From 1806 to 1814 Jefferson strove to have the expedition's history published, but the appearance of Biddle's work in the latter year by no means ended the usefulness of the manuscript journals in the eyes of the originator of the enterprise. Fully appreciating the value of the documents, the former president began a campaign to bring the material together under safe management. "The right to these papers is in the government," Jefferson declared, and he wished to reclaim them for the nation.  There was, however, no adequate national repository at the time, so Jefferson decided on the American Philosophical Society, with which he had been associated for so long, as the most reliable custodian for such items. As president of the society he was sure that the documents would receive proper care under that institution's stewardship. In fact, Jefferson was the first to obtain any materials from the expedition for inclusion in the society's archives, from the estate of Philadelphia naturalist Benjamin Smith Barton.
As noted in the Introduction, Lewis had discussed the intended publication of the history of the expedition with Barton in 1807 and may then have commissioned Barton to prepare the scientific portions of the work. Clark arranged for Barton to Carry to carry out this task in 1810, and in order to give both Biddle and Barton access to the journals, Clark decided to have the natural history portions of the daily journals copied into other notebooks for the naturalist's use. In many of the journals, passages are scored out and the words "copy for Dr. Barton" interlined or written in the margin. Biddle carried three such notebooks, Codices P, Q, and R (under Coues's system), from Fincastle to be turned over to Barton. Barton failed to carry out his assignment, but the three notebooks remained in his possession until his death in 1815 and were not used by Biddle for his edition. Biddle had access to the same material as Barton, since he had the regular journals from which the copies were made, but he did not utilize the scored passages in his volumes, and relatively little on natural history appears in the 1814 edition. Some years later, Biddle recalled his delivery to Barton: "My impression however is that the packet for Dr. Barton consisted of small notebooks and some papers. The books were chiefly extracts relative to natural history taken from the original journals." 
After Barton's death, José Corrèa da Serra, Portuguese diplomat and friend of Jefferson, recovered the three notebooks for Jefferson. Corrèa da Serra obtained one notebook from Barton's widow in March 1816 and sent it to Jefferson by way of the president's granddaughter, Ellen Wayles Randolph, who had been visiting Philadelphia. In June, Corrèa de Serra obtained three other notebooks from Barton's estate but discovered that one was not an item from the Lewis and Clark expedition and returned it to the widow. Jefferson deposited the three natural history journals with the society in November 1817. 
Lewis had entrusted the plant specimens from the expedition to the botanist Frederick Pursh, who carried a number of them off to Europe. He described many of them and applied Latin binomials, giving appropriate credit to Lewis and Clark. While some of the specimens disappeared, others eventually returned to America; all are now in the Academy of Natural Sciences of Philadelphia. Many of the zoological and ethnological specimens went to the artist and naturalist Charles Willson Peale, to be displayed in his Philadelphia museum, then the only public natural history museum in the country. After Peale's death they were scattered and virtually all are lost.  The botanical specimens at the academy will form a separate volume of this edition, and an introduction to that work will discuss the nature and provenance of that collection.
With Barton's material secure in the American Philosophical Society, Jefferson worked to get the remaining journals—those in Biddle's hands—into the society's vaults also. In fact, in September of 1816, at the same time he was working to recover the journals in Barton's estate, Jefferson began a correspondence to regain the "travelling pocket journals" for the government. Clark quickly authorized Biddle to deliver all the papers from the expedition to Jefferson but left Biddle the best judge of which papers to release. Clark also added certain stipulations concerning the documents: that John Ordway's journal be returned to him since the captains had personally purchased it from the sergeant; and that Clark, his heirs, or agents should have access to the papers at all times. 
In April 1818, Biddle supposedly turned over to the society all the materials he had in hand, with the exception of Ordway's journal, which he was supposed to return to Clark. Along with the materials, Biddle submitted a list of the items he was delivering to the society. That list and society accession records stand as the first small survey of Lewis and Clark documents.  The deposit included the following:
Fourteen volumes of the Pocket Journal
of Messrs. Lewis & Clark.
A volume of astronomical observations
and other matter by Captain Lewis.
A small copy book containing some notes
by Captain Lewis.
A rough draft of his letter to the
President from St. Louis announcing his return.
Two statistical tables of the Indian tribes
west of the Mississippi river made by
Governor Clark. 
