data-raw/seabirds.R

In ericmkeen/bangarang: Bangarang data tools for the Kitimat Fjord System

# Seabirds

library(dplyr)
library(readr)
library(ggplot2)

#===============================================================================
# 2013

sib <- read_csv("/Users/ekezell/Downloads/bangarang data/B13package/SIB13.csv")
head(sib)

sib %>% names
sib <- 
  sib %>% 
  mutate(wind_kph_raw = NA,
         wind_hdg_raw = NA,
         min = grp, 
         max = grp, 
         feed = NA,
         dir = NA,
         height = NA,
         plum1 = juv,
         plum2 = NA,
         plum3 = NA
         ) %>% 
  select(date:lat,
         lon = long,
         effort = eff,
         bft, 
         precip,
         knots = vess.spd,
         hdg = vess.hdg,
         wind_kph_raw,
         wind_hdg_raw,
         zone = in.strip,
         line = on.line,
         side = pos,
         best = grp,
         min, max,
         feed,
         motion = bhvr,
         dir,
         height,
         sp1 = spp1, per1 = spp1.per, plum1,
         sp2 = spp2, per2 = spp2.per, plum2,
         sp3 = spp3, per3 = spp3.per, plum3)

sib %>% names


sib$date %>% unique
sib$time %>% unique
sib$time <- stringr::str_pad(sib$time, width = 6, side='left',pad='0')

(yyyy <- substr(sib$date, 1,4))
(mo <- substr(sib$date, 5,6))
(dd <- substr(sib$date, 7,8))
(hh <- substr(sib$time, 1,2))
(mm <- substr(sib$time, 3,4))
(ss <- substr(sib$time, 5,6))
sib$date <- lubridate::as_datetime(paste0(yyyy,'-',mo,'-',dd,' ',hh,':',mm,':',ss))
sib$time <- NULL

sib %>% head
sib$zone %>% table
sib$zone <- NA
sib$line %>% table
sib$line <- NA

sib$sp1 %>% table
sib %>% names

(raw <- sib$motion)
raw %>% table
sib$motion[raw == 'FEED'] <- 'SIT'
sib$motion[raw == '1F'] <- NA
sib$motion[raw == 'FLOC'] <- 'FLY'
sib$motion[raw == 'STAT'] <- 'SIT'
sib$motion[raw == 'FLUS'] <- 'FLUSH'
sib$motion[raw == 'FLYN'] <- 'FLY'
sib$motion[raw == 'MIL'] <- 'SIT'
sib$motion %>% table

raw %>% table
sib$feed <- 'N'
sib$feed[raw == 'FEED'] <- 'Y'
sib$feed[raw == 'FLOC'] <- 'M'
sib$feed %>% table

sib$dir
sib$height

sib13 <- sib

#===============================================================================
# 2014

sib <- read_csv("/Users/ekezell/Downloads/bangarang data/B14package/2014_seabirds.csv")
head(sib)

sib %>% names

sib <- 
  sib %>% 
  mutate(height = NA) %>% 
  select(date, lat, lon = long,
         effort = eff,
         bft,
         precip,
         knots = spd,
         hdg,
         wind_kph_raw = app.spd,
         wind_hdg_raw = app.dir,
         zone:line, side, 
         best:max,
         feed:dir,
         height,
         sp1:plum3)

sib %>% head
sib14 <- sib

#===============================================================================
# 2015

sib <- read_csv("/Users/ekezell/Downloads/bangarang data/B15package/2015_seabirds.csv")
head(sib)

sib %>% names

sib$sp3 %>% table

sib <- 
  sib %>% 
  select(date, lat, lon = long,
         effort = eff,
         bft,
         precip,
         knots = spd,
         hdg,
         wind_kph_raw = app.spd,
         wind_hdg_raw = app.dir,
         zone:line, side, 
         best:max,
         feed:height,
         sp1:plum3)

sib %>% head
sib %>% names
sib15 <- sib

#===============================================================================

cbind(names(sib13), names(sib14), names(sib15))
sib <- rbind(sib13, sib14, sib15)

sib %>% nrow
sib %>% head
sib %>% tail

sib$hdg %>% sort %>% table

sib <- 
  sib %>% 
  mutate(hdg = as.numeric(hdg),
         wind_kph_raw = as.numeric(wind_kph_raw), 
         wind_hdg_raw = as.numeric(wind_hdg_raw),
         best = as.numeric(best),
         min = as.numeric(min),
         max = as.numeric(max),
         per1 = as.numeric(per1),
         per2 = as.numeric(per2),
         per3 = as.numeric(per3))

