The present article reports some ciphers used in 1662 by informants for Joseph Williamson (Wikipedia), who served Secretaries of State, Sir Edward Nicholas and Sir Henry Bennet (Lord Arlington), who succeeded Nicholas in October 1662.
By the time of the Civil War, numerical cipher was already common both for royalists (see here) and roundheads (see here). However, the cipher used in letters in French in February 1662 from one Richard Chauran was more old-fashined in that it used various symbols to enlarge the vocabulary of the numerical code. Chauran was an Orangist based in The Hague and apparently he also tackled French and Spanish ciphers (cf. [Chauran] to [Williamson], 12 February 1662, catalog entry of [Chauran?] to [Williamson?]. 7 May 1662, etc.).
Chauran's cipher was basically a numerical cipher with the numbers ranging from 1 to 100 but the same number could represent different words/letters/syllables by symbols above it. For example, the number 29 represents "puis" but 29m (which, in the convention as used in this article, denotes a number 29 with a symbol more or less like "m" above it) represents "s"; 29ω represents "r"; and 29" represents "fait". The number 33 represents "faire" but 33m represents "p": 33ω represents "a"; and 33" represents "pour"; and 33u represents "aucun"; 33: represents "ri". It appears numbers 10-33 with "m" or ω above them are reserved for single letters; numbers with a prime above them represent proper names such as 35' (Roy de Portugal), 61' (Calais), and 69' (Douvre); and other combinations are used for words and syllables. Not only the same numeral is used for many meanings but also the same word/syllable may be represented by various code numbers. For example, "que" is represented by 1^, 2:, 8", 30+, 47u, 74", 82, and 100u. There are also special symbols representing single letters.
Such a convention of using diacritical symbols rather than numbers above 100 to expand the vocabulary of the code is also seen in Spanish ciphers (e.g., Cg.9 (1574) discussed here and Cg.48 (1604-1618) discussed here).
A complete key of this cipher is preserved in PRO as SP 106/6, no. 32 (encoding table) and no. 33 (decoding table). The words and syllables are arranged in the alphabetical order in the encoding table , whereas the decoding table gives sequences of numerically ordered entries under each of the diacritic marks. Although this is not a pure numerical cipher, it has a structure of two-part code.
A letter (in French) of 15 February 1662 from one Wickfort, another of Williamson's informants, who was occasionally mentioned in Chauran's letters, uses the same cipher as Chauran's discussed above. According to the PRO catalog, this cipher (PRO SP 106/6 no. 32) is also used by Wickfort in his letters of 5 March, 19 April, 26 April, 3 May, and 14 May 1662.
His letter of 5 May 1662 used a similar but different cipher: SP 106/6, no. 31 (decoding table) and no. 35 (encoding table). This new cipher uses numbers up to 999. In particular, it uses 30-271 with an overbar, 401-507 with a breve, 500-618 with a plus (+), 400-508 with a circumflex (^), 500-557 with a polliwog-like diacritic (an overbar with a small circle at the left end), 800-999 without diacritics, and 801-980 with a prime. The figures with a prime are reserved for proper names. Numbers 1-135 without diacritics, 1-135 with double dots, 1-135 with a u above them, and 1-137 with a crossed u above them represent single letters and frequently used syllables.
PRO SP 106/6 no. 34 is a decoding table of a similar cipher with a vocabulary in Spanish. It uses 1-211 without diacritics, 1-210 with an overbar, 1-211 with a double bar, 1-211 with triple dots, 1-210 with m, 1-220 with a crossed circle, 1-240 with a grave ("un tiret a rebour"), 1-239 with a double prime ("deux virgule"), 1-234 with a %-like sign (or ./. "une barre et deux points"). Single letters are scattered at several groups in these figures rather than forming their own section.
Another informant, an Orangist based in Leeuwarden (Van Ruyven, aka De Bacquoy) used a usual numerical cipher in his letters (in French) to Willamson.
Low numbers appear to represent single letters.
Numbers above around 50 represent two series of words and syllables genrally arranged in alphabetical order: 51 (accord), 64 (affaire), 270 (France), 595 (votre), 626 (Zelande); 688 (ad), 700 (au), 732 (de), 747 (er), 753 (et), 939 (vo).
Public Record Office (PRO) SP 84/165 (An online catalogue is here.)
GALE CENGAGE Learning, State Papers Online (pdf) ... carries an image of a portion of a letter from Chauran to Williamson dated 12 February 1662.