data-raw/RivOtter_DwellsDams.R

In h-a-graham/beavertools: Tools to monitor the expansion of beaver populations and predict future territory capacity.

# File to read in the ROBT dwelling and dam data recorded during annual surveys.
# These signs will be used as confirmatory signs to establish if areas of impact can be classified as territories.
# Data was super messy so has been collected and put into a single Geopackage.


library(sf)
library(here)
library(tidyverse)
library(lubridate)
library(ggspatial)


# --------- functions-----------

# Prep_sf_obj
prep_data <- function(.data, type, season){
  .data %>%
    select(EDITTED, geom) %>%
    rename(RecordDate = EDITTED)%>%
    mutate(RecordDate = dmy_hms(RecordDate)) %>%
    mutate(SignType = type) %>%
    mutate(SurveySeason = season)

}


# ---------- load data -----------------

# pre 15
Dwell_Pre15 <- read_sf('data-raw/Otter_survey_raw/Dam_Dwelling.gpkg', layer='Dwelling_Pre15') %>%
  prep_data(., 'Dwelling', 'Pre 2015')

# Winter 15 - 16
Dwell_15_16 <- read_sf('data-raw/Otter_survey_raw/Dam_Dwelling.gpkg', layer='Dwelling_15_16') %>%
  prep_data(., 'Dwelling', '2015 - 2016')

Dam_15_16 <- read_sf('data-raw/Otter_survey_raw/Dam_Dwelling.gpkg', layer='Dam_15_16') %>%
  prep_data(., 'Dam', '2015 - 2016')

# Winter 16 -17
Dwell_16_17 <- read_sf('data-raw/Otter_survey_raw/Dam_Dwelling.gpkg', layer='Dwelling_16_17') %>%
  prep_data(., 'Dwelling', '2016 - 2017')

Dam_16_17 <- read_sf('data-raw/Otter_survey_raw/Dam_Dwelling.gpkg', layer='Dam_16_17') %>%
  prep_data(., 'Dam', '2016 - 2017')

# Winter 17 - 18
Dwell_17_18 <- read_sf('data-raw/Otter_survey_raw/Dam_Dwelling.gpkg', layer='Dwelling_17_18') %>%
  prep_data(., 'Dwelling', '2017 - 2018')

Dam_17_18 <- read_sf('data-raw/Otter_survey_raw/Dam_Dwelling.gpkg', layer='Dam_17_18') %>%
  prep_data(., 'Dam', '2017 - 2018')

# Winter 18 - 19
Dwell_18_19 <- read_sf('data-raw/Otter_survey_raw/Dam_Dwelling.gpkg', layer='Dwelling_18_19') %>%
  prep_data(., 'Dwelling', '2018 - 2019')

Dam_18_19 <- read_sf('data-raw/Otter_survey_raw/Dam_Dwelling.gpkg', layer='Dam_18_19') %>%
  prep_data(., 'Dam', '2018 - 2019')

# Witer 19 - 20
Dwell_19_20 <- read_sf('data-raw/Otter_survey_raw/Dam_Dwelling.gpkg', layer='Dwelling_19_20') %>%
  prep_data(., 'Dwelling', '2019 - 2020')

Dam_19_20 <- read_sf('data-raw/Otter_survey_raw/Dam_Dwelling.gpkg', layer='Dam_19_20') %>%
  prep_data(., 'Dam', '2019 - 2020')


# Witer 19 - 20
Dwell_20_21 <- read_sf(file.path(here::here(), 'data-raw', 'Otter_survey_raw', 'Otter_FS_20_21', 'Dwellings16.SHP')) %>%
  rename(geom=geometry)%>%
  prep_data(., 'Dwelling', '2020 - 2021')

Dam_20_21 <- read_sf(file.path(here::here(), 'data-raw', 'Otter_survey_raw', 'Otter_FS_20_21', 'Dam16.SHP')) %>%
  rename(geom=geometry)%>%
  prep_data(., 'Dam', '2020 - 2021')



#  --------------- combine data ---------------------------------

RivOtter_OtherSigns <- list(Dwell_Pre15, Dwell_15_16, Dam_15_16, Dwell_16_17, Dam_16_17, Dwell_17_18, Dam_17_18,
                    Dwell_18_19, Dam_18_19, Dwell_19_20, Dam_19_20, Dwell_20_21, Dam_20_21) %>%
  bind_rows() %>%
  mutate(SurveySeason = fct_relevel(SurveySeason, 'Pre 2015')) %>%
  mutate(SignType = fct_relevel(SignType, 'Dwelling'))%>%
  select(SurveySeason, RecordDate, SignType, geom)


# Check sf dataframe
ggplot() +
  ggspatial::annotation_map_tile(type = 'osmgrayscale', zoomin = 0, alpha = 0.8) +
  layer_spatial(RivOtter_OtherSigns, aes(colour=SignType) ,alpha = 0.7) +
  coord_sf(crs = sf::st_crs(RivOtter_OtherSigns), datum =  sf::st_crs(RivOtter_OtherSigns)) +
  facet_wrap(~SurveySeason) +
  scale_colour_brewer(palette = 'Dark2') +
  theme_bw()


#export the dataset to the data folder.
usethis::use_data(RivOtter_OtherSigns, overwrite = TRUE)