Methodology Employed in The Marlowe-Shakespeare Continuum
Authorship attribution studies prior to the second half of the 20th century centered around parallels—similarities of thought or expression between a work of known authorship and a work whose authorship was in question. Unfortunately, some of the parallels were common phrases, or untested to determine how uncommon they were; claimed on the basis of an exceedingly small known body of work by an author; or made due to commonplace similarities of thought. They also failed to take into account the possibility of parody.
In the latter part of the 20th century, attention shifted to a “stylometric” examination of texts for linguistic preferences (“pish,” “i’th,” “‘em”), contractions, and rare words within an author’s canon. Researchers including Cyrus Hoy and David J. Lake made great progress with 17th century texts, helping to distinguish authorship of works in the Francis Beaumont and John Fletcher folios, and to pin down which plays were written by Thomas Middleton. The attribution of the 17th century Pericles to George Wilkins and William Shakespeare was aided by the fact that both the play and the texts used to differentiate Wilkins were written close together in time. It was slower going with 16th century plays, however, which exhibit fewer uncommon linguistic preferences.
With the advent of computers, “computational stylistics” came to the fore, with machines counting function words (“and,” “but,” “in”), lexical words (conjunctions, pronouns, prepositions), or performing principal components analysis derived from applied linear algebra, to find the most frequent words and filter out the others. The results of such studies are, on the whole, unconvincing. Sir Brian Vickers, a respected authority in the field of authorship attribution who appreciates studies that pay attention to language and directly engage with the text, wrote, “Two independent surveys [of computer-assisted attribution studies] by leading practitioners have made the same diagnosis—that the discipline is in a permanent state of confusion.” 
Stylometric studies must be based on assumptions, including the assumption that an author wrote all the words in the works that are employed to establish his baseline vocabulary and linguistic preferences, and that, for the purposes of such baselines, works written several years apart by the same author are treated identically. I was unwilling to make such assumptions.
Instead, I gravitated back in the direction of parallels with a powerful, new tool at my disposal: the searchable Early English Books Online-Text Creation Partnership (EEBO) database. I employed it to develop two new techniques: Matches and Near Matches, and Rare Scattered Word Clusters.
Matches and Near Matches
Parallels in language between plays vary in quality. I sought to locate occasions where linguistic repetition existed and was quite uncommon with the help of EEBO, comprised of 32,863 full texts of works written from 1472 to 1700 at the time of my study.
When a word, phrase, or juxtaposition occurs in EEBO in two or more works I posit to involve the hand of the same person, plus no more than one additional occurrence within forty years of the known or approximate date of authorship, it is called a “Match.” “Near Matches” are terms found in such works plus no more than fifteen other pieces within the 32,863 texts of EEBO.
Here’s an example of an EEBO Match between Titus Andronicus (Shakespeare’s portion) and Marlowe’s Edward II:
What’s this but libelling against the Senate (IV.iv.17)
What call you this but private libelling
Against the earl of Cornwall and my brother? (Sc. vi.34-5)
—EEBO Match: But fby.5 libelling against. ("Fby.5" means the second term follows within five words of the first.)
Authors did copy each other, but a large number of Matches and Near Matches between the work in question and a variety of works by a known author is an important indication that the same hand was involved.
A large number of Matches/Near Matches could, however be due to intentional parody. In The Marlowe-Shakespeare Continuum, I show why I believe that the anonymousThe Taming of a Shrew (a forerunner to The Taming of the Shrew) was a self-parody by Marlowe and Nashe, and Soliman and Perseda was a parody of self and others by Thomas Kyd. A large number of Matches and Near Matches also could represent an extreme case of one playwright copying another, and so I support my attributions with other authorship detection devices: Rare Scattered Word Clusters, Strong Parallels, Other Similarities, Image Clusters, Biographical Connections, and Logic.
Rare Scattered Word Clusters
A Rare Scattered Word Cluster is two to four words or phrases that occur within 100 words of each other in the two works identified plus no more than one other time in EEBO, with at least one of the instances spread out over three or more lines. The reason I stipulate that one of the occurrences be spread out over at least three lines is to lessen the likelihood that it was caused by one author copying another. A Rare Scattered Word Cluster is a robust indication of a single mind at work.
