2. patch analysis

packages

# library(reshape)
# library(ggplot2)
# library(dplyr)
# library(yarrr)
# source('./fncs/21_patch_statistics.R')

data

Dataset including the patch size for every location of roe and red deer location dataset.

• aniyr: unique identifier for animal-year
• study_areas_id: unique identifier study area as defined in the eurodeer database
• sex: biological sex of the animal
• animals_id: unique identifier of animal as defined in the eurodeer database
• acquisition_time: UTC date and time corresponding to a location
• x: x-coordinate of the location using Spatial Reference Identifier SRID 3035
• y: y-coordinate of the location using Spatial Reference Identifier SRID 3035
• forest_density: forest density percentage of the location as defined by the Tree Cover Density Dataset (TCD)
• corine_land_cover_2012_vector_code: land cover classification code of the location as defined by Corine Land Cover - Vector (CLC).
• timex: time in utc
• datex: date
• yearx: year
• mid_or_noon: midnight or noon
• doyx: day of the year
• min: minimum doy in dataset
• max: maximum doy in dataset
• diff_doy: total number of days as defined by the interval (minimum doy to maximum doy)
• timex: time in utc
• prop: overall proportion of locations in the forest as defined by TCD
• prop_night: proportion of locations in the forest during the night as defined by TCD
• prop_day: proportion of locations in the forest during the day as defined by TCD
• count: overall number of locations on which calculations are based
• count_night: number of locations during the night on which calculations are based
• count_day: number of locations during the day on which calculations are based
• TCD_forest_patch_size: patch size in squared meter of forest patch of a location as defined by TCD
  
• CLC_forest_patch_size: patch size in squared meter of forest patch of a location as defined by CLC
  
• TCD_open_patch_size: patch size in squared meter of open patch of a location as defined by TCD
• CLC_open_patch_size: patch size in squared meter of open patch of a location as defined by CLC

# ce <- read.csv2('../data/2_patchsize/red.csv',dec = ',')
# ca <- read.csv2('../data/2_patchsize/roe.csv',dec = ',')
# head(ce)
# head(ca)

Apply patch_stat function

# # CALCULATE NUMBER OF PATCHES AND NUMBER OF FIXES IN A PATCH SMALLER THAN 25 HECTARE 
# patch_ce_l <- patch_statistics(ce, patchsize = 250000)
# patch_ca_l <- patch_statistics(ca, patchsize = 250000)

nr of small patches

First, we calculated the number of patches per individual. Then we sum up all the patches over all populations per species.

# # NR OF PATCHES 
# patch_nr_ce <- patch_ce_l[[1]] 
# patch_nr_ce$species <- 'red'
# patch_nr_ca <- patch_ca_l[[1]] 
# patch_nr_ca$species <- 'roe'
# 
# patch_nr <- rbind(patch_nr_ce,patch_nr_ca)
# patch_nr <- melt(patch_nr, id=c("species","animals_id")) 
# 
# # STATISTICS ABOUT NR OF PATCHES PER INDIVIDUAL OVER ALL POPULATIONS PER SPECIES 
# (r <- group_by(patch_nr, species, variable) %>% 
#     summarise(sum = sum(value), 
#               mean= mean(value), 
#               median=median(value), 
#               max=max(value),
#               min=min(value)))
# barplot(r$sum, 
#         cex.names=0.6,
#         names.arg=c(paste0(r$species, ' ' , r$variable)), 
#         main='total number of patches over all population')

nr of fixes in patches < 25 hectares

First, we calculated the proportion of fixes that is in a patch smaller than 25 hectare, for each individual. Then, we calculate the mean of that proportion over all populations (and thus all individuals)

# patch_fx_ce <- patch_ce_l[[2]]
# patch_fx_ce$species <- 'red'
# patch_fx_ca <- patch_ca_l[[2]] 
# patch_fx_ca$species <- 'roe'
# 
# patch_fx <- rbind(patch_fx_ce,patch_fx_ca)
# (r <- group_by(patch_fx, species, variable) %>% 
#     summarise(mean= mean(Freq), 
#               median=median(Freq), 
#               max=max(Freq),
#               min=min(Freq)))
# barplot(r$mean, 
#         cex.names=0.6,
#         names.arg=c(paste0(r$species, ' ', r$variable)), 
#         main='mean proportion of fixes in small patches (<25ha) per individual over all populations')
# #boxplot(Freq ~ species + variable, data=patch_fx, cex.axis=0.6, main='proportion of fixes in small patches (<25 ha) per individual')
# pirateplot(Freq ~ variable  + species, data=patch_fx, cex.axis=0.6, main='proportion of fixes in small patches (<25 ha) per individual')