2, col = "green") +
  tmap::tm_shape(aoi_region) +
  tmap::tm_borders(lwd = 1, col = "blue") +
  tmap::tm_shape(aoi_site) +
  tmap::tm_borders(lwd = 2, col = "red")

Figure 1d: Interactive map showing site boundary, national borders, and national bounding box

Import Basemap

# zoom = 8 returns scale of 1:2,000,000
basemap_4m = maptiles::get_tiles(
  bbox_region, 
  zoom      = 8, 
  crop      = T,
  provider  = "CartoDB.Positron"
)

tmap::tmap_mode("plot")
country_map = tmap::tm_shape(vbox_country) + tm_borders(lwd = 0.0, col = "black") +
  tmap::tm_shape(basemap_4m) + tm_rgb(alpha=0.2) + 
  tmap::tm_shape(aoi_site) + tm_borders(lwd=2, col = "red", fill="#e28672", fill_alpha=0.5) +
  tmap::tm_shape(aoi_region) + tm_borders(lwd = 0.5, col = "black") +
  tmap::tm_compass(type="4star", size=1.1, color.dark = "gray60", text.color="gray60",position=c("LEFT", "TOP")
    ) 

tmap::tmap_save(country_map, 
                "/Users/seamus/Repos/map-templates/assets/outputs/02-country-map.png"
                )
country_map

Figure 1e: Interactive map showing site boundary, national borders, and downloaded basemap.

Build Map

main_map = tmap::tmap_grob(site_map)
inset_map = tmap::tmap_grob(country_map)

locator_map = ggdraw() +
  draw_plot(main_map) +
  draw_plot(inset_map, x = -0.39, y=0.4, height = 0.45)

Save output

ggsave(locator_map, "/Users/seamus/Repos/map-templates/assets/outputs/03-locator-map.png")

1.3 Render Maps

locator_map

Figure 1f: Locator map showing site area and location at 1:4,000,000 & 1:150,000 scales

Environment Setup

easypackages::packages(
  "bslib", 
  "cols4all", "covr", "cowplot", 
  "dendextend", "digest","DiagrammeR","dtwclust", "downlit", 
  "e1071", "exactextractr","elevatr", 
  "FNN", "future", 
  "gdalcubes", "gdalUtilities", "geojsonsf", "geos", "ggplot2", "ggstats", 
  "ggspatial", "ggmap", "ggplotify", "ggpubr", "ggrepel", "giscoR", 
  "hdf5r", "httr", "httr2", "htmltools",
  "jsonlite", 
  "kohonen", 
  "leaflet.providers", "leafem", "libgeos","luz","lwgeom", "leaflet", "leafgl",
  "mapedit", "mapview", "maptiles", "methods", "mgcv", 
  "ncdf4", "nnet", 
  "openxlsx", "parallel", "plotly", 
  "randomForest", "rasterVis", "raster", "Rcpp", "RcppArmadillo", 
  "RcppCensSpatial","rayshader", "RcppEigen", "RcppParallel", 
  "RColorBrewer", "reactable", "rgl", "rsconnect","RStoolbox", "rts", 
  "s2", "sf", "scales", "sits","spdep", "stars", "stringr","supercells", 
  "terra", "testthat", "tidyverse", "tidyterra","tools", 
  "tmap", "tmaptools", "terrainr", 
  "xgboost",
  prompt = F)