After their deposition in 1818, the journals remained in the vaults of the American Philosophical Society, obscure and almost unused, until their discovery by Elliott Coues in 1892. Late in that year Coues obtained permission to take them to his home in Washington, D.C., and there he set to work to classify, collate, describe, and arrange in chronological order those important documents. Working tirelessly throughout the Christmas season, Coues by mid-January 1893 had completed his survey of the journals deposited by Jefferson and Biddle and presented a report of his findings to the society. Coues explained that he had discovered "18 bound note books, and 12 small parcels of other Mss., making in all 30 codices . . . something like 2,000 written pages." Coues found thirteen volumes bound in red morocco, the so-called red books, which he designated as Codices D through P; four notebooks bound in marble-covered boards, which he labeled Codices A, B, Q, and R; a single journal bound in brown leather, which he called Codex C; and twelve loose parcels (many containing sheets torn from the red and marble-covered books), which he covered and interspersed with the other codices and which he arranged as Codices Aa, Ba, Fa, Fb, Fc, Fd, Fe, Ia, La, Lb, S and T. He designated those fragments according to the notebook journal to which each was closest in time. Thus, Lewis's Codex Aa contains entries for two days in the same period of some three months covered by Clark's Codex A. In his report Coues also gave descriptions of each codex that until this day have stood as the definitive survey of the journals. 
Coues was not the first to codify the journals. Clark had numbered some of the journals during the expedition and used the numbers in cross-references. Codices A, B, and C he called numbers 1, 2, and 3; Voorhis No. 1 (to be discussed below) was his number 4; and Codex G was number 5. Although his cross-references are not so direct, Clark seems to have used the numbers 6, 7, and 8 to designate Codices H and I and Voorhis No. 2. Later, Biddle imposed his own numbering system, and present Codices A–N became notebooks 1–14. Clark apparently adopted Biddle's numbering system when the men worked on the journals together at Fincastle. Several of the double-lettered codices (like Codex Fb) are cross-references to Clark's regular journals using Biddle's numbers rather than the captain's own system from the expedition. This edition will use Coues's system. 
Lewis and Clark made their daily entries in journals that Coues called Codices A–N, and the loose sheets he arranged as double-lettered codices. Codices A–N were the "fourteen volumes of the Pocket Journal of Messrs. Lewis & Clark" deposited by Biddle. Biddle would not have listed the double-lettered items separately. In his time they were not individually bound documents but were probably separated or loosely inserted into the regular notebooks when Coues discovered them. The contents of the remaining six notebooks and covered sheets that Coues designated as Codices O, P, Q, R, S, and T are quite dissimilar to the other journals. Lewis and Clark apparently reserved them for noting miscellaneous observations and events, and for that reason they are here called the specialized journals. 
While in the East after the expedition in 1807, Lewis made arrangements with other persons besides Barton to aid him in publishing the results of the transcontinental trip. He turned to Ferdinand Rudolph Hassler, a Swiss mathematician at West Point, for help with the astronomical observations that he and Clark had so carefully taken on the trip. When in 1810 Clark began to collect the papers left in Lewis's estate, he noticed that the book of astronomical observations was missing and queried Hassler on its whereabouts. We must assume that Lewis left such a notebook with Hassler. Strong evidence suggests that Hassler had one of the red books from the journey, an item Biddle listsed as a "volume of astronomical observations and other matter by Captain Lewis." This is the notebook that Coues labeled Codex O. 
Codex O is actually in two parts and is completely in Lewis's hand. The first part is filled with astronomical observations from May 18, 1804, to March 30, 1805; the second part is a summary of the principal affluents of the Missouri River from Camp Dubois to Fort Mandan, with information about streams higher up gleaned from Indian testimony. The notebook was prepared at Fort Mandan based on the captains' field notes, their on-the-spot astronomical observations, and their discussions with Indians and traders. It is generally believed that this notebook was sent to Jefferson in April 1805, as the permanent party of the Corps of Discovery started out of Fort Mandan and as another group returned to St. Louis carrying a boatload of artifacts, papers, and specimens to be forwarded to the president. Codex O would have been among the papers sent to Jefferson. If so, then Lewis would have regained the journal from the president in early 1807 and probably turned it over to Hassler at that time. 
As far as can be determined, Hassler made only one mention of the journal in his possession. Calling it "a fair copy, which I see has many faults in writing," Hassler wrote that "my journal in hands goes till Fort Mandan [point of observation] No. 51." Codex O is the only notebook that answers the desecription. Daily entries in the regular journals often carried the longitude and latitude readings within the text, but the reading for point of observation No. 51 is found only in Codex O. By 1810 Hassler was asking to see the original diaries so he could examine all the astronomical observations made during the expedition, but Biddle was unwilling to let them go. Thus, Hassler may have been hampered in his work, and he later complained that he could have finished the work in 1807 if he had received all the material then.  Nothing is known of Codex O again until 1817 when Jefferson was attempting to bring all the journals together, at which time it was reported that Hassler had "given up the calculations in despair." It is unknown when Hassler relinquished the journal in his possession, but it was among the papers that Biddle delivered to the society in April 1818. 
