Although the only one of the R Yair's works that is fully extant is his Chavas Yair, he also left behind over 46 volumes of writings in manuscripts. A large part of which was to have been a vast encyclopedic work called Eitz Chaim. All that we have of this is the introduction (printed together with Chavas Yair) and an index (Yair Nesiv) with which one can get a taste of the vastness of the project.
An excellent overview of R' Yair Chaim's life and major works can be found in the JQR 1891 V. 3(this is an English summary of a larger work in German). Here is a small excerpt:
The merest glance at the extent of this collection gives some idea of its richness; a thorough examination of the multiplicity and scientific tone of its contents changes our wonder to admiration. Thus the first volume consisted of 237 leaves, the table of contents of which occupies twenty-four closely written folio pages of the index. The headings that succeed each other in miscellaneous order are somewhat as follows:- Talmud, Agada, Legalism, Ritual, Bible, Homiletics, Ethics, Philosophy, Cabbala, History, and general Criticism.
The variety of the contents, and the rays of light that break through the mental darkness of the period may be illustrated by a few examples from this work. Thus in one passage he asserts that even ethical writings in German are of more value than the greatest and most ingenious Tal-mudical works that are not based upon truth. Elsewhere he excuses the Polish Talmudists for their deficient knowledge of the Bible. The story of two women who agreed that the one who died first should relate to the survivor her experiences after death,' seems to him to be as well worth noting down as the impressive rebuke he administered to his co-religionists for certain defects (and their causes) that had crept into divine service. At one time he inveighs against the misunderstanding of Christian commentators of the Talmudical saying, "Keep back your children from reading," as well as against the reproaches levelled against the Jews for their ignorance of the interpretation of Holy Writ, and then his philosophical reflections cause him to soar aloft to a height whence he recognises how the Biblical verse (Ps. civ. 31) has this profound meaning, that God will only rejoice in the future, for at the present time each day reveals some new imper-fection in the world.
At one time he is defending Abraham Ibn Ezra against the imputation that in his exegesis he disregarded Rabbinical tradition, and at another he traces the development of the system of hospitality among the ancients, and the origin of the so-called Pletten, i.e., the bills for the payment of the expenses of poor students and travellers to whom hospitality was shown. In one passage he seeks reasons for declaring the drawing and hanging up of one's own portrait, and that of one's relatives to be perfectly allowable; in another he puzzles himself about the phenomenon that in a mirror the human face does not seem to turn from right to left. He is as anxious to settle the question whether Maimuni possessed a knowledge of Hebrew grammar, poetry and metre, as whether the Joseph Hacohen mentioned in the Mishna may not be the author of Josippon.
In this part he is engaged in questions of natural science, as, e.g., about objects that are visible and yet cannot be perceived by the sense of touch, and vice versa [A"H- See Chavas Yair No. 233] , or about the query, why drunkem men have thought or presenttiments that are more correct then other men. He further speaks of the superstitious notions of about hobgoblins, elves , and litle fairies as he had read about them in the popular literature of his time.
[ ענין בן תמליון . ושאין חמא על מי שמגדלו בביתו ודברים רבים ראיתי בספרי א"ה וקוראים לו קאבאלד ובכינוי פולדר גייסטער והם דמות ילדים קטנים בלבוש יפה רואין ואינם נראין וכל משרתי הבית משימי' להן בזמן קבוע קערה בתבשיל לאכול הוא עושה להם כל מיני עבודת הבית ובפרט לנקות הרפת ושאר עבודות הבהמות ובלבד שלא ילעיגו עליו או ירבה עליו דברי בזיון ושאר פרטי ענינין ומעשיו שהיו ומהותו לדעתם לא רציתי להאריך]
On the בן תמלין - see TB Mei'lah 17a.
"Especially rich in material was Vol. VII., that contained 282 leaves, and is described in the index from p. 89a-104a. Here he had written out his father's commentary to the tractate of the Mishna, called Kinnim, with his own criticisms and the replies thereto of the author. Natural science, history, and literature were here gathered together pell-mell. The pigmies (Alriunchen) are as much a point of interest to him as the query whether the human race has really deteriorated in stature, strength, and longevity."
The enumeration of the Messianic movements in Jewish history, is as important an object of solicitude as the fixing the date of the composition of the legal code of Joseph Karo, at the years 1522-1542. He makes a note of the supposed introduction of Hebrew words into other languages, such as the word "baar" into German, or the word " null," into Latin, and, like a harbinger of the study of folk-lore, he comments upon the appearance of Talmudical tales in other literatures. Like the Christian theologians, he raises the question, how America was peopled after the flood, and makes use of an opinion of Philo to help him to disprove that Cain married his sister. He holds in pious respect every Jewish custom, but nevertheless reads polemical writings against Judaism, and adduces remarks collected from Wagenseil's works. He
is as much interested in the personal individuality of Bachya b. Joseph, as he is eager to defend Maimuni against the suspicions of Abravanel.
But even if he has not come down to posterity with all the ripe produce of his life's work, nevertheless he has become so deeply impressed upon their memory as to have his name preserved as one of the most prominent men of genius, one of the most important phenomena among the German Jews of the seventeenth century, who, though having his nature deeply rooted in the past was still in advance of his time, and who will always be regarded as the forerunner of the study of Judaism in a historical and scientific spirit.