Runtime Log

devtools::session_info()
## ─ Session info ───────────────────────────────────────────
##  setting  value
##  version  R version 4.3.0 (2023-04-21)
##  os       macOS 15.7.1
##  system   aarch64, darwin20
##  ui       X11
##  language (EN)
##  collate  en_US.UTF-8
##  ctype    en_US.UTF-8
##  tz       America/Vancouver
##  date     2025-11-03
##  pandoc   3.8 @ /opt/local/bin/ (via rmarkdown)
##  quarto   1.7.33 @ /usr/local/bin/quarto
## 
## ─ Packages ───────────────────────────────────────────────
##  package            * version    date (UTC) lib source
##  abind              * 1.4-8      2024-09-12 [1] CRAN (R 4.3.3)
##  ape                  5.8-1      2024-12-16 [1] CRAN (R 4.3.3)
##  assertthat           0.2.1      2019-03-21 [1] CRAN (R 4.3.3)
##  backports            1.5.0      2024-05-23 [1] CRAN (R 4.3.3)
##  base64enc            0.1-3      2015-07-28 [1] CRAN (R 4.3.3)
##  bit                  4.6.0      2025-03-06 [1] CRAN (R 4.3.3)
##  bit64                4.6.0-1    2025-01-16 [1] CRAN (R 4.3.3)
##  bitops               1.0-9      2024-10-03 [1] CRAN (R 4.3.3)
##  boot                 1.3-32     2025-08-29 [1] CRAN (R 4.3.0)
##  brew                 1.0-10     2023-12-16 [1] CRAN (R 4.3.3)
##  brio                 1.1.5      2024-04-24 [1] CRAN (R 4.3.3)
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##  bslib              * 0.9.0      2025-01-30 [1] CRAN (R 4.3.3)
##  cachem               1.1.0      2024-05-16 [1] CRAN (R 4.3.3)
##  callr                3.7.6      2024-03-25 [1] CRAN (R 4.3.3)
##  car                  3.1-3      2024-09-27 [1] CRAN (R 4.3.3)
##  carData              3.0-5      2022-01-06 [1] CRAN (R 4.3.3)
##  caret                7.0-1      2024-12-10 [1] CRAN (R 4.3.3)
##  class                7.3-23     2025-01-01 [1] CRAN (R 4.3.3)
##  classInt             0.4-11     2025-01-08 [1] CRAN (R 4.3.3)
##  cli                  3.6.5      2025-04-23 [1] CRAN (R 4.3.3)
##  clue                 0.3-66     2024-11-13 [1] CRAN (R 4.3.3)
##  cluster              2.1.8.1    2025-03-12 [1] CRAN (R 4.3.3)
##  coda                 0.19-4.1   2024-01-31 [1] CRAN (R 4.3.3)
##  codetools            0.2-20     2024-03-31 [1] CRAN (R 4.3.1)
##  colorspace           2.1-1      2024-07-26 [1] CRAN (R 4.3.3)
##  cols4all           * 0.9        2025-08-28 [1] CRAN (R 4.3.0)
##  contfrac             1.1-12     2018-05-17 [1] CRAN (R 4.3.3)
##  coro                 1.1.0      2024-11-05 [1] CRAN (R 4.3.3)
##  corpcor              1.6.10     2021-09-16 [1] CRAN (R 4.3.3)
##  countrycode          1.6.1      2025-03-31 [1] CRAN (R 4.3.3)
##  covr               * 3.6.4      2023-11-09 [1] CRAN (R 4.3.1)
##  cowplot            * 1.2.0      2025-07-07 [1] CRAN (R 4.3.3)
##  crayon               1.5.3      2024-06-20 [1] CRAN (R 4.3.3)
##  crosstalk            1.2.2      2025-08-26 [1] CRAN (R 4.3.0)
##  cubature             2.1.4      2025-06-02 [1] CRAN (R 4.3.3)
##  data.table           1.17.8     2025-07-10 [1] CRAN (R 4.3.3)
##  DBI                  1.2.3      2024-06-02 [1] CRAN (R 4.3.3)
##  deldir               2.0-4      2024-02-28 [1] CRAN (R 4.3.3)
##  dendextend         * 1.19.1     2025-07-15 [1] CRAN (R 4.3.0)
##  deSolve              1.40       2023-11-27 [1] CRAN (R 4.3.3)
##  devtools             2.4.5      2022-10-11 [1] CRAN (R 4.3.0)
##  DiagrammeR         * 1.0.11     2024-02-02 [1] CRAN (R 4.3.1)
##  dichromat            2.0-0.1    2022-05-02 [1] CRAN (R 4.3.3)
##  digest             * 0.6.37     2024-08-19 [1] CRAN (R 4.3.3)
##  doParallel           1.0.17     2022-02-07 [1] CRAN (R 4.3.3)
##  downlit            * 0.4.4      2024-06-10 [1] CRAN (R 4.3.3)
##  dplyr              * 1.1.4      2023-11-17 [1] CRAN (R 4.3.1)
##  dtw                * 1.23-1     2022-09-19 [1] CRAN (R 4.3.3)
##  dtwclust           * 6.0.0      2024-07-23 [1] CRAN (R 4.3.3)
##  e1071              * 1.7-16     2024-09-16 [1] CRAN (R 4.3.3)
##  easypackages         0.1.0      2016-12-05 [1] CRAN (R 4.3.0)
##  elevatr            * 0.99.0     2023-09-12 [1] CRAN (R 4.3.0)
##  ellipsis             0.3.2      2021-04-29 [1] CRAN (R 4.3.3)
##  elliptic             1.4-0      2019-03-14 [1] CRAN (R 4.3.3)
##  evaluate             1.0.5      2025-08-27 [1] CRAN (R 4.3.0)
##  exactextractr      * 0.10.0     2023-09-20 [1] CRAN (R 4.3.1)
##  extrafont            0.19       2023-01-18 [1] CRAN (R 4.3.3)
##  extrafontdb          1.0        2012-06-11 [1] CRAN (R 4.3.3)
##  farver               2.1.2      2024-05-13 [1] CRAN (R 4.3.3)
##  fastmap              1.2.0      2024-05-15 [1] CRAN (R 4.3.3)
##  flexclust            1.5.0      2025-02-28 [1] CRAN (R 4.3.3)
##  FNN                * 1.1.4.1    2024-09-22 [1] CRAN (R 4.3.3)
##  forcats            * 1.0.0      2023-01-29 [1] CRAN (R 4.3.0)
##  foreach              1.5.2      2022-02-02 [1] CRAN (R 4.3.3)
##  Formula              1.2-5      2023-02-24 [1] CRAN (R 4.3.3)
##  fs                   1.6.6      2025-04-12 [1] CRAN (R 4.3.3)
##  future             * 1.67.0     2025-07-29 [1] CRAN (R 4.3.0)
##  future.apply         1.20.0     2025-06-06 [1] CRAN (R 4.3.0)
##  FuzzyNumbers         0.4-7      2021-11-15 [1] CRAN (R 4.3.3)
##  FuzzyNumbers.Ext.2   3.2        2017-09-05 [1] CRAN (R 4.3.3)
##  gdalcubes          * 0.7.1      2025-03-20 [1] CRAN (R 4.3.3)
##  gdalUtilities      * 1.2.5      2023-08-10 [1] CRAN (R 4.3.0)
##  generics             0.1.4      2025-05-09 [1] CRAN (R 4.3.3)
##  geojsonsf          * 2.0.3      2022-05-30 [1] CRAN (R 4.3.3)
##  geos               * 0.2.4      2023-11-30 [1] CRAN (R 4.3.3)
##  ggmap              * 4.0.1      2025-04-07 [1] CRAN (R 4.3.3)
##  ggplot2            * 3.5.2      2025-04-09 [1] CRAN (R 4.3.3)
##  ggplotify          * 0.1.2      2023-08-09 [1] CRAN (R 4.3.0)
##  ggpubr             * 0.6.1      2025-06-27 [1] CRAN (R 4.3.3)
##  ggrepel            * 0.9.6      2024-09-07 [1] CRAN (R 4.3.3)
##  ggsignif             0.6.4      2022-10-13 [1] CRAN (R 4.3.0)
##  ggspatial          * 1.1.10     2025-08-24 [1] CRAN (R 4.3.0)
##  ggstats            * 0.10.0     2025-07-02 [1] CRAN (R 4.3.3)
##  giscoR             * 0.6.1      2025-08-11 [1] Github (rOpenGov/giscoR@adfed30)
##  globals              0.18.0     2025-05-08 [1] CRAN (R 4.3.0)
##  glue                 1.8.0      2024-09-30 [1] CRAN (R 4.3.3)
##  gmm                  1.9-1      2025-08-26 [1] CRAN (R 4.3.0)
##  gower                1.0.2      2024-12-17 [1] CRAN (R 4.3.3)
##  gridExtra            2.3        2017-09-09 [1] CRAN (R 4.3.3)
##  gridGraphics         0.5-1      2020-12-13 [1] CRAN (R 4.3.3)
##  gtable               0.3.6      2024-10-25 [1] CRAN (R 4.3.3)
##  hardhat              1.4.2      2025-08-20 [1] CRAN (R 4.3.0)
##  hdf5r              * 1.3.12     2025-01-20 [1] CRAN (R 4.3.3)
##  hexbin               1.28.5     2024-11-13 [1] CRAN (R 4.3.3)
##  hms                  1.1.3      2023-03-21 [1] CRAN (R 4.3.0)
##  htmltools          * 0.5.8.1    2024-04-04 [1] CRAN (R 4.3.3)
##  htmlwidgets          1.6.4      2023-12-06 [1] CRAN (R 4.3.1)
##  httpuv               1.6.16     2025-04-16 [1] CRAN (R 4.3.3)
##  httr               * 1.4.7      2023-08-15 [1] CRAN (R 4.3.0)
##  httr2              * 1.2.1      2025-07-22 [1] CRAN (R 4.3.0)
##  hypergeo             1.2-14     2025-03-24 [1] CRAN (R 4.3.3)
##  interp               1.1-6      2024-01-26 [1] CRAN (R 4.3.3)
##  ipred                0.9-15     2024-07-18 [1] CRAN (R 4.3.3)
##  iterators            1.0.14     2022-02-05 [1] CRAN (R 4.3.3)
##  jpeg                 0.1-11     2025-03-21 [1] CRAN (R 4.3.3)
##  jquerylib            0.1.4      2021-04-26 [1] CRAN (R 4.3.3)
##  jsonlite           * 2.0.0      2025-03-27 [1] CRAN (R 4.3.3)
##  KernSmooth           2.23-26    2025-01-01 [1] CRAN (R 4.3.3)
##  knitr                1.50       2025-03-16 [1] CRAN (R 4.3.3)
##  kohonen            * 3.0.12     2023-06-09 [1] CRAN (R 4.3.3)
##  later                1.4.4      2025-08-27 [1] CRAN (R 4.3.0)
##  lattice            * 0.22-7     2025-04-02 [1] CRAN (R 4.3.3)
##  latticeExtra         0.6-30     2022-07-04 [1] CRAN (R 4.3.3)
##  lava                 1.8.1      2025-01-12 [1] CRAN (R 4.3.3)
##  lazyeval             0.2.2      2019-03-15 [1] CRAN (R 4.3.3)
##  leafem             * 0.2.5      2025-08-28 [1] CRAN (R 4.3.0)
##  leafgl             * 0.2.2      2024-11-13 [1] CRAN (R 4.3.3)
##  leaflegend           1.2.1      2024-05-09 [1] CRAN (R 4.3.3)
##  leaflet            * 2.2.2      2024-03-26 [1] CRAN (R 4.3.1)
##  leaflet.providers  * 2.0.0      2023-10-17 [1] CRAN (R 4.3.3)
##  leafpop              0.1.0      2021-05-22 [1] CRAN (R 4.3.0)
##  leafsync             0.1.0      2019-03-05 [1] CRAN (R 4.3.0)
##  libgeos            * 3.11.1-3   2025-03-19 [1] CRAN (R 4.3.3)
##  lifecycle            1.0.4      2023-11-07 [1] CRAN (R 4.3.3)
##  listenv              0.9.1      2024-01-29 [1] CRAN (R 4.3.3)
##  logger               0.4.0      2024-10-22 [1] CRAN (R 4.3.3)
##  lubridate          * 1.9.4      2024-12-08 [1] CRAN (R 4.3.3)
##  luz                * 0.5.0      2025-07-29 [1] CRAN (R 4.3.0)
##  lwgeom             * 0.2-14     2024-02-21 [1] CRAN (R 4.3.1)
##  magrittr             2.0.4      2025-09-12 [1] CRAN (R 4.3.0)
##  mapedit            * 0.7.0      2025-04-20 [1] CRAN (R 4.3.3)
##  maptiles           * 0.10.0     2025-05-07 [1] CRAN (R 4.3.3)
##  mapview            * 2.11.2     2023-10-13 [1] CRAN (R 4.3.1)
##  MASS                 7.3-60.0.1 2024-01-13 [1] CRAN (R 4.3.1)
##  Matrix               1.6-5      2024-01-11 [1] CRAN (R 4.3.1)
##  matrixcalc           1.0-6      2022-09-14 [1] CRAN (R 4.3.3)
##  MCMCglmm             2.36       2024-05-06 [1] CRAN (R 4.3.1)
##  memoise              2.0.1      2021-11-26 [1] CRAN (R 4.3.3)
##  mgcv               * 1.9-3      2025-04-04 [1] CRAN (R 4.3.0)
##  microbenchmark       1.5.0      2024-09-04 [1] CRAN (R 4.3.3)
##  mime                 0.13       2025-03-17 [1] CRAN (R 4.3.3)
##  miniUI               0.1.2      2025-04-17 [1] CRAN (R 4.3.3)
##  ModelMetrics         1.2.2.2    2020-03-17 [1] CRAN (R 4.3.3)
##  modeltools           0.2-24     2025-05-02 [1] CRAN (R 4.3.3)
##  MomTrunc             6.1        2024-10-28 [1] CRAN (R 4.3.3)
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##  ncdf4              * 1.24       2025-03-25 [1] CRAN (R 4.3.3)
##  nlme               * 3.1-168    2025-03-31 [1] CRAN (R 4.3.3)
##  nnet               * 7.3-20     2025-01-01 [1] CRAN (R 4.3.3)
##  openxlsx           * 4.2.8      2025-01-25 [1] CRAN (R 4.3.3)
##  parallelly           1.45.1     2025-07-24 [1] CRAN (R 4.3.0)
##  pillar               1.11.0     2025-07-04 [1] CRAN (R 4.3.3)
##  pkgbuild             1.4.8      2025-05-26 [1] CRAN (R 4.3.3)
##  pkgconfig            2.0.3      2019-09-22 [1] CRAN (R 4.3.3)
##  pkgload              1.4.0      2024-06-28 [1] CRAN (R 4.3.3)
##  plotly             * 4.11.0     2025-06-19 [1] CRAN (R 4.3.3)
##  plyr                 1.8.9      2023-10-02 [1] CRAN (R 4.3.3)
##  png                  0.1-8      2022-11-29 [1] CRAN (R 4.3.3)
##  prettyunits          1.2.0      2023-09-24 [1] CRAN (R 4.3.3)
##  pROC                 1.19.0.1   2025-07-31 [1] CRAN (R 4.3.0)
##  processx             3.8.6      2025-02-21 [1] CRAN (R 4.3.3)
##  prodlim              2025.04.28 2025-04-28 [1] CRAN (R 4.3.3)
##  profvis              0.4.0      2024-09-20 [1] CRAN (R 4.3.3)
##  progress             1.2.3      2023-12-06 [1] CRAN (R 4.3.1)
##  progressr            0.15.1     2024-11-22 [1] CRAN (R 4.3.3)
##  promises             1.3.3      2025-05-29 [1] CRAN (R 4.3.3)
##  proxy              * 0.4-27     2022-06-09 [1] CRAN (R 4.3.3)
##  ps                   1.9.1      2025-04-12 [1] CRAN (R 4.3.3)
##  purrr              * 1.1.0      2025-07-10 [1] CRAN (R 4.3.0)
##  R6                   2.6.1      2025-02-15 [1] CRAN (R 4.3.3)
##  randomForest       * 4.7-1.2    2024-09-22 [1] CRAN (R 4.3.3)
##  rappdirs             0.3.3      2021-01-31 [1] CRAN (R 4.3.3)
##  raster             * 3.6-32     2025-03-28 [1] CRAN (R 4.3.3)
##  rasterVis          * 0.51.6     2023-11-01 [1] CRAN (R 4.3.3)
##  rayshader          * 0.37.3     2024-02-21 [1] CRAN (R 4.3.1)
##  rbibutils            2.3        2024-10-04 [1] CRAN (R 4.3.3)
##  RColorBrewer       * 1.1-3      2022-04-03 [1] CRAN (R 4.3.3)
##  Rcpp               * 1.1.0      2025-07-02 [1] CRAN (R 4.3.3)
##  RcppArmadillo      * 14.6.0-1   2025-07-02 [1] CRAN (R 4.3.3)
##  RcppCensSpatial    * 0.3.0      2022-06-27 [1] CRAN (R 4.3.0)
##  RcppEigen          * 0.3.4.0.2  2024-08-24 [1] CRAN (R 4.3.3)
##  RcppParallel       * 5.1.11-1   2025-08-27 [1] CRAN (R 4.3.0)
##  RCurl                1.98-1.17  2025-03-22 [1] CRAN (R 4.3.3)
##  Rdpack               2.6.4      2025-04-09 [1] CRAN (R 4.3.3)
##  reactable          * 0.4.4      2023-03-12 [1] CRAN (R 4.3.0)
##  readr              * 2.1.5      2024-01-10 [1] CRAN (R 4.3.1)
##  recipes              1.3.1      2025-05-21 [1] CRAN (R 4.3.3)
##  relliptical          1.3.0      2024-02-07 [1] CRAN (R 4.3.1)
##  remotes              2.5.0      2024-03-17 [1] CRAN (R 4.3.3)
##  reshape2             1.4.4      2020-04-09 [1] CRAN (R 4.3.0)
##  rex                  1.2.1      2021-11-26 [1] CRAN (R 4.3.3)
##  rgl                * 1.3.24     2025-06-25 [1] CRAN (R 4.3.3)
##  rlang                1.1.6      2025-04-11 [1] CRAN (R 4.3.3)
##  rmarkdown            2.29       2024-11-04 [1] CRAN (R 4.3.3)
##  rpart                4.1.24     2025-01-07 [1] CRAN (R 4.3.3)
##  rsconnect          * 1.5.1      2025-08-28 [1] CRAN (R 4.3.0)
##  RSpectra             0.16-2     2024-07-18 [1] CRAN (R 4.3.3)
##  rstatix              0.7.2      2023-02-01 [1] CRAN (R 4.3.0)
##  RStoolbox          * 1.0.2.1    2025-02-03 [1] CRAN (R 4.3.3)
##  rstudioapi           0.17.1     2024-10-22 [1] CRAN (R 4.3.3)
##  rts                * 1.1-14     2023-10-01 [1] CRAN (R 4.3.3)
##  Rttf2pt1             1.3.12     2023-01-22 [1] CRAN (R 4.3.3)
##  Ryacas0              0.4.4      2023-01-12 [1] CRAN (R 4.3.3)
##  s2                 * 1.1.9      2025-05-23 [1] CRAN (R 4.3.3)
##  sandwich             3.1-1      2024-09-15 [1] CRAN (R 4.3.3)
##  sass                 0.4.10     2025-04-11 [1] CRAN (R 4.3.3)
##  satellite            1.0.6      2025-08-21 [1] CRAN (R 4.3.0)
##  scales             * 1.4.0      2025-04-24 [1] CRAN (R 4.3.3)
##  sessioninfo          1.2.3      2025-02-05 [1] CRAN (R 4.3.3)
##  settings             0.2.7      2021-05-07 [1] CRAN (R 4.3.3)
##  sf                 * 1.0-22     2025-08-25 [1] Github (r-spatial/sf@3660edf)
##  shiny                1.11.1     2025-07-03 [1] CRAN (R 4.3.3)
##  shinyjs              2.1.0      2021-12-23 [1] CRAN (R 4.3.0)
##  shinyWidgets         0.9.0      2025-02-21 [1] CRAN (R 4.3.3)
##  sits               * 1.5.2      2025-02-12 [1] CRAN (R 4.3.3)
##  sp                 * 2.2-0      2025-02-01 [1] CRAN (R 4.3.3)
##  spacesXYZ            1.6-0      2025-06-06 [1] CRAN (R 4.3.3)
##  spData             * 2.3.4      2025-01-08 [1] CRAN (R 4.3.3)
##  spdep              * 1.4-1      2025-08-31 [1] CRAN (R 4.3.0)
##  stars              * 0.6-8      2025-02-01 [1] CRAN (R 4.3.3)
##  StempCens            1.2.0      2025-06-11 [1] CRAN (R 4.3.3)
##  stringi              1.8.7      2025-03-27 [1] CRAN (R 4.3.3)
##  stringr            * 1.5.2      2025-09-08 [1] CRAN (R 4.3.0)
##  supercells         * 1.0.0      2024-02-11 [1] CRAN (R 4.3.1)
##  survival             3.8-3      2024-12-17 [1] CRAN (R 4.3.3)
##  svglite              2.2.1      2025-05-12 [1] CRAN (R 4.3.3)
##  systemfonts          1.2.3      2025-04-30 [1] CRAN (R 4.3.3)
##  tensorA              0.36.2.1   2023-12-13 [1] CRAN (R 4.3.3)
##  terra              * 1.8-60     2025-07-21 [1] CRAN (R 4.3.0)
##  terrainr           * 0.7.6      2025-07-25 [1] CRAN (R 4.3.0)
##  testthat           * 3.2.3      2025-01-13 [1] CRAN (R 4.3.3)
##  textshaping          1.0.3      2025-09-02 [1] CRAN (R 4.3.0)
##  tibble             * 3.3.0      2025-06-08 [1] CRAN (R 4.3.3)
##  tidyr              * 1.3.1      2024-01-24 [1] CRAN (R 4.3.1)
##  tidyselect           1.2.1      2024-03-11 [1] CRAN (R 4.3.1)
##  tidyterra          * 0.7.2      2025-04-14 [1] CRAN (R 4.3.3)
##  tidyverse          * 2.0.0      2023-02-22 [1] CRAN (R 4.3.0)
##  timechange           0.3.0      2024-01-18 [1] CRAN (R 4.3.3)
##  timeDate             4041.110   2024-09-22 [1] CRAN (R 4.3.3)
##  tlrmvnmvt            1.1.2      2022-06-09 [1] CRAN (R 4.3.3)
##  tmap               * 4.1        2025-05-12 [1] CRAN (R 4.3.3)
##  tmaptools          * 3.2        2025-01-13 [1] CRAN (R 4.3.3)
##  tmvtnorm             1.6        2023-12-05 [1] CRAN (R 4.3.3)
##  torch                0.16.0     2025-08-21 [1] CRAN (R 4.3.0)
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##  units                0.8-7      2025-03-11 [1] CRAN (R 4.3.3)
##  urlchecker           1.0.1      2021-11-30 [1] CRAN (R 4.3.3)
##  usethis              3.1.0      2024-11-26 [1] CRAN (R 4.3.3)
##  uuid                 1.2-1      2024-07-29 [1] CRAN (R 4.3.3)
##  vctrs                0.6.5      2023-12-01 [1] CRAN (R 4.3.3)
##  viridis              0.6.5      2024-01-29 [1] CRAN (R 4.3.1)
##  viridisLite          0.4.2      2023-05-02 [1] CRAN (R 4.3.3)
##  visNetwork           2.1.2      2022-09-29 [1] CRAN (R 4.3.0)
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##  xfun                 0.53       2025-08-19 [1] CRAN (R 4.3.0)
##  xgboost            * 1.7.11.1   2025-05-15 [1] CRAN (R 4.3.3)
##  XML                  3.99-0.18  2025-01-01 [1] CRAN (R 4.3.3)
##  xml2                 1.4.0      2025-08-20 [1] CRAN (R 4.3.0)
##  xtable               1.8-4      2019-04-21 [1] CRAN (R 4.3.3)
##  xts                * 0.14.1     2024-10-15 [1] CRAN (R 4.3.3)
##  yaml                 2.3.10     2024-07-26 [1] CRAN (R 4.3.3)
##  yulab.utils          0.2.1      2025-08-19 [1] CRAN (R 4.3.0)
##  zeallot              0.2.0      2025-05-27 [1] CRAN (R 4.3.3)
##  zip                  2.3.3      2025-05-13 [1] CRAN (R 4.3.3)
##  zoo                * 1.8-14     2025-04-10 [1] CRAN (R 4.3.3)
## 
##  [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
##  * ── Packages attached to the search path.
## 
## ──────────────────────────────────────────────────────────