Codices P, Q, and R already had some specialized material in them and also contained many blank pages. As such, they were ideal for another purpose; those three notebooks were used for transferring the natural history material from the regular journals, so that both Biddle and Barton could have access to expedition documents at the same time. Lewis, the naturalist of the expedition, apparently placed some miscellaneous observations of plants and animals in the notebooks. Codex Q had Lewis's zoological notes from July 30, 1804, to about January 1806. Codex R contained Lewis's botanical notes from May 10 to November 17, 1804, and a zoological note on "a bird of the Corvus genus" (black-headed jay). Codex P had only a few pages of weather information and only a couple of lines of daily entry writing, which are overwritten and barely readable. Biddle or Clark apparently tore the pages of daily entry material out of the notebook to use the blank pages on either side for copying purposes. Coues found the daily entry pages (Lewis's remarks for September 9–11, 1805) as loose sheets, which he covered and labeled Codex Fc. Coues failed to note, however, that the loose pages came from Codex P and that the entry for September 10 in Codex Fc stops abruptly in midsentence. It connects very nicely with words in Lewis's hand upside down from the main text on p. 80 of Codex P.
Clark started copying the natural history material into Codex P, following some of Lewis's writing in the first pages of the notebook. He began with April 9, 1805, immediately after the group left Fort Mandan and where the first natural history material occurs at that time. Several lines into the copied entry another hand takes up the copying. In fact, there appear to be two hands at work on copying besides Clark, who wrote only a few lines here and there in Codex P. Biddle does not seem to have done any of the copying in any of the three Codices, P, Q, and R, and it may be that the copying was completed before Biddle arrived at Fincastle. The identity of the copyist or the copyists remains a mystery. It may be that Clark hired a clerk from Fincastle or someone earlier at St. Louis, or perhaps a family member did the work. The copyist made a number of errors. For instance, incorrect dates appear for some entries and several entries may be combined under a single date. Also, some of the material designated "copy for Dr. Barton" was overlooked, such as an entry for September 20, 1805, in Codex Fd. Biddle may have noticed this oversight later, for a note by Biddle in the codex calls attention to this passage. 
The copying in Codex P ends with an entry for February 17, 1806, and the few remaining pages of the journal are filled with Lewis's weather data—placed there during the trip or immediately thereafter. During the period of this copied material (April 9, 1805, through February 17, 1806) there exists a large gap in Lewis's regular journal-keeping. The hiatus is roughly from August 26, 1805, to January 1, 1806, with only a few scattered entries of daily events (such as the material in Codex Fc) but with no natural history notes. It is noteworthy that the copied entries in Codex P fall off dramatically during this same period. There are only two notebook pages of natural history notes for seven days (October 17, 23, November 19, 29, December 9, 27, and 31, 1805). The entries are fewer and shorter for this period than for those either preceding or following it. All the material comes from Clark's journals at the society, which Coues labeled Codices H and I. Perhaps Lewis kept no regular journal during this time; at least, it is apparent that neither Clark nor Biddle had access to additional Lewis items for copying into the notebook.
After filling up the available space in Codex P, the copyist began to enter material into Codex R. The first entry takes up where Codex P left off, February 18, 1806, and the copying continues until March 11, 1806, when the notebook is filled. Again an unknown writer is at work on the copying; the copyist appears to be the second person who was working on Codex P. Clark apparently did no copying in this codex or in Codex Q, but he may have written directions for Barton here and there in both books. The copyist finally turned to Codex Q to enter the remaining natural history material, and it appears that the same person completed both Codices R and Q. Codex Q carries the natural history matter from March 11 to August 10, 1806, about when Lewis stopped his journal writing. There were several blank pages left in the journal after the final copied entry so the copyist placed additional specialized material on those pages in order to fill out the notebook. The final few pages were copied from Clark's journals and include entries that precede the initial date of April 9, 1805, in Codex P (i.e., February 12, 27, 1805, and August 22, 24, September 1, 17, 1804). 