sib %>% head

effort$precip %>% table
sib$precip %>% table
sib$precip[sib$precip == 'CLR'] <- 'clear'
sib$precip[sib$precip == 'CLR 210 245'] <- 'clear'
sib$precip[sib$precip == 'DRZ'] <- 'drizzle'
sib$precip[sib$precip == 'FOG'] <- 'fog'
sib$precip[sib$precip == 'HAZ'] <- 'haze'
sib$precip[sib$precip == 'POR'] <- 'pouring'
sib$precip %>% table

sib$knots %>% plot
sib$lat %>% plot
sib$lat[sib$lat > 53.8] <- NA
sib$lon %>% plot
sib$lon[sib$lon < -129.8] <- NA
sib$lon[sib$lon > -123] <- NA

sib$hdg %>% plot
sib$wind_kph_raw %>% plot
sib$wind_hdg_raw %>% plot

sib$zone %>% table
sib$zone[sib$zone == '4'] <- 'OUT'

sib$line %>% table

sib$bft %>% table

sib$side %>% table
sib$side[sib$side == '6'] <- NA
sib$side[sib$side == '8'] <- NA
sib$side[sib$side == 'WBW'] <- NA
sib$side[sib$side == 'LB STAR'] <- 'STAR'
sib$side[sib$side == 'BW HELM'] <- 'HELM'
sib$side[sib$side == 'MIDL'] <- 'HELM'

sib$best %>% plot
sib$min %>% plot
sib$max %>% plot
sib$per1 %>% plot
sib$per2 %>% plot
sib$per3 %>% plot

sib <- 
  sib %>% 
  mutate(per1 = ifelse(is.na(per1), 0, per1)) %>% 
  mutate(per3 = ifelse(is.na(per3), 0, per3)) %>% 
  mutate(per2 = ifelse(per3 == 0, (100 - per1), per2))

sib$date %>% plot

sib$plum1 %>% table
sib$plum1[sib$plum1 == '100'] <- NA
sib$plum1[sib$plum1 == 'FALSE'] <- NA
sib$plum1[sib$plum1 == 'TRUE'] <- NA