Following is a Rare Scattered Word Cluster for Titus Andronicus (Shakespeare portion), The Jew of Malta (Marlowe portion), Marlowe’s II Tamburlaine, and the anonymous Edward III, which numerous Shakespeare experts now attribute to the Bard. In only these four plays in EEBO do we find: Flint* near.100 heart* near.100 unrelenting*. ("Near.100" means the second term is located within 100 words of the first.) The Edward III and The Jew of Malta excerpts also include “breast(s),” while II Tamburlaine contains “bosom.”
Listen, fair madam, let it be your glory
To see her tears, but be your heart to them
As unrelenting flint to drops of rain. (II.iii.139-41)
With what a flinty bosom should I joy
The breath of life and burden of my soul,
If, not resolved into resolvèd pains,
My body’s mortifièd lineaments
Should exercise the motions of my heart,
Pierced with the joy of any dignity!
O father, if the unrelenting ears
Of death and hell be shut against my prayers (V.iii.185-92)
Edward Plantagenet, in the name of God,
As with this armour I impall thy breast,
So be thy noble unrelenting heart
Walled in with flint of matchless fortitude,
That never base affections enter there. (III.iii.179-83)
The Jew of Malta:
And having all, you can request no more,
Unless your unrelenting flinty hearts
Suppress all pity in your stony breasts,
And now shall move you to bereave my life. (I.ii.141-4)
Strong Parallels and Other Similarities
Strong Parallels and Other Similarities consist of two or more passages that do not contain Matches or Near Matches but possess sufficient points in common to be worthy of note. Here’s an example from Romeo and Juliet (Shakespeare portion) and The Jew of Malta (Marlowe portion).
Romeo and Juliet:
But soft, what light through yonder window breaks?
It is the east, and Juliet is the sun. (II.i.44-5)
The Jew of Malta:
But stay, what star shines yonder in the east?
The lodestar of my life, if Abigall. (II.i.41-2)
Shakespeare’s mind operated via Image Clusters, or groupings of image associations, according to Caroline Spurgeon, author of Shakespeare’s Imagery.
An association between Helen of Troy and “face,” “thousand,” and “ships” runs like a thread through various works I attribute to Marlowe:
Doctor Faustus (Marlowe portion):
No marvel though the angry Greeks pursued
With ten years’ war the rape of such a queen,
Whose heavenly beauty passeth all compare. (Sc. xiii.27-9)
Was this the face that launched a thousand ships
And burnt the topless towers of Ilium? (Sc. xiii.90-1)
II Tamburlaine (Marlowe):
Helen, whose beauty summoned Greece to arms
And drew a thousand ships to Tenedos (II.iv.87-8)
The Taming of a Shrew (Anonymous. DM: Marlowe and Nashe self parody):
More fair then was the Grecian Helena
For whose sweet sake so many princes di[e]de,
That came with thousand shippes to Tenedos. (li. 258-60)
Dido, Queen of Carthage (Marlowe):
Tell him, I never vowed at Aulis’ gulf
The desolation of his native Troy,
Nor sent a thousand ships unto the walls (V.i.202-4)
Richard II (Shakespeare):
Was this face the face
That every day under his household roof
Did keep ten thousand men? (IV.i.271-3)
Troilus and Cressida (Shakespeare):
Is she worth keeping? Why, she is a pearl
Whose price hath launched above a thousand ships (II.ii.80-81)
All’s Well That Ends Well (Shakespeare):
‘Was this fair face the cause’, quoth she,
‘Why the Grecians sackèd Troy? (I.iii.69-70)
Was this a face
To be expos’d against the warring winds? (IV.vi.28-9)
As Gary Taylor wrote, “Biographical evidence cannot often be found, but cannot easily be dismissed when present.” 
Juliet was sixteen years old in the main source for Romeo and Juliet, Arthur Brooke’s poem The Tragical History of Romeus and Juliet, and scholars are not sure why Shakespeare made her younger. According to the play, Juliet was born on Lammas Eve (August 20). Christopher Marlowe had a sister named Joan (or Jane) who was baptized on Lammas Eve and married young, at age 12 ½. She died in childbirth a year later, when she was the same age as Juliet.  Marlowe had a personal reason to view the death of a newly married girl not yet fourteen years old as particularly tragic.