Codex S is the least complex of the specialized journals, and its circumstances have been fairly well known since Coues's time. It was the item Biddle called "a rough draft of his [Lewis's] letter to the President announcing his return." It consists of two letters by Lewis on letter paper rather than on notebook paper torn from the journals. The first, dated September 23, 1806, was written to Jefferson and is probably a draft or a retained copy. Jefferson's copy, in his papers at the Library of Congress, contains many small variations from the codex but no substantial differences. The second letter was dated September 21, 1806, and ends in midsentence at the bottom of a page indicating that additional pages are missing. The letter has no addressee, but Coues thought it was intended for the president; Thwaites conjectured that it may have been a draft of a letter that Lewis promised Jefferson in his letter of September 23. If so, however, why the confusion of dates? Donald Jackson believed from the poor penmanship of the letters that they were written on the boats before the men reached St. Louis on September 23. Moreover, it appeared to him that the date "23" had been added some time after the letter was originally written. Thus, the dates on the letters may not be a true indication of the order or time of their execution. After September 23, the captains' opportunity for writing diminished greatly as they were feted and honored everywhere. 
The provenance of Codex T was not apparent to Coues and Thwaites because material unknown to either of them had to come into the archives of the society before the codex would be matched to its missing pages. Moreover, it does not appear on Biddle's list or in the society's accession records. It must have come with the Biddle deposit, but because it was a loose sheet, it went unrecorded until Coues's time—as did the double-lettered codices. In 1913, Charles and Edward Biddle deposited in the Library of Congress thousands of papers accumulated by their grandfather, Nicholas Biddle. In examining the papers prior to their delivery, one grandson discovered manuscripts associated with the Lewis and Clark expedition. These important documents were in time donated to the society and will be discussed below. One item, however, is necessary to understanding the contents of Codex T. 
Among the papers of the Biddle family deposit was a small notebook of forty-eight pages covered with loose boards. The sheets appear to be letter paper cut to a size of about six inches by four inches and used by Clark as a field notebook in place of the regular notebooks. The little field book contains mainly miscellaneous items and is almost exclusively in Clark's hand but with occasional notes by Lewis. Most important perhaps is Clark's field draft of his notes for January 6–10, 1806 (misdated 1805 in the notebook), when he and a small party visited the whale site on the Pacific coast near their winter camp at Fort Clatsop in present Oregon. As might be expected for a field notebook, the entries are irregularly placed and in many instances are nearly illegible. 
Near the end of the notebook is a section in which Clark seems to be correcting some of his earlier estimates of courses and distances of the outbound journey. There are also passages that lay out the most advantageous route across portions of the trip with listings of various geographic points along the way. This material was probably written near the end of the expedition since Clark's route on the Yellowstone River in July and August 1806 is mentioned. The very last material seems to be a summing up of the party's trip from Fort Mandan in April 1805, to Fort Clatsop on the Pacific coast, and the return. The writing ends in midsentence on the last page where the Corps has reached the western slope of the Rocky Mountains in May and June 1806. It is here that the text of Codex T matches that of the field notebook and continues the narrative of the return journey until Clark reached the confluence of the Yellowstone and Missouri rivers. In fact, several words from the text of the field notebook are repeated on the first line of Codex T. The one problem with linking the two conclusively is that the paper differs considerably. Codex T is one sheet, apparently of letter paper, measuring about seven and one-fourth inches by four and one-half inches. Clark may have filled his little notebook and turned to a convenient scrap of paper to finish his writing. Later the scrap piece and notebook became separated while in Biddle's possession and arrived at the society in different accessions: Codex T in 1818 and the field notebook a century later. So exactly do the texts match that they will be combined in the new edition. 
Coues apparently overlooked two items listed in Biddle's 1818 deposit and did not include them in his description of materials in the American Philosophical Society. The first was "a small copy book containing some notes by Captain Lewis." This notebook has no resemblance to the red or marble-covered journals and is apparently a book that Lewis used some years before the expedition without filling. Into this notebook he placed some botanical notes from the expedition, but for the most part the pages are filled with weather data. For this reason it is here called the Weather Diary. The weather entries are in the hands of both Lewis and Clark, but Lewis has done a greater share of the writing. The notes cover the period from January 1, 1804, to April 9, 1805, but entries fall off sharply after May 14, 1804, as the expedition got underway from Camp Dubois. Indeed, there are only nine entries between May 14 and September 19, when consistent entries resume, and these nine entries are concerned with natural history observations rather than meteorological matter. This notebook could have returned with the boatload of items destined for Jefferson in April 1805, it could have crossed the continent with the captains, or it may have been buried in one of the caches established by the Corps. Since weather data was also kept in the regular journals, it is not clear whether Biddle used this notebook or the daily-entry journals for the weather tables appended to his work. 
