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README.md
acquisitions.csv
allCetaceanData.csv
survivalRates.csv

README.md

This folder contains all of the data used in The Pudding article Free Willy and Flipper by the Numbers published in July 2017.

Below you'll find metadata for each file.

acquisitions.csv

  • What is this?: For a whale or dolphin to reside under human care, it must have been captured from the ocean, born in captivity, or rescued. This dataset provides aggregate counts of whales and dolphins that joined the US captive animal population, along with their acquisition methods, between 1938 and May 7, 2017.
  • Source(s): The data used to create this aggregated set came from the US National Marine Mammal Inventory (original data requested on June 15, 2015 via FOIA available here) and from Ceta-Base. Data from Ceta-Base were downloaded May 7, 2017. The complete, cleaned, non-aggregated dataset can be found in allCetaceanData.csv.
  • Last Modified: May 7, 2017
  • Contact Information: Amber Thomas
  • Spatial Applicability: United States
  • Temporal Applicability: March 1, 1938 - May 7, 2017
  • Variables (Columns):
Header Description Data Type
AcqYear The year that an animal joined the captive US community. For captive-born animals, the AcqYear is the year of birth, whereas for wild-caught or rescued animals, AcqYear is the year of capture or rescue. number
Born The aggregate number of cetaceans that were born in captivity during a calendar year. This number only includes live births (i.e., miscarriages and stillbirths are not included in this count). number
Capture The aggregate number of cetaceans that were captured and spent some period of time living in captivity in the US during a calendar year. number
Rescue The aggregate number of cetaceans that were rescued and were deemed unreleasable during a calendar year. It is possible (and even quite likely) that several more animals were rescued in the US each year and either died or were released. This count only includes the animals that survived but could not be released and thus joined the captive US community. number
  • Other Notes: The 25 animals in the database that were transferred from non-US facilities to US facilities are not included in these counts. Of those 25 animals, the most-recently captured was caught in 1997, housed in Mexico for 7+ years and transferred to a US facility in 2005.

allCetaceanData.csv

  • What is this?: A collection of all data that I could find on whales and dolphins that spent some period of time captive in the US between 1938 and May 7, 2017.
  • Source(s): The data used to create this aggregated set came from the US National Marine Mammal Inventory (original data requested on June 15, 2015 via FOIA available here) and from Ceta-Base. Data from Ceta-Base were downloaded May 7, 2017.
  • Last Modified: May 7, 2017
  • Contact Information: Amber Thomas
  • Spatial Applicability: United States
  • Temporal Applicability: March 1, 1938 - May 7, 2017
  • Variables (Columns):
Header Description Data Type
species The common name for an individual animal's species (e.g., Bottlenose, Killer whale; orca etc.) text
id One or more individual identification numbers assigned to an animal. Note: Not all individual animals have an ID number. If an animal has no number, it is denoted as NA. text
name An individual animal's name. Some animals have been known by more than one name. Where possible, the additional name(s) are noted in Notes. text
sex An individual animal's sex.
M = male
F = female
U = unknown
text
accuracy The accuracy of an animal's birth date (i.e., birth dates for wild-caught animals are estimated).
a = actual date
e = estimated date
u = unknown
text
birthYear The year that an individual animal was born (see Accuracy to determine if that birth year is known or estimated). If a birth year is unknown and not estimated, it is coded as NA. number
acquisition The method through which an animal was acquired and brought into the captive cetacean group.
Born = animal was born in captivity
Capture = animal was captured from the ocean
Rescue = animal was rescued (e.g., had stranded or required medical intervention) and was deemed unreleasable.
Note: If the recorder was unsure how an animal was acquired, they may have included a ? with the above code (e.g., born?).
text
originDate The year that an animal entered captivity. For a wild-caught or rescued animal, this will be the year that they were rescued/captured. For captive-born animals, this will be the same as the birth year. Unknown dates are encoded as NA. date
originLocation The location that an animal originated from. For captured/rescued animals this is an approximate location in the ocean (e.g., Atlantic Ocean or Gulf of Mexico, MS, US), but for animals born in captivity it will list the facility where the animal was born. text
mother The name of an animal's biological mother (if known). Note: Some names contain species scientific names (e.g., Cindy (T.t. gilli)). Unknown names are encoded as NA. text
father The name of an animal's biological father (if known). Note: Some names contain species scientific names (e.g., Jethro (T.t. gilli)). Unknown names are encoded as NA. text
transfers A list of facilities that an animal was transferred to, with the approximate dates that they were transferred (e.g., SeaWorld Orlando to New England Aquarium (22-Feb-1982) to Dolphin Research Center (23-Oct-1991)). If no transfers are known, this field is encoded as NA. text
currently The location where a living animal currently resides (as of May 7, 2017) or the last location where an animal lived before it died. If an animal's last location is unknown it is encoded as Unknown. text
region The region of the world where the animal either currently or most-recently lived. text
status The current status of an animal.
Alive = animal is still alive and living in captivity (as of May 7, 2017)
Died = animal has been confirmed as dead.
Stillbirth = Calf that died before birth.
Miscarriage = Calf that was miscarried before full-term gestation.
Released = Animal had lived in captivity for some period of time but has since been released to the ocean.
Unknown = The animal's current status is unknown.
Note: When the recorder of an animal's status wasn't sure exactly what happened to the animal, they may have included a ? with the above code (e.g., stillbirth?).
text
statusDate The date that an animal's status changed. For living animals, the status date is NA, but for animals that have died or been released, this is their date of death or release. date
COD The animal's reported cause of death. For living animals, this is NA.
Note: Use these data with caution. COD is reported differently between facilities and are not always reported by a pathologist that can properly identify the cause of death.
text
transferDate The date an animal was transferred into the US. For animals that were born in the US, this is NA. date
transfer The types of transfers that an animal has been involved with.
US = The animal was only transferred between facilities in the US
Foreign = The animal was transferred from outside of the US into the US.
text
entryDate The date that an individual animal entered the US captive population. For captive-born animals, this is their birth date or the day they were transferred to a facility in the US. For captured or rescued animals, this is either the date that they were captured/rescued or the day that they were transferred from a foreign facility to a US one. date