---
title: "Field Sites"
execute:
  echo: true
format:
  html:
    toc: true
    toc-location: right
    toc-depth: 4
    toc-title: "**On this page**"
    number-sections: false
    highlight-style: pygments
    page-layout: article

editor_options: 
  markdown: 
    wrap: 60
---

```{r}
#| warning: false
#| message: false
#| include: false
#| echo: false
#| comment: NA

options(repos = c(CRAN = "https://cloud.r-project.org"),
        htmltools.dir.version = FALSE, 
        htmltools.preserve.raw = FALSE
        )

knitr::opts_chunk$set(
  echo = TRUE, 
  message = FALSE, 
  warning = FALSE,
  error = FALSE, 
  comment = NA, 
  tidy.opts = list(width.cutoff = 60)
  ) 

#install.packages("easypackages")
#pak::pkg_install(c(
#libs = c(
easypackages::packages(
  "bslib", 
  "cols4all", "covr", "cowplot", 
  "dendextend", "digest","DiagrammeR","dtwclust", "downlit", 
  "e1071", "exactextractr","elevatr", 
  "FNN", "future", 
  "gdalcubes", "gdalUtilities", "geojsonsf", "geos", "ggplot2", "ggstats", 
  "ggspatial", "ggmap", "ggplotify", "ggpubr", "ggrepel", "giscoR", 
  "hdf5r", "httr", "httr2", "htmltools",
  "jsonlite", 
  "kohonen", 
  "leaflet.providers", "leafem", "libgeos","luz","lwgeom", "leaflet", "leafgl",
  "mapedit", "mapview", "maptiles", "methods", "mgcv", 
  "ncdf4", "nnet", 
  "openxlsx", "parallel", "plotly", 
  "randomForest", "rasterVis", "raster", "Rcpp", "RcppArmadillo", 
  "RcppCensSpatial","rayshader", "RcppEigen", "RcppParallel", 
  "RColorBrewer", "reactable", "rgl", "rsconnect","RStoolbox", "rts", 
  "s2", "sf", "scales", "sits","spdep", "stars", "stringr","supercells", 
  "terra", "testthat", "tidyverse", "tidyterra","tools", 
  "tmap", "tmaptools", "terrainr", 
  "xgboost",
  prompt = F)

#installed_libs <- libs %in% rownames(installed.packages())
#if(any(installed_libs == F)){install.packages(libs[!installed_libs])}
#invisible(lapply(libs, library, character.only = T))

#lib = .libPaths()[[1L]], upgrade = F, ask = F, dependencies = T)
#mapviewOptions(fgb = FALSE)
sf::sf_use_s2(use_s2 = FALSE)
```

```{css, echo=FALSE, class.source = 'foldable'}
div.column {
    display: inline-block;
    vertical-align: top;
    width: 50%;
}

#TOC::before {
  content: "";
  display: block;
  height:200px;
  width: 200px;
  background-image: url('https://raw.githubusercontent.com/seamusrobertmurphy/map-templates/refs/heads/main/assets/outputs/01-site-map.png');
  background-size: contain;
  background-position: 50% 50%;
  padding-top: 80px !important;
  background-repeat: no-repeat;
}
```