Biddle's other item of deposit undetected by Coues was "two statistical tables of the Indian tribes west of the Mississippi river made by Governor Clark." The first of the two tables was the "Estimate of Eastern Indians," originally executed by Clark at Fort Mandan. At least two copies were made—one sent to the secretary of war in April 1805, which is now lost, and a second copy, which is now at the society. Jefferson prepared his own Message from the President . . . (1806), in which he included a "Statistical View of Indian Nations," from the secretary's copy. There are differences between Jefferson's printed version and the manuscript at the society, to be noted when the material appears in this edition. The other table, now called "Estimate of Western Indians," Clark probably prepared at Fort Clatsop. Clark's "Western Indians" were those west of the Rocky Mountains. The estimate in this statistical table may have come from notes already written into Codex I, with revisions of tribal numbers and changes from the original codex draft from place to place. Variations with the codex will be noted in this edition. 
Other journals from the expedition reemerged in 1903, items that Clark had retained after the return of the Corps of Discovery. In August of that year Thwaites discovered a wealth of journals, maps, letters, and other material in the New York home of Julia Clark Voorhis and her daughter Eleanor Glasgow Voorhis. Julia had obtained the material from the estate of her father, George Rogers Hancock Clark, the fourth child of William Clark. The Voorhis manuscripts were a golden find of hitherto unknown materials and are now deposited as the Voorhis Collection in the Missouri Historical Society, St. Louis.  The letters relating to the expedition have appeared in Jackson's work, while the maps are printed in the Atlas of the present edition and are for the most part at Yale University. Some of the miscellaneous material will appear in this and subsequent volumes of this edition or will be useful in annotating journal items.
The principal items of the Voorhis journals consist of five notebooks—four like the red books at the American Philosophical Society and one a field book bound in rough elkskin. The first three red books are standard daily-entry journals in Clark's hand and cover the periods of April 7–July 3, 1805 (Voorhis No. 1), January 30–April 3, 1806 (Voorhis No. 2), and April 4–June 6, 1806 (Voorhis No. 3). The fourth red book, also by Clark, has no daily-entry material but rather carries miscellaneous material including weather data, distance estimates, botanical and zoological notes, statistics on Indians, a few longitudinal and latitudinal readings, and additional notes from later periods. The Elkskin-bound Journal covers the period from September 11 to December 31, 1805, and is clearly a notebook that Clark kept in the field; the material is repeated in Clark's Codices G, H, and I at Philadelphia.  There is an additional red book in the Voorhis Collection, but it is filled with memoranda unrelated to the expedition. On the outside front cover that notebook carries the words, "9 to 12 Augt. 1806" but has no entries for that period. As noted in the Introduction, Codex Lb at Philadelphia covers those very dates in Lewis's hand and must originally have been pages from that notebook.
The Voorhis Collection also includes an unbound Orderly Book that was once a part of one of the marble-covered books. The orders cover the period from April 1, 1804, to January 1, 1806, and occur once or twice a month from February to August 1804; then come two orders for October 1804, and a final one for January 1806. The orders are in the handwriting of Lewis, Clark, and Ordway, in about equal proportions. Two earlier orders by Lewis (February 20 and March 3, 1804) are on letter paper and are not repeated in the Orderly Book; one fragment of letter paper carries part of an order by Clark (April 7, 1804) which appears in full in the book in Ordway's hand. It may be that Lewis and Clark were writing the orders separately and then transferring them to the Orderly Book.
Two other items from the Voorhis Collection appear to be field notes kept by Clark. One is an apparent first draft of daily-entry notes from April 16 to 21, 1806, that is repeated by Clark in Voorhis No. 3. The other field draft covers the dates July 13–19 and July 24–August 3, 1806, while Clark was on the Yellowstone River. Thwaites did not print this latter material, probably because he thought it too repetitious of existing entries in Clark's Codex M; it will be printed in this edition. The writing is almost exlusively course and distance notes but much more extensive than that written in the regular journals. The gap in the journal-writing occurs because the Yellowstone party camped for several days in July in order to build canoes to float the remainder of the river, so no course and distance record was needed. 