Christopher Marlowe read the first three books of Edmund Spenser’s The Faerie Queene (FQ) at least three years prior to their publication in 1590 (the rest of FQ appeared in 1596). The language of FQ heavily influenced I and II Tamburlaine, c. 1587. The 1590 edition of FQ was 18,081 lines long (606 pages), not counting dedications. So far as I can determine, the earliest occurrence of the phrase “distressed plight” was in the FQ manuscript Marlowe read, where it appears twice: “Into most deadly danger and distressed plight” (II.12.11), and “To comfort me in my distressed plight” (III.5.35). Marlowe's I Tamburlaine picked up the last half of FQ’s III.5.35: “Ah, shepherd, pity my distressèd plight” (I.ii.7).
In the Shakespeare portion of Titus Andronicus, c. 1591-3 we find: “And rather comfort his distressèd plight” (IV.iv.32). Titus Andronicus did not take this language from I Tamburlaine, but rather directly from the line I Tamburlaine echoed in FQ, stitching on the word “comfort” from FQ III.5.35. It is not logical that two separate authors would remember the same line from Spenser’s 18,081-line poem.
A detailed compilation of similarities causes me to attribute the authorship of certain plays to Christopher Marlowe in The Marlowe-Shakespeare Continuum.
The Trapped Fox Approach?
Some 19th and early 20th-century Stratfordian scholars assigned all or part of II Henry VI, III Henry VI and Titus Andronicus to Christopher Marlowe and, indeed, in The Marlowe-Shakespeare Continuum, I present numerous uncommon similarities between these three plays and the works of Marlowe. Although contemporary scholars have been loath to attribute any part of the Shakespeare canon to Marlowe, it is possible that, like a fox caught in a trap, some might try to gnaw off these three plays and give them to Marlowe in order to save the rest of the canon for Shakspere. They are among the least performed of the Shakespeare works, and Titus Andronicus is a gory, horror-filled play.
The problem with this approach is that II Henry VI and III Henry VI share so many linguistic and plot similarities with Richard III. The two earlier plays set up the action and the character of Richard of Gloucester. And if you give Marlowe Richard III, one of Shakespeare's greatest (albeit early) plays, to my mind, the argument is over. As for Titus Andronicus, it is quite well-connected to Shakespeare's Venus and Adonis and The Rape of Lucrece. To offer one example, below is a Rare Scattered Word Cluster between a Shakespeare portion of Titus Andronicus and Venus and Adonis for Shed* near.100 flower* near 100 fresh* near.100 heart*. The excerpts share not only words but also the imagery of blood being shed upon flowers.
Quintus. Upon whose leaves are drops of new-shed blood
As fresh as morning's dew distilled on flowers?
A very fatal pace it seems to me.
Speak, brother. Hast thou hurt thee with a fall?
Martius. O brother, ith the dismall'st object hurt
That ever eye with sight made heart lament (II.iii.200-5)
Venus and Adonis:
Wishing her cheeks were gardens full of flowers,
So they were dewed with such distilling showers...
Knocks at my heart, and whispers in mine ear
That if I love thee, I thy death should fear;
And, more than so, presenteth to mine eye
The picture of an angry chafing boar,
Under whose sharp fangs on his back doth lie
An image like thyself, all stained with gore,
Whose blood upon the fresh flowers being shed (65-6, 659-65)
No, the Trapped Fox Approach, gnawing off part of the canon for Marlowe to be able to attribute the rest of it to William Shakspere of Stratford, will not work.
 Brian Vickers, “Shakespeare and Authorship Studies in the Twenty-First Century,” Shakespeare Quarterly 62 (2011): 106-42, 114.
 Gary Taylor, “The Canon and Chronology of Shakespeare’s Plays,” in Stanley Wells and Gary Taylor, William Shakespeare. A Textual Companion (Oxford: Clarendon Press, 1987), 77.
 Louis Ule, Christopher Marlowe (1564-1607). A Biography (New York: Carlton Press, 1995), 2-3.