## 1.0 Overview

Site map templates to help field teams navigate a site,
illustrating settlements, boundaries, and access routs, and
locator maps showing geographic locations within local and
national contexts.

## 1.1 Site Maps

### Import AOI

```{r site-aoi}
#| warning: false
#| message: false
#| eval: true
#| echo: true
#| comment: NA

crs_master = sf::st_crs('epsg:4326')
aoi_site   = sf::read_sf("../assets/inputs/chilwa_watershed_4326.shp") |>
  sf::st_cast() |> sf::st_transform(crs_master)
bbox_site  = terrainr::add_bbox_buffer(aoi_site, 20000, "meters")
vbox_site = terra::vect(bbox_site)

tmap::tmap_mode("view")
tmap::tm_shape(aoi_site) +
  tmap::tm_borders(col = "red") +
  tmap::tm_basemap("Esri.WorldImagery")
```

Figure 1a: Interactive map showing project boundary and
ESRI's basemap

### Import Basemap

```{r site-basemap, cache=T}
#| warning: false
#| message: false
#| echo: true
#| eval: true
#| comment: NA

# zoom = 12 sources basemap at scale of 1:150,000
basemap_150k = maptiles::get_tiles(
  bbox_site, 
  zoom      = 10, 
  crop      = T,
  provider  = "OpenTopoMap"
)

tmap::tmap_mode("view")
tmap::tm_shape(basemap_150k) + tmap::tm_rgb() + 
  tmap::tm_shape(aoi_site) +
  tmap::tm_borders(col="red")
```

Figure 1b: Site map showing project boundary and downloaded
basemap `OpenTopoMap`

### Build Map

```{r customize-site-map}
#| warning: false
#| message: false
#| echo: true
#| eval: false
#| comment: NA
tmap::tmap_mode("plot")
site_map = tmap::tm_shape(basemap_150k) + tmap::tm_rgb() + 
  tmap::tm_shape(aoi_site) +
  tmap::tm_borders(lwd = 1, col = "red") +
  tmap::tm_graticules(lines=T,labels.rot=c(0,90),lwd=0.2) +
  tmap::tm_credits("EPSG:4326", position = c("left", "bottom")) +
  tmap::tm_scale_bar(
    c(0, 10, 20, 40), 
    position = c("RIGHT", "BOTTOM"), 
    text.size = .5
    ) +
  tmap::tm_compass(
    type = "4star", size = 1.5,
    color.dark = "gray60", text.color = "gray60",
    position = c("left", "top")
    ) 
```

### Save output

```{r save-site-map}
#| warning: false
#| message: false
#| echo: true
#| eval: false
#| comment: NA

# `width` & `height` controls output resolution 
# `dpi` controls size of map attributes relative to output resolution
tmap::tmap_save(site_map, width=15120, height=15120, asp=0, dpi=600,
  "/Users/seamus/Repos/map-templates/assets/outputs/01-site-draft.png"
  )
site_map
```

![Figure 1c: Site Map rendered with customized attributes
and resolution
(`15120x15120`)](https://raw.githubusercontent.com/seamusrobertmurphy/map-templates/refs/heads/main/assets/outputs/01-site-map.png)