Why did Clark not leave the materials with Biddle after their visit at Fincastle in 1810 or else turn them over to the American Philosophical Society in 1817 when Jefferson was attempting to bring all the expedition materials together in a safe depository? It is certain that Biddle at least saw the Voorhis journals, because in one (Voorhis No. 4) he has jotted some queries and requests to Clark. Probably he viewed the journals at Fincastle, scribbled in the notes, but left Clark to take them back to St. Louis. Thwaites's answer to the question of Clark's reason for keeping the journals was that much of the material was repetitious of other journals and that some items may have been deemed of less historical significance. Clark probably reasoned that Biddle had the same coverage in Lewis's notebooks and thus his own were superfluous. This would have been particularly true of Voorhis No. 2, which was written during a period when Clark was largely copying Lewis's notes verbatim. Of course, the Elkskin-bound Journal material was also repeated for Biddle, and in a neater, more legible format, in some red books. 
In 1913, besides the small notebook that fits with Codex T, Biddle's grandsons discovered other expedition items among their grandfather's papers. The heirs recovered all the items associated with the expedition from the Library of Congress where they had been placed and deposited them with the American Philosophical Society between 1915 and 1917.  One of the more important pieces was the journal kept by Lewis, and later Clark, of the preliminary trip from Pittsburgh to Camp Dubois, from August 30 to December 12, 1803, here called the Eastern Journal. In spite of a two-month gap, the entries cover a period of which little had previously been known. Besides the important information about this portion of the expedition, the notebook also contains extensive notes by Biddle, probably made during his visit with Clark in April 1810. The ninety-three pages of notes, rather than the daily entries in the Eastern Journal, might explain why Biddle retained the notebook. Actually, these notes are only the latter portion of the notes he made at Fincastle; the remainder are in a notebook like the marble-covered books, which forms another items of the Biddle family deposit. A great number of pages are missing from the front of that book and it is quite possible that the Orderly Book at St. Louis was once under the covers. Perhaps Biddle tore the orderly pages from the book at Fincastle to utilize the remaining blank pages, gave the orders to Clark, and when he had filled the unused pages simply continued his writing on blank pages of the Eastern Journal. 
After editor Quaife had completed his work of publishing the Eastern Journal and Ordway's journal, the Biddle family presented more expedition items to the society, but none were as exciting as Ordway's or the Eastern Journal. One group of manuscripts in that deposit, called the "three memo books," includes the Biddle notebook in which were written points of discussion with Clark at Fincastle in 1810 (the companion to the notes in the Eastern Journal), Clark's notebook with the first draft for January 6–10, 1806 (discussed above in connection with Codex T), and a journal kept by Clark on a trip to make a treaty with the Osages in 1808. 
The final manuscripts in the Biddle family's donation are called the "seven manuscript items." Five of those items—all in Clark's hand and never before published—will be included in this edition at appropriate spots: (1) "The Countrey and Rivers in advance or above the Mandans"; (2) and (4) "A Slight view of the Missouri River"; (3) "A Summary Statement of the Rivers & Creeks which fall into the Missouri"; and (5) "[A statistical?] view of the Indian Nations inhabitating the territory of Louisiana and the countries adjacent to its northern and western boundaries." The first and third items are very similar to material in Lewis's Codex O and may have been preliminary notes for that codex. Items two and four appear to have once been a single document and will be combined when printed. The last item may have been a preliminary version of the tabular statement on the Eastern Indians. Of the two items that are not included in this edition, one (6) is labeled "Extracts from Capt. Mackay's Journal." It is printed elsewhere and is discussed in the introduction to this edition's Atlas. The final item (7) is a sheet that may have served as a wrapper for the other six pieces and is marked on one side in Clark's hand "For Mr Biddle." On the reverse it has some jottings by Clark in answer to queries by Biddle. The jottings may have been a draft for Clark's letter to Biddle of December 7, 1810, and the "seven manuscript items" were probably enclosures with that letter. Those items for the most part, then, were probaly copied into Codex O and the Estimate of Eastern Indians during the stay at Fort Mandan. 
Why did Biddle retain the "seven manuscript items" instead of turning it over to the American Philosophical Society with the other expedition manuscripts in 1818? Recall that Clark had left Biddle "the best judge of the papers to be delivered" to the society. Biddle probably viewed the items as drafts that were duplicated in the notebooks that he gave to the society. Moreover, he may have considered them as Clark's personal papers since they came to him later and were not a part of the materials he received at Fincastle. Biddle probably did not return them to Clark through some oversight, similar to his keeping of Ordway's journal and the Eastern Journal. When Biddle placed expedition materials with the society in 1818, he noted that he was depositing the manuscripts that he had received from Clark in the spring of 1810—"the papers & documents deemed necessary for the publication of the Travels." Thus it seems that Biddle had separated the two groups of documents in his own mind as he had also separated them before his deposit. 