survivalRates.csv

  • What is this?: Calculated values of Annual and Daily Survival Rates of Bottlenose Dolphins, Killer Whales (orcas), Beluga Whales, and Pacific White-Sided Dolphins in Captivity between 1939 and 2017.
  • Source(s) & Methodology: The data used to create this aggregated set came from the US National Marine Mammal Inventory (original data requested on June 15, 2015 via FOIA available here) and from Ceta-Base. Data from Ceta-Base were downloaded May 7, 2017. The entire course of cetacean captivity has been equally split into three temporal groups (1939 - 1964, 1965 - 1990, 1991 - 2017) . Annual Survival Rate (ASR) was calculated for the entire population of animals that entered captivity during each group as described in DeMaster and Drevenak (1988). Due to small sample sizes and to compare to wild animal ASR, age-specific survival rates were not calculated. Animals that died at younger than 60 days of age (or within the first 60 days after capture) were excluded from analysis, to compare to similarly calculated wild values. Animals that were transferred from non-US facilities were included in these data, starting at the date that they joined the US population.
  • Last Modified: May 7, 2017
  • Contact Information: Amber Thomas
  • Spatial Applicability: United States
  • Temporal Applicability: March 1, 1938 - May 7, 2017
  • Variables (Columns):
Header Description Data Type
species The common name for a species (e.g., Bottlenose, Killer whale; orca etc.) text
yearGroup Denotes which of the 3 groups of years the following values have been calculated for.
A = 1939 - 1964
B = 1965 - 1990
C = 1991 - 2017.
text
sumAnimalDays The total number of days that animals were alive and in captivity in the US between January 1st of the starting year and December 31st of the ending year (except for Group C, where total days were calculated between January 1st 1991 and May 7, 2017). number
count Total number of animals living in captivity in the US during a group of years. number
DSR Daily Survival Rate. Calculated as 1 - (count / sumAnimalDays) number
ASRLow Low estimate of Annual Survival Rate. Calculated as (DSR - (1.96 * (sqrt(DSR * (1 - DSR) / sumAnimalDays)))) ^ 365.25. number
ASRHigh High estimate of Annual Survival Rate. Calculated as (DSR + (1.96 * (sqrt(DSR * (1 - DSR) / sumAnimalDays)))) ^ 365.25. number
ASR Estimate of Annual Survival Rate. Calculated as DSR ^ 365.25. number
  • Calculations: Using R, the above values can be calculated from the values within allCetaceanData.csv with the following script:
library(tidyverse)

years <- c(1939:1964, 1965:1990, 1991:2017)

yearGroups <- as.data.frame(years) %>% 
            mutate(group = ifelse(years < 1985, "A",
                ifelse(years > 1991, "C", "B")))

animalDays3 <- allCetaceanData %>% 
	filter(Status == "Alive" | Status == "Died",
         !(Status == "Died" & is.na(statusDate))) %>% 
	mutate(entryDate = ymd(entryDate),
        entryYear = year(entryDate),
        yearGroup = ifelse(entryYear <= 1964, "A",
                ifelse(entryYear > 1991, "C", "B")),
                max = ifelse(yearGroup == "A" & (statusDate < ymd("1964-12-31")), "Died", 
                ifelse(yearGroup == "B" & (statusDate < ymd("1991-12-31")), "Died", ifelse(yearGroup == "C" & (statusDate < ymd("2016-12-31")), "Died", "Survived")))) %>% 
	mutate(max = ifelse(is.na(max), "Survived", max)) %>% 
	mutate(minA = pmin(statusDate, ymd("1964-12-31"), na.rm = TRUE),
        minB = pmin(statusDate, ymd("1991-12-31"), na.rm = TRUE),
        minC = pmin(statusDate, ymd("2016-12-31"), na.rm = TRUE),
        min = if_else(yearGroup == "A", minA,
                if_else(yearGroup == "B", minB,
                    if_else(yearGroup == "C", minC, ymd("2017-05-01"))))) %>%
	select(-minA, -minB, -minC) %>% 
	mutate(animalDays = min - entryDate) %>% 
	filter(!animalDays < 60) %>% 
	filter(Species == "Bottlenose" | Species == "Beluga" | Species == "Killer Whale; Orca" | Species == "White-sided, Pacific") %>% 
	group_by(Species, yearGroup) %>% 
	mutate(totalAnimalDays = sum(animalDays, na.rm = TRUE)) %>% 
	group_by(Species, max, yearGroup) %>% 
	summarise(sumAnimalDays = mean(totalAnimalDays),
        count = n()) %>% 
	filter(max == "Died") %>% 
	mutate(sumAnimalDays = as.numeric(sumAnimalDays)) %>% 
	mutate(DSR = 1 - (count / sumAnimalDays),
         ASRlow = (DSR - (1.96 * (sqrt(DSR * (1-DSR) / sumAnimalDays)))) ^ 365.25,
         ASRhigh = (DSR + (1.96 * (sqrt(DSR * (1-DSR) / sumAnimalDays)))) ^ 365.25,
         ASR = DSR ^ 365.25) %>% 
	ungroup()