## 1.2 Locator Maps

### Import AOI

```{r locator-map}
#| warning: false
#| message: false
#| echo: true
#| eval: true
#| comment: NA

aoi_country = giscoR::gisco_get_countries(country = "Malawi", resolution = "3") |>
  st_cast() |> st_transform(crs_master)
aoi_region = giscoR::gisco_get_countries(
  country = c("Malawi", "Zambia", "Tanzania", "Mozambique"), resolution = "3") |>
  st_cast() |> st_transform(crs_master)

bbox_site  = terrainr::add_bbox_buffer(aoi_site, 20000, "meters")
bbox_country = terrainr::add_bbox_buffer(aoi_country, 40000, "meters")
bbox_region = terrainr::add_bbox_buffer(aoi_region, 80000, "meters")

vbox_site = vect(bbox_site)
vbox_region = vect(bbox_region)
vbox_country = terra::vect(terra::ext(vect(aoi_country)) * 1.3) |> sf::st_as_sf()
sf::st_crs(vbox_country) <- "epsg:4326" 

# Interactive map mode: "view" 
tmap::tmap_mode("view")
tmap::tm_shape(vbox_country) +
  tmap::tm_borders(lwd = 2, col = "green") +
  tmap::tm_shape(aoi_region) +
  tmap::tm_borders(lwd = 1, col = "blue") +
  tmap::tm_shape(aoi_site) +
  tmap::tm_borders(lwd = 2, col = "red")
```

Figure 1d: Interactive map showing site boundary, national
borders, and national bounding box

### Import Basemap

```{r locator-basemap}
#| warning: false
#| message: false
#| echo: true
#| eval: false
#| comment: NA

# zoom = 8 returns scale of 1:2,000,000
basemap_4m = maptiles::get_tiles(
  bbox_region, 
  zoom      = 8, 
  crop      = T,
  provider  = "CartoDB.Positron"
)

tmap::tmap_mode("plot")
country_map = tmap::tm_shape(vbox_country) + tm_borders(lwd = 0.0, col = "black") +
  tmap::tm_shape(basemap_4m) + tm_rgb(alpha=0.2) + 
  tmap::tm_shape(aoi_site) + tm_borders(lwd=2, col = "red", fill="#e28672", fill_alpha=0.5) +
  tmap::tm_shape(aoi_region) + tm_borders(lwd = 0.5, col = "black") +
  tmap::tm_compass(type="4star", size=1.1, color.dark = "gray60", text.color="gray60",position=c("LEFT", "TOP")
    ) 

tmap::tmap_save(country_map, 
                "/Users/seamus/Repos/map-templates/assets/outputs/02-country-map.png"
                )
country_map
```

![Figure 1e: Interactive map showing site boundary, national
borders, and downloaded
basemap.](https://raw.githubusercontent.com/seamusrobertmurphy/map-templates/refs/heads/main/assets/outputs/02-country-map.png)

### Build Map

```{r customize-locator-map}
#| warning: false
#| message: false
#| echo: true
#| eval: false
#| comment: NA

main_map = tmap::tmap_grob(site_map)
inset_map = tmap::tmap_grob(country_map)

locator_map = ggdraw() +
  draw_plot(main_map) +
  draw_plot(inset_map, x = -0.39, y=0.4, height = 0.45)
```

### Save output

```{r output-map}
#| warning: false
#| message: false
#| echo: true
#| eval: false
#| comment: NA

ggsave(locator_map, "/Users/seamus/Repos/map-templates/assets/outputs/03-locator-map.png")
```

## 1.3 Render Maps

```{r}
#| warning: false
#| message: false
#| echo: true
#| eval: false
#| comment: NA

locator_map
```

![Figure 1f: Locator map showing site area and location at
1:4,000,000 & 1:150,000
scales](https://raw.githubusercontent.com/seamusrobertmurphy/map-templates/refs/heads/main/assets/outputs/03-locator-map.png){fig-align="center"}

#### Environment Setup

```{r}
#| warning: false
#| message: false
#| eval: false
#| comment: NA

easypackages::packages(
  "bslib", 
  "cols4all", "covr", "cowplot", 
  "dendextend", "digest","DiagrammeR","dtwclust", "downlit", 
  "e1071", "exactextractr","elevatr", 
  "FNN", "future", 
  "gdalcubes", "gdalUtilities", "geojsonsf", "geos", "ggplot2", "ggstats", 
  "ggspatial", "ggmap", "ggplotify", "ggpubr", "ggrepel", "giscoR", 
  "hdf5r", "httr", "httr2", "htmltools",
  "jsonlite", 
  "kohonen", 
  "leaflet.providers", "leafem", "libgeos","luz","lwgeom", "leaflet", "leafgl",
  "mapedit", "mapview", "maptiles", "methods", "mgcv", 
  "ncdf4", "nnet", 
  "openxlsx", "parallel", "plotly", 
  "randomForest", "rasterVis", "raster", "Rcpp", "RcppArmadillo", 
  "RcppCensSpatial","rayshader", "RcppEigen", "RcppParallel", 
  "RColorBrewer", "reactable", "rgl", "rsconnect","RStoolbox", "rts", 
  "s2", "sf", "scales", "sits","spdep", "stars", "stringr","supercells", 
  "terra", "testthat", "tidyverse", "tidyterra","tools", 
  "tmap", "tmaptools", "terrainr", 
  "xgboost",
  prompt = F)
```

#### Runtime Log

```{r seesion-info}
devtools::session_info()
```