The history of the Clark Field Notes, as indicated in the Introduction to this volume, is both simple and mysterious. There seems no reason to doubt that those sixty-seven sheets, aptly desecribed as "rough" notes, were written by Clark at Camp Dubois and on the journey up the Missouri on the dates given, as preliminary notes for his notebook journals. As explained in the Introduction, it seems likely though not certain that Clark sent the River Journal to Jefferson from Fort Mandan in April 1805, at the same time sending the Duois Journal to his brother Jonathan Clark for safekeeping. Apparently he retrieved the River Journal from Jefferson on his return in 1807; at any rate, he evidently put the Dubois and River journals together at some time, for they were found in one bundle. Biddle evidently saw the River Journal in 1810, since he made notations of the dates on most of the sheets, but he either did not take them with him after visiting Fincastle that year or returned them to Clark later. How they made their way from Clark's possession to General Hammond's desk in St. Paul is unknown. 
The federal government sought to gain possession of the Field Notes after their discovery in 1953 on the ground that the expedition had been a government enterprise and all documents produced on the journey were public property. This doctrine, once established, could have applied equally well to the expedition documents at the American Philosophical Society and the Missouri Historical Society. Jefferson might have agreed, considering his statement that "the right to these papers is the government," but the federal courts did not sustain this view. The Field Notes are now in the keeping of the Beinecke Library at Yale University, along with most of the original maps. 
A final journal, here called Lewis's Astronomy Notebook, is a relatively new discovery that has never before been printed. This is apparently a child's copybook that Lewis used before the expedition when he visited Philadelphia and trained with Robert Patterson in taking astronomical observations. Patterson placed instructions and examples in the book, and it is filled with tables, charts, and explanations for celestial sightings in both men's hands. It even contains actual observations from May 20 and 21, 1805. It also includes a map by Lewis given him by Yellept, principal chief of the Wallas Wallas, about April 27, 1806, during the party's final days on the Columbia River. The map and observations will appear at appropriate places in this edition. The book's provenance before 1928 is a mystery. It was purchased in that year by the State Historical Society of Missouri, Columbia, from the heirs of William Clark Breckenridge (no relation to the captain), a noted St. Louis collector of Missouriana. It was first discovered by John Logan Allen, and the map was printed in his Passage through the Garden. 
Enlisted Men's Journals
Another of the large remaining questions concerning the journals of the Lewis and Clark expedition is whether the presently known records of the enlisted men are complete. Faced with a knowledge of repeated discoveries of expedition manuscripts over the years, no one would state unequivocally that we now have the total literary records of the expedition. Moreover, it is well known that there are great gaps in the subordinates' writings, as there are in the captains', and often in such a haphazard arrangement as to imply the existence of additional notes. The known journals of the enlisted men can be quickly but not definitively explained. Sergeant Patrick Gass's original journal is missing, and all that remains of his writing is the severely edited version done by McKeehan, which is discussed in the Introduction.
The journal of Sergeant Charles Floyd, at the State Historical Society of Wisconsin, is brief because the author died early in the trip (August 20, 1804) near present Sioux City, Iowa. Floyd's journal was probably sent to his relatives in Kentucky in April 1805 with the returning crew. Thwaites discovered Floyd's journal in 1893 among the papers of Lyman Draper, former head of the State Historical Society of Wisconsin, but it is not now clear how Draper came to have the journal. Draper received a large collection of Clark materials from John Croghan, Clark's nephew, and the Floyd journal may have been among those items. Draper also corresponded with Mary Lee Walton, a sister of Floyd, and she may have been the source for the journal, although nothing in their correspondence indicates it. Or, Draper may have gotten the journal from some unknown person at an unknown date. His records of acquisition are practically nonexistent, and the journal's provenance has long been lost. 
Private Joseph Whitehouse's journal is in two versions, both now at the Newberry Library, Chicago. The first version is the private's original manuscript and is in three parts bound under a single cover of animal hide, perhaps elkskin. The journal covers the period from May 14, 1804, to November 6, 1805. When Thwaites discovered the journal in 1903, it was in the hands of Gertrude Haley, whose acquisition of the notebook is somewhat obscure. Thwaites learned that about the time of his death (date unknown), Whitehouse gave the journal to Canon de Vivaldi, an Italian priest. In about 1860, Vivaldi deposited it with the New York Historical Society where it remained until 1893, when he gave Mrs. Haley and her husband an order for it because the couple had advanced him some money. Thwaites became aware of its existence when Mrs. Haley attempted to sell it to the Library of Congress. He persuaded his publisher, Dodd, Mead, and Company, to make the purchase. After Thwaites completed his editing, the journal was sold to Edward Everett Ayer, a Chicago collector of rare books, who eventually donated it to the Newberry Library. The journal is largely in Whitehouse's handwriting, but Clark and at least two other persons have also written in the notebook. The journal contains a number of gaps, most notably from January 21 through April 30, 1805. 