sib$plum2 %>% table
sib$plum2[sib$plum2 == '000'] <- NA

sib$plum3 %>% table
sib$plum3[sib$plum3 == '000'] <- NA

sib$sp1 %>% unique %>% sort
sib$sp1[sib$sp1 == 'Alcidspp.'] <- 'ALCD'
sib$sp1[sib$sp1 == 'Arctictern'] <- 'ARTE'
sib$sp1[sib$sp1 == 'Bald'] <- 'BAEA'
sib$sp1[sib$sp1 == 'Baldeagle'] <- 'BAEA'
sib$sp1[sib$sp1 == 'Baldeagle100'] <- 'BAEA'
sib$sp1[sib$sp1 == 'Black-leggedkittiwake'] <- 'BLKI'
sib$sp1[sib$sp1 == 'Blackscoter'] <- 'BLSC'
sib$sp1[sib$sp1 == "Bonaparte'sgull"] <- 'BOGU'
sib$sp1[sib$sp1 == "Bonaparte'sgullHer"] <- 'BOGU'
sib$sp1[sib$sp1 == 'Californiagull'] <- 'CAGU'
sib$sp1[sib$sp1 == "Cassin'sauklet"] <- 'CAAU'
sib$sp1[sib$sp1 == 'Comm/Pac'] <- 'LOON'
sib$sp1[sib$sp1 == 'CommonLoon'] <- 'COLO'
sib$sp1[sib$sp1 == 'Commonmurre'] <- 'COMU'
sib$sp1[sib$sp1 == 'Commontern'] <- 'COTE'
sib$sp1[sib$sp1 == 'Fork-tailedstormpetrel'] <- 'FTSP'
sib$sp1[sib$sp1 == 'Glaucous-wingedgull'] <- 'GWGU'
sib$sp1[sib$sp1 == 'GlaucousWingedGull'] <- 'GWGU'
sib$sp1[sib$sp1 == 'H/C/Ggull'] <- 'HTCG'
sib$sp1[sib$sp1 == 'GULLS'] <- 'GULL'
sib$sp1[sib$sp1 == 'H/Cgull'] <- 'HTCG'
sib$sp1[sib$sp1 == 'Herringgull'] <- 'HEGU'
sib$sp1[sib$sp1 == 'HERG'] <- 'HEGU'
sib$sp1[sib$sp1 == 'hummingbird'] <- 'HUMM'
sib$sp1[sib$sp1 == 'Hummingbird'] <- 'HUMM'
sib$sp1[sib$sp1 == 'HUMR'] <- 'HUMM'
sib$sp1[sib$sp1 == 'Jaegersp.'] <- 'PAJA'
sib$sp1[sib$sp1 == 'Kittiwakesp.'] <- 'BLKW'
sib$sp1[sib$sp1 == 'Largegull'] <- 'LAGU'
sib$sp1[sib$sp1 == 'M/Bgull'] <- 'MBGU'
sib$sp1[grep('marb',tolower(sib$sp1))] <- 'MAMU'
sib$sp1[sib$sp1 == 'Mewgull'] <- 'MEGU'
sib$sp1[sib$sp1 == 'Parasiticjaeger'] <- 'PAJA'
sib$sp1[sib$sp1 == 'Pacificloon'] <- 'PALO'
sib$sp1[sib$sp1 == 'PacificLoon'] <- 'PALO'
sib$sp1[sib$sp1 == 'Pelagiccormorant'] <- 'PECO'
sib$sp1[sib$sp1 == 'Phal spp.'] <- 'RNPH'
sib$sp1[sib$sp1 == 'Pigeonguillemot'] <- 'PIGU'
sib$sp1[sib$sp1 == 'PORT'] <- NA
sib$sp1[sib$sp1 == 'Red-neckedphalarope'] <- 'RNPH'
sib$sp1[sib$sp1 == 'Red-throatedLoon'] <- 'RTLO'
sib$sp1[sib$sp1 == 'Rhinocerosauklet'] <- 'RHAU'
sib$sp1[sib$sp1 == 'Smallgull'] <- 'SMGU'
sib$sp1[sib$sp1 == 'Storm-petrel'] <- 'FTSP'
sib$sp1[sib$sp1 == 'STPE'] <- 'FTSP'
sib$sp1[sib$sp1 == 'Surfbird'] <- 'SURF'
sib$sp1[sib$sp1 == 'Surfscoter'] <- 'SUSC'
sib$sp1[sib$sp1 == 'Surfscoter100'] <- 'SUSC'
sib$sp1[sib$sp1 == 'W/H/C'] <- 'WHCG'
sib$sp1[sib$sp1 == 'W/H/Cgull'] <- 'WHCG'
sib$sp1[sib$sp1 == 'Westerngull'] <- 'WEGU'
sib$sp1[sib$sp1 == "Wilson'sphalarope"] <- 'RNPH'

sib$sp2 %>% unique %>% sort
sib$sp2[sib$sp2 == "100"] <- NA
sib$sp2[sib$sp2 == "ABE"] <- 'BAEA'
sib$sp2[sib$sp2 == "EMK"] <- NA
sib$sp2[sib$sp2 == "WBW"] <- NA
sib$sp2[sib$sp2 == "KLB"] <- NA
sib$sp2[sib$sp2 == "S"] <- NA
sib$sp2[sib$sp2 == "SW"] <- NA
sib$sp2[sib$sp2 == "Kitti"] <- 'BLKW'
sib$sp2[sib$sp2 == "Mew gull"] <- 'MEGU'
sib$sp2[sib$sp2 == "W/H/C gull"] <- 'WHCG'

sib$sp3 %>% table
sib$sp3[sib$sp3 == "W/H/C gull"] <- 'WHCG'

sib$effort %>% table
sib$effort[sib$effort == '0'] <- 'off'
sib$effort[sib$effort == '1'] <- 'transect'
sib$effort[sib$effort == '2'] <- 'station'
sib$effort[sib$effort == '4'] <- 'with whale'
sib$effort[sib$effort == '5'] <- 'casual'

#===============================================================================
# Save it

sib %>% head

seabirds <- sib
save(seabirds, file='data-raw/seabirds.rds')
use_data(seabirds, overwrite=TRUE)

document()
data(seabirds)
seabirds %>% head