Pairing criteria included type of ship (i.e., destroyer, cruiser, tender), Pacific location, and service near to the time of CROSSROADS.

The initial selection plan was amended twice. First, because CROSSROADS occurred in the summer of 1946, well after demobilization efforts had gotten under way following World War II, ships in the Atlantic were chosen when it was impossible to find sufficient ships of a given type in the Pacific. Second, because selected control ships did not always supply sufficient numbers of personnel for the comparison cohort to match the desired rating distribution, additional control ships were selected to provide supplements. The additional ships maintain the type of ship choice initially derived from the to-be-matched participant ship.

As discussed above, DNA supplied MFUA with lists of potential control ships; MFUA selected actual control ships from those lists. To identify the enlisted men on these ships, microfilmed muster rolls were obtained from the National Archives. Each muster roll of a Navy ship from the CROSSROADS era provides, for a given date, the complete list in alphabetical order of enlisted personnel on board that particular ship, showing name, service number, and rank/rating (for example, "MMI" is machinist mate, first class).

We selected Navy enlisted controls in such a way that they would have the same rating distribution as participants and would have served on the same types of ships. Before keying individual control names, MFUA developed a distribution of ranks and ratings (based on distribution within participant units) required from each control ship to create a balanced comparison cohort. A muster roll was selected for a control ship, and once the ship identifying information was entered into the computer, the program randomly selected a letter of the alphabet at which keying of the muster roll data for that ship was begun. As each individual rank and rating was entered, it was compared to the distribution of participant ranks and ratings for a specific ship or ship type. If a particular category had not already been filled, the keyer was allowed to enter the corresponding name and military service number. As more names were entered, more rank-rating categories were filled up, and the program accepted fewer names. Although the original software was programmed to match each individual's participant ship to a single control ship, it was later modified to match the type of participant ship to the type of control ship (e.g., submarine to submarine, destroyer to destroyer, etc.). The identification of control officers relied on a different source—deck logs—because Navy officers are not routinely listed on muster rolls.

Marine controls were selected, by and large, in the same way as Navy controls, starting from ship muster rolls. Because 52 percent had missing military service numbers (MSN), the Marine Corps Stat list was searched for MSN; the majority of missing numbers were found. Also, there was no random alphabetical starting point for keying and no range checks on keyed data because, for each selected control unit, the entire list was keyed.

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