In 1966 a paraphrased a version of Whitehouse's journal was discovered in Philadelphia. That year, George W. White, a professor of geology from the University of Illinois, Urbana, was visiting Sessler's bookstore in the city and was shown the paraphrase. He informed Donald Jackson, a colleague at Illinois, of his find. Jackson had edited the Letters of the Lewis and Clark Expedition in 1962 and immediately realized the journal's significance. He reported the find to the Newberry Library and that institution soon purchased it. The paraphrased version is important for a number of reasons: it fills the gaps in Whitehouse's original piece; it extends the journal-keeping to April 2, 1806; and it reveals that the private probably kept a journal for the remainder of the expedition. This revelation is apparent from a notation preceding the entry of March 23, 1806, which reads, "Volume 2nd." The paraphrased notebook did not allow space for further entries after April 2, which may have been entered in another book now lost. 
The provenance of the paraphrased version is even more obscure than that of the original. The original cover of the notebook had a label that read, "Journal of Captains Lewis and Clark's Expedition. Written by Joseph Whitehouse. Property of E. Clarence Lighthall Mustin A.M. 5851." Before the words "Property of. . ." the words "Formerly the" have been added by another hand and then below "5851" the phrase "Presented to George S. Mustin A.D. 1850." Jackson did a considerable amount of editing work on this journal but eventually decided that there was too little that was new to warrant its publication. It will appear in this edition. During his work Jackson attempted to discover more about Whitehouse and the Mustins but was largely unsuccessful. He also had little success in tracing the journal back beyond Sessler's bookstore because the previous owner of the journal had died. Perhaps someday more information will be discovered, or the remainder of the paraphrased version may be found, or even the whole of the original. 
An examination of Biddle's papers by his grandsons in 1913 led to the discovery of important expedition documents that Biddle, for some reason, had not turned over to the American Philosophical Society. The finding on one volume of the journal of Sergeant John Ordway, for which Thwaites had searched in vain, led to a further search, which turned up not only the rest of the Ordway journal but the Eastern Journal and other papers. Ordway's journal, covering every day of the expedition in three notebooks and written by one of the more literate enlisted men, provides a useful supplement to the captains' accounts. One notebook is a marble-covered piece like Codices A, B, Q, and R, while the others are bound with loose boards or left unbound. Biddle had use of the sergeant's journal while preparing the 1814 History, and a few words scribbled here and there in the books may be his writing. Clark had requested that Biddle return the three volumes to him after using them, because they had been purchased by Clark from the sergeant. Biddle failed to comply, perhaps through an oversight, and the books remained among his papers for a century. 
Lewis had directed all the sergeants to keep diaries, so we should assume that Sergeant Nathaniel Pryor—besides Gass, Floyd, and Ordway—kept a journal, but one has never been found, if it ever existed. Importantly, Clark had specifically directed Pryor to keep a journal when the men separated in July 1806, for Pryor to travel on a special mission to the Mandan Indian villages. Pryor's mission failed prematurely. When he reunited with Clark he discovered that he had left his saddlebags behind, which contained his "papers," but he was able to retrieve the bags before the day was out. Those "papers" may have been journals, but we have no journals by Pryor today. There is one other journal known to be missing—that of Private Robert Frazer—for which a prospectus was published in 1806, but no book ever appeared.
In all, we can count a total of six journals by enlisted men, yet Lewis wrote from Fort Mandan that seven of the men were keeping journals. Lewis may have been excluding Floyd since he had died earlier, leaving us to locate two other journalists. George Shannon has traditionally been thought to have kept a journal, but that seems doubtful. Shannon personally assisted Biddle at Philadelphia during work on the 1814 paraphrase, and although he praised the young man's intelligence and help, the editor never referred to a diary by Shannon, but he did allude to those of Ordway and Gass (the latter probably being the printed version rather than the original). There is some evidence that Private Alexander Willard kept a journal and that it was accidentally destroyed. It could be that Lewis was including Floyd in his count and thus only one other journalist has to be found, and that would be Willard. Lewis's seven journalists, then, would include: Gass, Ordway, Frazer, Pryor, Whitehouse, and perhaps Floyd and Willard.