Navigating-the-Wild-in-R-Course

Materials and lesson plans for course in data processing, wrangling, and visualization for wildlife ecologists, taught by Dr. K Whitney Hansen and Dr. Johannes De Groeve. Hosted by Dr. Emily Bennitt at University of Botswana's Okavango Research Institute

Lesson 01 can be found here.

Part of the material for Lesson 01 has been adapted from Dr. Simona Piccardi's data organizational workshop materials (https://github.com/picardis).

Lessons 04 part 2 and 05 were adapted from Dr. Brian Smith's movement data workshop materials (https://github.com/bsmity13).

• www: Navigating-the-Wild-in-R
• repository: Navigating-the-Wild-in-R

Directory Structure

The repository contains the following files and directories:

``` ├── Navigating-the-Wild-in-R-Course.Rproj ├── README.md ├── additionalmaterials │   ├── 01simdata.R │   ├── 01simhabitat.R │   ├── 02simdata.R │   ├── 04pt2lecture.html │   ├── 04refs.bib │   ├── HSFexercise.html │   └── ICTWS 2025 Workshop.pptx ├── code │   ├── lesson02.R │   ├── lesson02pt2.R │   ├── lesson03.R │   ├── lesson04.R │   ├── lesson04pt2.R │   ├── lesson05.R │   └── lesson05pt2.R │   ├── exercisesolutions │   │   ├── 02solutions.R │   │   ├── 02pt2solutions.R │   │   ├── 03solutions.R │   │   ├── 04solutions.R │   │   ├── 04pt2solutions.R │   │   └── 05HSFsolution.R │   ├── fun │   │   ├── bcrw.R │   │   └── reclasslanduse.R ├── data │   ├── lesson02 │   │   ├── CAcounties.geojson │   │   ├── CAcounties.qmd │   │   ├── CAprotectedareas.geojson │   │   ├── CAprotectedareas.gpkg │   │   ├── CAprotectedareas.qmd │   │   ├── CAroads.geojson │   │   ├── CAroads.qmd │   │   ├── areasvalid.gpkg │   │   ├── landcover.tif │   │   ├── slope.tif │   │   └── treecover.tif │   ├── lesson03 │   │   ├── floridadetections.rda │   │   └── floridastack.tif │   ├── lesson04 │   │   ├── fawndata.rda │   │   ├── texasmove.rda │   │   └── texasstack.tif │   └── lesson05 │   ├── habitat.tif │   ├── simgpshsf.csv │   └── simgpsssf.csv ├── index.html ├── output │   ├── CAprotectedareasclipped.geojson │   ├── CAroadsclipped.geojson │   ├── countyPAs.geojson │   ├── extractedrastervalues.csv │   ├── lowpreysites.jpg │   ├── mypoints.geojson │   ├── myraster.tif │   ├── myshapefile.geojson │   ├── randompointsbigbasin.csv │   ├── randompointssantaclara.csv │   ├── rasterstack.tif │   ├── slope.tif │   ├── speciescountsbymonth.jpg │   ├── speciesdetections.rda │   └── toppredatorsites.jpg ├── repo_tree.txt

```

code-directory

lessons are stored in the code-directory.

| File(s)/Directories | Description | |:--------------------|:------------| | bcrw.R | function for Lesson 04 | | reclass_landuse.R | function for Lesson 05 | | lesson_01.html | Lesson link: data organization and introduction to Rprojects, GitHub, and more- hosted externally on Johannes De Groeve's gitlab website | | lesson_02.R | Lesson file: basic spatial operations (basic spatial data types, vector operations | | lesson_02pt2.R | Lesson file: basic spatial operations part 2 (sampling points, raster wrangling) | | lesson_03.R | Lesson file: using tidyverse and wrangling detection data | | lesson_04.R | Lesson file: processing movement data | | lesson_04pt2.R | Lesson file: understanding and plotting homeranges | | lesson_05.R | Lesson file: testing habitat selection functions using simulated data | | lesson_05pt2.R | Lesson file: testing step selection functions using simulated data |

data-directory

Raw and processed datasets are stored in the data-directory. Datasets are described in more detail in the above scripts.

| File(s)/Directories | Description | |:---------------------|:------------| | CA_counties.geojson | Lesson 2 data: County designation for California | | CA_counties.qmd | Lesson 2 data: qmd | | CAprotectedareas.geojson | Lesson 2 data: Protected area designation for California (geojson version) | | CAprotectedareas.gpkg | Lesson 2 data: Protected area designation for California (gpkg version) | | CAprotectedareas.qmd | Lesson 2 data: qmd | | CA_roads.geojson | Lesson 2 data: Roads in California | | CA_roads.qmd | Lesson 2 data: qmd | | landcover.tif | Lesson 2 data: Raster layer designating landcover types in California | | slope.tif | Lesson 2 data: Raster layer designating slope in California | | treecover.tif | Lesson 2 data: Raster layer designating tree and shrub cover in California | | florida_detections.rda | Lesson 3 data: RDA file combining camera observations dataframe and camera locations spatial object for Florida camera trap study | | florida_stack.tif | Lesson 3 data: Stack of raster layers combining landcover types in Florida study site | | fawn_data.rda | Lesson 4 data: RDA file combining deer movement data from South Texas and a spatial features of roads across study sites | | texas_move.rda | Lesson 4 data: RDA file of fawn mortality data | | texas_stack.tif | Lesson 4 data: Stack of raster layers combining landcover types in Texas study site | | habitat.tif | Lesson 05 data: simulated habitat data | | simgpshsf.csv | Lesson 05 data: simulated movement data for HSF | | simgpsssf.csv | Lesson 05 data: simulated movement data for SSF |