The roots of the expedition of Meriwether Lewis and William Clark were already lengthy by the time of the Louisiana Purchase in April 1803. Thomas Jefferson's curiosity about the West was lifelong, sustained by his broad scientific interests and his hopes and dreams for the future of the United States. For at least twenty years before he launched Lewis and Clark across two thousand miles into immortality, Jefferson had planned for a transcontinental expedition starting up the Missouri River. In 1783, while serving in Congress, he asked the frontier Revolutionary War hero George Rogers Clark (the older brother of William) to consider leading a privately sponsored expedition to explore the West. Then, as later, he feared that Britain might secure a foothold west of the Mississippi (then the western boundary of the United States) and forestall American expansion. George Rogers Clark declined the offer. 
A few years later, while minister to France, Jefferson encouraged the hopes of John Ledyard, an American veteran of Captain James Cook's third voyage to the Pacific. Ledyard planned to travel eastward across Siberia, secure passage on a ship to some point on the western coast of North America, and then strike out alone across the continent. It was a far-fetched project at best, and the suspicious Russians frustrated it by expelling Ledyard from their country. 
In 1792 Jefferson, then secretary of state under Washington, and various friends and associates in the American Philosophical Society in Philadelphia tried to interest Dr. Moses Marshall, a physician and botanist from Philadelphia, in undertaking an expedition up the Missouri. They offered a reward of a thousand guineas to Marshall if he could provide proof of having reached the "South Sea," but apparently nothing came of the suggestion. 
The following year, Jefferson sponsored a more promising effort by André Michaux, a French botanist. Acting for the American Philosophical Society, Jefferson sent Michaux west to "find the shortest & most convenient route of communication between the U. S. & the Pacific ocean, within the temperate latitudes, & to learn such particulars as can be obtained of the country through which it passes, it's productions, inhabitants & other interesting circumstances." Avoiding Spanish authorities who might try to stop him, Michaux was to ascend the Missouri and, from its headwaters, locate the easiest route to some major stream flowing into the Pacific. Here already was the basic outline of the Lewis and Clark exploration. To appreciate how ambitious the scheme was it must be remembered that most of the territory Michaux was to traverse and the people who inhabited it were either little known or wholly unknown to Europeans. Moreover, Jefferson had every reason to believe that the Spanish government, which claimed jurisdiction over Louisiana, would be hostile to the project. Only ten years later Jefferson could provide Lewis and Clark with far more information about the lower Missouri and the Pacific Coast than he was able to give Michaux. In any event, Michaux became involved in international intrigues and never crossed the Mississippi. 
Jefferson made no further serious attempt to promote the exploration of the trans-Mississippi West until he became president in 1801; then, circumstances made the project seem not only feasible but also vitally necessary. As president, Jefferson was in a better position to launch such an expedition and to insure adequate financing; in the same year, world political conditions seemed, more than ever, to threaten the preemption of the West by some other nation.
By the time Jefferson entered the White House, there had been several significant advances in knowledge of the country beyond the Mississippi. In 1792, the American sea-going trader Captain Robert Gray had discovered and named the Columbia River. In the same year, Captain George Vancouver of the British Navy had made a thorough survey of the northwest coast, sending one of his officers about one hundred miles up the great river. In the same decade, fur traders from St. Louis, acting under the authority of the Spanish government, moved up the Missouri as far as the villages of the Mandans in present North Dakota. John Thomas Evans, who reached the Mandans in 1796, received instructions from his employer, James Mackay, that seem to anticipate Jefferson's instructions to Lewis and Clark. Evans was asked to ascend the Missouri to its headwaters, inquire of the Indians about a river flowing "toward the setting sun," and descend this stream to the Pacific. Along the way he was to collect specimens of animals and plants and to be "very accurate in his observations concerning the nations." Evans in fact got no farther than the Mandans, where he found British traders extending their commercial network from Canada. Evans's detailed maps of the Missouri from present northeast Nebraska to the Mandan villages were eventually of great assistance to Lewis and Clark. 
