CA_HAB_Bulletin

Marine Mammal Stranding Data

marine_mammal = read_csv('TMMC_data.csv')

## Parsed with column specification:
## cols(
##   .default = col_character(),
##   Acc_number = col_integer(),
##   Latitude = col_double(),
##   Longitude = col_double(),
##   Admit_Weight_kg = col_double(),
##   Admit_Length_cm = col_double(),
##   Dispo_Weight_kg = col_double(),
##   Dispo_Length_cm = col_double()
## )

## See spec(...) for full column specifications.

marine_mammal_test = marine_mammal %>%
  select(Age_Class, Sex, Common_Name, Strand_Date, Stranding_City, Stranding_County,Stranding_Locality,Latitude, Longitude, Disposition) %>%
  mutate(Strand_Date = as.Date(Strand_Date, format ="%m/%d/%Y")) %>%
  mutate(Year = format(as.Date(Strand_Date, format="%m/%d/%Y"), "%Y")) %>% 
  mutate(Year_Month = format(as.Date(Strand_Date), "%Y-%m")) %>% 
  group_by(Year_Month) %>% #Age_Class, 
  summarize(Counts = length(Year_Month))

marine_mammal_test_date = marine_mammal %>%
  select(Age_Class, Sex, Common_Name, Strand_Date, Stranding_City, Stranding_County,Stranding_Locality,Latitude, Longitude, Disposition) %>%
  na.omit() %>%
  mutate(Strand_Date = as.Date(Strand_Date, format ="%m/%d/%Y")) %>%
  mutate(Year = format(as.Date(Strand_Date, format="%m/%d/%Y"), "%Y")) %>% 
  mutate(Year_Month = format(as.Date(Strand_Date), "%Y-%m")) %>% 
  group_by(Strand_Date, Age_Class) %>% #Age_Class, 
  summarize(Counts = length(Strand_Date))

marine_mammal_year = marine_mammal %>%
  select(Age_Class, Sex, Common_Name, Strand_Date, Stranding_City, Stranding_County,Stranding_Locality,Latitude, Longitude, Disposition) %>%
  na.omit() %>%
  mutate(Strand_Date = as.Date(Strand_Date, format ="%m/%d/%Y")) %>%
  mutate(Year = format(as.Date(Strand_Date, format="%m/%d/%Y"), "%Y")) %>% 
  mutate(Year_Month = format(as.Date(Strand_Date), "%Y-%m")) %>% 
  group_by(Year) %>% #Age_Class, 
  summarize(Counts = length(Year))

marine_mammal_year_ageclass = marine_mammal %>%
  select(Age_Class, Sex, Common_Name, Strand_Date, Stranding_City, Stranding_County,Stranding_Locality,Latitude, Longitude, Disposition) %>%
  na.omit() %>%
  mutate(Strand_Date = as.Date(Strand_Date, format ="%m/%d/%Y")) %>%
  mutate(Year = format(as.Date(Strand_Date, format="%m/%d/%Y"), "%Y")) %>% 
  mutate(Year_Month = format(as.Date(Strand_Date), "%Y-%m")) %>% 
  group_by(Year, Age_Class) %>% #, 
  summarize(Counts = length(Year))

Plots

marine_mammal = read_csv('TMMC_data.csv')

## Parsed with column specification:
## cols(
##   .default = col_character(),
##   Acc_number = col_integer(),
##   Latitude = col_double(),
##   Longitude = col_double(),
##   Admit_Weight_kg = col_double(),
##   Admit_Length_cm = col_double(),
##   Dispo_Weight_kg = col_double(),
##   Dispo_Length_cm = col_double()
## )

## See spec(...) for full column specifications.

# dygraph_test = marine_mammal %>%
#   select(Age_Class, Sex, Common_Name, Strand_Date, Stranding_City, Stranding_County,Stranding_Locality,Latitude, Longitude, Disposition) %>%
#   na.omit() %>%
#   mutate(Strand_Date = as.Date(Strand_Date, format ="%Y/%d/%m")) %>%
#   mutate(Year_Month = format(as.Date(Strand_Date), "%Y-%m")) %>% 
#   group_by(Year_Month) %>% 
#   summarize(Counts = length(Year_Month))

dygraph_test = marine_mammal %>%
  select(Age_Class, Sex, Common_Name, Strand_Date, Stranding_City, Stranding_County,Stranding_Locality,Latitude, Longitude, Disposition) %>%
  na.omit() %>%
  mutate(Strand_Date = as.Date(Strand_Date, format ="%m/%d/%Y")) %>%
  mutate(Year = format(as.Date(Strand_Date, format="%m/%d/%Y"), "%Y")) %>% 
  mutate(Year_Month = format(as.Date(Strand_Date), "%Y-%m")) %>% 
  group_by(Year_Month) %>% #Age_Class, 
  summarize(Counts = length(Year_Month))

dygraph_test$Year_Month = as.yearmon(dygraph_test$Year_Month, "%Y-%m")
don2 = xts(x=dygraph_test$Counts, order.by = dygraph_test$Year_Month)

#dygraph_test$Strand_Date = ymd(dygraph_test$Strand_Date) 
#don = xts(x=dygraph_test$Counts, order.by = dygraph_test$Strand_Date)

dygraph(don2, main = "Sea Lion Strandings", xlab = "", ylab= "Sea Lion Strandings") %>%
  dyOptions(labelsUTC = TRUE, fillGraph=TRUE, fillAlpha=0.4, drawGrid = T, drawPoints = T) %>% #colors="#D8AE5A"
  dyRangeSelector() %>%
  dyAxis("x", valueRange = c(1990, 2018))

  #dyCrosshair(direction = "vertical") %>%
  #dyHighlight(highlightCircleSize = 5, highlightSeriesBackgroundAlpha = 0.2, hideOnMouseOut = FALSE)  %>%
  #dyRoller(rollPeriod = 1)