Telemetry Reports for Tag Owners

#optional subsetted dataset to use: detections with releases filtered out!

tqcs_matched_10_11_no_release <- tqcs_matched_10_11 %>%
  filter(receiver != "release")

#optional full dataset to use: detections with releases filtered out!

tqcs_matched_10_11_full_no_release <- tqcs_matched_10_11_full %>%
  filter(receiver != "release")

base <- get_stamenmap(
  bbox = c(left = min(tqcs_matched_10_11$longitude),
           bottom = min(tqcs_matched_10_11$latitude),
           right = max(tqcs_matched_10_11$longitude),
           top = max(tqcs_matched_10_11$latitude)),
  maptype = "terrain-background",
  crop = FALSE,
  zoom = 8)


#add your releases and detections onto your basemap

tqcs_map <-
  ggmap(base, extent='panel') +
  ylab("Latitude") +
  xlab("Longitude") +
  geom_point(data = tqcs_matched_10_11,
             aes(x = longitude,y = latitude), #specify the data
             colour = 'blue', shape = 19, size = 2) #lots of aesthetic options here!

#view your tagging map!

tqcs_map

#set your basemap

geo_styling <- list(
  fitbounds = "locations", visible = TRUE, #fits the bounds to your data!
  showland = TRUE,
  landcolor = toRGB("gray95"),
  subunitcolor = toRGB("gray85"),
  countrycolor = toRGB("gray85")
)

#decide what data you're going to use

tqcs_map_plotly <- plot_geo(tqcs_matched_10_11, lat = ~latitude, lon = ~longitude)

#add your markers for the interactive map

tqcs_map_plotly <- tqcs_map_plotly %>% add_markers(
  text = ~paste(catalognumber, scientificname, paste("Date detected:", datecollected),
                paste("Latitude:", latitude), paste("Longitude",longitude),
                paste("Detected by:", detectedby), paste("Station:", station),
                paste("Contact:", contact_poc, contact_pi), sep = "<br />"),
  symbol = I("square"), size = I(8), hoverinfo = "text"
)

#Add layout (title + geo stying)

tqcs_map_plotly <- tqcs_map_plotly %>% layout(
  title = 'TQCS Detections<br />(2010-2011)', geo = geo_styling
)

#View map

tqcs_map_plotly

# summary of animals you've tagged

tqcs_tag_summary <- tqcs_tag %>%
  mutate(UTC_RELEASE_DATE_TIME = ymd_hms(UTC_RELEASE_DATE_TIME)) %>%
  #filter(UTC_RELEASE_DATE_TIME > '2019-06-01') %>% #select timeframe, specific animals etc.
  group_by(year = year(UTC_RELEASE_DATE_TIME), COMMON_NAME_E) %>%
 summarize(count = n(),
            Meanlength = mean(LENGTH..m., na.rm=TRUE),
            minlength= min(LENGTH..m., na.rm=TRUE),
            maxlength = max(LENGTH..m., na.rm=TRUE),
            MeanWeight = mean(WEIGHT..kg., na.rm = TRUE))

#view our summary table

tqcs_tag_summary

#Average location of each animal, without release records

tqcs_matched_10_11_no_release %>%
  group_by(catalognumber) %>%
  summarize(NumberOfStations = n_distinct(station),
            AvgLat = mean(latitude),
            AvgLong =mean(longitude))

#First we need to make a tagname column in the tag metadata (to match the Detection Extract), and figure out the enddate of the tag battery.

tqcs_tag <- tqcs_tag %>%
  mutate(enddatetime = (ymd_hms(UTC_RELEASE_DATE_TIME) + days(EST_TAG_LIFE))) %>% #adding enddate
  mutate(tagname = paste(TAG_CODE_SPACE,TAG_ID_CODE, sep = '-')) #adding tagname column

#Now we join by tagname, to the detections without the release information

tag_joined_dets <-  left_join(x = tqcs_matched_10_11_no_release, y = tqcs_tag, by = "tagname")

#make sure the redeployed tags have matched within their deployment period only

tag_joined_dets <- tag_joined_dets %>%
  filter(datecollected >= UTC_RELEASE_DATE_TIME & datecollected <= enddatetime)

View(tag_joined_dets)

# Avg length per location

tqcs_tag_det_summary <- tag_joined_dets %>%
  group_by(detectedby, station, latitude, longitude)  %>%  
  summarise(AvgSize = mean(LENGTH..m., na.rm=TRUE))

tqcs_tag_det_summary

# count detections per transmitter, per array

tqcs_matched_10_11_no_release %>%
  group_by(catalognumber, detectedby, commonname) %>%
  summarize(count = n()) %>%
  select(catalognumber, commonname, detectedby, count)

# list all receivers each fish was seen on, and a number_of_receivers column too

receivers <- tqcs_matched_10_11_no_release %>%
  group_by(catalognumber) %>%
  mutate(stations = (list(unique(station)))) %>% #create a column with a list of the stations
  dplyr::select(catalognumber, stations)  %>% #remove excess columns
  distinct_all() %>% #keep only one record of each
  mutate(number_of_stations = sapply(stations, length)) %>% #sapply: applies a function across a List - in this case we are applying length()
  as.data.frame()