The catalyst, however, of Jefferson's decision to launch the expedition was apparently the publication of Alexander Mackenzie's Voyages from Montreal … through the Continent of North America, to the Frozen and Pacific Oceans (London, 1801); therein Mackenzie, a partner in the North West Company of Canada, described his 1789 trip to the Arctic Ocean and his 1792–93 journey across the Rockies to the coast of present British Columbia. He had made the first crossing of the continent north of Mexico and had discovered what he took to be the upper reaches of the Columbia. Having proved that such a crossing was possible, he urged in his book that Britain develop the transcontinental route, in order to secure the fur trade and open commerce with Asia. Here again was the danger that Jefferson had long feared—British preemption of the far West. 
Many historians have seen Jefferson's appointment of Meriwether Lewis as his private secretary in 1801 as evidence that he intended from the first to send the young man on a western expedition, especially since Lewis's knowledge of the "western country" was a factor in Jefferson's choice. Historian Donald Jackson argues that there is no proof of such an intention and suggests that Jefferson may have wished to make use of Lewis's knowledge of the army to weed out officers with Federalist leanings. Although Jefferson had stated the contrary, Lewis's frontier experience, especially with Indians, was meager. One should not forget, however, that Lewis had volunteered in 1793 for the expedition for which Michaux was actually chosen and that in 1805 he would write of the transcontinental exploration as "a darling project of mine for the last ten years." 
In any case, it was Lewis that Jefferson now selected to lead the enterprise on which he had definitely determined by the end of 1802. Born in Virginia in 1774, Lewis had served as an army officer in the Northwest Territory for several years and had some experience with wilderness travel. His formal education was slight by present standards, but he was well read and had the scientific interests that characterized so many of Jefferson's friends. What Jefferson really wanted was "a person who to courage, prudence, habits & health adapted to the woods, & some familiarity with the Indian character, joins a perfect knoledge of botany, natural history, mineralogy & astronomy." His knowledge of Lewis and his acquaintance with the American scientific community told him that Lewis was as close to such a paragon as he could realistically hope to find. 
The Louisiana Purchase did not prompt the expedition to explore west of the Mississippi; Lewis was already on his way across the Appalachians in the summer of 1803 when Jefferson sent him definite word of the diplomatic windfall that had occurred in Paris the previous April. Jefferson's hopes had always pointed toward eventual American penetration of the lands beyond the Mississippi, but the French decision to sell this vast territory presented the United States with an opportunity of which the president could only have dreamed for the distant future. Now an expedition became all the more important as an inspection and an assertion of sovereignty over the new empire. 
Jefferson and Lewis agreed that there must be a second-in-command competent to carry on if something were to happen to the commander; Lewis's choice was his old army friend William Clark. Four years older than Lewis, he had also served several years in the army on the frontier and had been Lewis's immediate superior for a time. After resigning his captain's commission in 1796, he had engaged in family business in Kentucky and Indiana. Clark had visited Lewis in Washington and had made Jefferson's acquaintance. In accepting Lewis's offer, Clark wrote, "The enterprise &c. is Such as I have long anticipated"; his words suggest that the two friends had discussed the possibility of such an expedition, and that Jefferson may have earlier given them both some hint of his plans. 
Lewis and Clark have become inseparable in history, and some historians, in order to distinguish them, have emphasized the contrasts in their personalities. Lewis is stereotyped as the moody, sensitive intellectual, Clark as the tough, pragmatic, barely literate frontiersman. The differences existed, but they may have been exaggerated. Lewis quite adequately demonstrated his mastery of wilderness craft on his great journey, and the expedition did not suffer as a result of Lewis's "hypochondriac affections," which even Jefferson noted in his protégé. If Clark's spelling was versatile and his grammar rough hewn—in a day when the rules were less firmly established than today—Lewis was not altogether a model in those respects, in spite of his more elegant literary style. Both were largely self-educated by today's standards. Clark lacked polish, but neither his vocabulary nor his ideas were those of a backwoodsman. 
Jefferson's conception of the expedition encompassed far more than geographic discovery, important as that was. It would be arbitrary to distinguish between his "practical" and "scientific" goals, for Jefferson, a true son of the Enlightenment, believed all knowledge to be of some benefit. He characterized the enterprise as "purely literary"—devoted to gathering and disseminating scientific knowledge—in sounding out the Spanish minister on his government's possible reaction to the expedition; the minister was understandably skeptical. After the Louisiana Purchase, of course, the practical aspect of the expedition became more immediately relevant. 