View(receivers)

animal_id_summary <- tqcs_matched_10_11_no_release %>%
  group_by(catalognumber) %>%
  summarise(dets = length(catalognumber),
            stations = length(unique(station)),
            min = min(datecollected),
            max = max(datecollected),
            tracklength = max(datecollected)-min(datecollected))

View(animal_id_summary)

#try with tqcs_matched_10_11_full_no_release if you're feeling bold! takes ~30 secs

tqcs_matched_10_11_no_release  %>%
  mutate(datecollected=ymd_hms(datecollected)) %>% #make datetime
  mutate(year_month = floor_date(datecollected, "months")) %>% #round to month
  group_by(year_month) %>% #can group by station, species etc.
  summarize(count =n()) %>% #how many dets per year_month
  ggplot(aes(x = (month(year_month) %>% as.factor()),
             y = count,
             fill = (year(year_month) %>% as.factor())
  )
  )+
  geom_bar(stat = "identity", position = "dodge2")+
  xlab("Month")+
  ylab("Total Detection Count")+
  ggtitle('TQCS Detections by Month (2010-2011)')+ #title
  labs(fill = "Year") #legend title

#Use the color scales in this package to make plots that are pretty,
#better represent your data, easier to read by those with colorblindness, and print well in grey scale.
library(viridis)

# monthly latitudinal distribution of your animals (works best w >1 species)

tqcs_matched_10_11 %>%
  group_by(m=month(datecollected), catalognumber, scientificname) %>% #make our groups
  summarise(mean=mean(latitude)) %>% #mean lat
  ggplot(aes(m %>% factor, mean, colour=scientificname, fill=scientificname))+ #the data is supplied, but no info on how to show it!
  geom_point(size=3, position="jitter")+   # draw data as points, and use jitter to help see all points instead of superimposition
  #coord_flip()+   #flip x y, not needed here
  scale_colour_manual(values = "blue")+ #change the colour to represent the species better!
  scale_fill_manual(values = "grey")+
  geom_boxplot()+ #another layer
  geom_violin(colour="black") #and one more layer


#There are other ways to present a summary of data like this that we might have chosen.
#geom_density2d() will give us a KDE for our data points and give us some contours across our chosen plot axes.

tqcs_matched_10_11 %>% #doesnt work on the subsetted data, back to original dataset for this one
  group_by(month=month(datecollected), catalognumber, scientificname) %>%
  summarise(meanlat=mean(latitude)) %>%
  ggplot(aes(month, meanlat, colour=scientificname, fill=scientificname))+
  geom_point(size=3, position="jitter")+
  scale_colour_manual(values = "blue")+
  scale_fill_manual(values = "grey")+
  geom_density2d(size=7, lty=1) #this is the only difference from the plot above

#anything you specify in the aes() is applied to the actual data points/whole plot,
#anything specified in geom() is applied to that layer only (colour, size...)

# per-individual density contours - lots of plots: called facets!
tqcs_matched_10_11 %>%
  ggplot(aes(longitude, latitude))+
  facet_wrap(~catalognumber)+ #make one plot per individual
  geom_violin()

# an easy abacus plot!

abacus_animals <-
  ggplot(data = tqcs_matched_10_11_no_release, aes(x = datecollected, y = catalognumber, col = detectedby)) +
  geom_point() +
  ggtitle("Detections by animal") +
  theme(plot.title = element_text(face = "bold", hjust = 0.5)) +
  scale_color_viridis(discrete = TRUE)

abacus_animals

abacus_stations <-
  ggplot(data = tqcs_matched_10_11_no_release,  aes(x = datecollected, y = station, col = catalognumber)) +
  geom_point() +
  ggtitle("Detections by station") +
  theme(plot.title = element_text(face = "bold", hjust = 0.5)) +
  scale_color_viridis(discrete = TRUE)

abacus_stations

# track movement using geom_path!!

tqcs_subset <- tqcs_matched_10_11_no_release %>%
  dplyr::filter(catalognumber %in%
                  c('TQCS-1049282-2008-02-28', 'TQCS-1049281-2008-02-28'))

View(tqcs_subset)

movMap <-
  ggmap(base, extent = 'panel') + #use the BASE we set up before
  ylab("Latitude") +
  xlab("Longitude") +
  geom_path(data = tqcs_subset, aes(x = longitude, y = latitude, col = commonname)) + #connect the dots with lines
  geom_point(data = tqcs_subset, aes(x = longitude, y = latitude, col = commonname)) + #layer the stations back on
  scale_colour_manual(values = c("red", "blue"), name = "Species")+ #
  facet_wrap(~catalognumber)+
  ggtitle("Inferred Animal Paths")

#to size the dots by number of detections you could do something like: size = (log(length(animal)id))?

movMap