Jefferson's final instructions of June 1803, formidable in their scope even to the modern reader, reflect the broad range of interests of the third president. In a day of less rigid academic specialization when the distinction between professional and amateur was not fixed, Jefferson could be not only a political leader but president of the American Philosophical Society, then the principal group promoting scientific endeavor in the United States. Jefferson himself was perhaps the nation's leading expert on the geography of the trans-Mississippi West, and geographic discovery was, of course, one of his principal purposes for the expedition. Lewis and Clark made the last search up the Missouri for the fabled Northwest Passage; they would find that previous conceptions of a single ridge of mountains or a "pyramidal height of land," offering an easy portage from the headwaters of the Missouri to those of the Columbia, were illusions. It remained for Lewis and Clark to discover that the Rockies were a complex series of ranges hundreds of miles wide. Clark's great map of the West, published in 1814, would in itself have justified the expedition. 
Jefferson had much more in mind, however. The captains were to open a highway for the American fur trade, to win over the Indians from Spanish or British influence, and to lay the foundation for what Jefferson hoped would be a carefully regulated trade and intercourse with the Indians that would avoid some of the evils of unrestrained competition and interracial conflict so common in American experience. Further, they were to observe and record the whole range of natural history and ethnology of the area and the possible resources for future settlers. Jefferson expected a great deal of two infantry officers, but they met the challenge. 
Lewis, a student of plants and animals since boyhood, made significant additions to zoological and botanical knowledge, providing the first scientific descriptions of many new species. Only in recent decades have his contributions been fully appreciated. The captains also made the first attempt at a systematic record of the meteorology of the West and less successfully attempted to determine the latitude and longitude of significant geographical points. 
Jefferson's instructions also reflected his lifelong interest in ethnology, and in carrying them out Lewis and Clark displayed an objectivity and tolerance rare in their generation. Lacking the conceptual tools of the modern anthropologist, they nonetheless provided the first general survey of the life and material culture of the village Indians of the Missouri, the Rocky Mountain tribes, and those of the Northwest Coast. They also achieved, on the whole, a record for peaceful cooperation with the Indians that few of their predecessors or successors could equal. 
In the spring of 1803 Lewis traveled to Philadelphia to purchase supplies for the expedition and to complete training in astronomy, natural history, health, and ethnology by consulting with the leading lights of the American Philosophical Society, all friends of Jefferson. At Lancaster, Pennsylvania, he spent three weeks with Andrew Ellicott, mathematician and astronomer, who instructed him in the technique of determining latitude and longitude and advised him on the purchase of navigational instruments. After his arrival in Philadelphia in early May, Lewis received further instruction and advice in the same subjects from Robert Patterson, Irish-born professor of mathematics at the University of Pennsylvania. Benjamin Rush, the most eminent American physician of the day, advised him on the purchase of medicines and on general health care, besides providing him with a questionnaire for use in his ethnological inquiries. Benjamin Smith Barton, professor of natural history and botany and author of the first textbook on botany written in the United States, advised Lewis in a field in which the young Virginian was already much interested, as did Caspar Wistar, professor of anatomy and the leading American authority on fossils. 
In addition to his studies, Lewis roamed the business establishments of the city, purchasing the extensive and varied collection of items needed for the expedition. Mosquito netting, ink powder, thermometers, Indian trade beads, waterproof lead canisters for gunpowder, cooking utensils, and clothing all went to make up the 3,500 pounds of equipment to be carried across the continent. 
Having prepared himself intellectually and having secured as much equipment as he could in the East, Lewis crossed the Appalachians in the summer of 1803, supervised the construction of his keelboat in Pittsburgh, and started down the Ohio on August 31. He picked up Clark at Clarksville, Indiana, and gathered the first of their recruits. Both leaders were commissioned officers in the army, and most of their men were enlisted in the army, some signed up especially for the trip, others already in the service and detailed for the expedition by their commanding officers. Lewis expected that Clark would hold the same captain's rank as he, but red tape in the Department of War resulted in Clark's receiving only a second lieutenant's commission. They concealed this embarrassing fact from the men, and Clark is always "Capt. C." in Lewis's journals. There was no disturbance in their remarkably harmonious relationship, and Lewis apparently treated Clark as "equal in every point of view," a partner whose abilities were complementary to his own. Nonetheless the situation irked Clark, who had been a captain in his earlier period of service and Lewis's superior officer. After the expedition's return he sent the commission back to the secretary of war as soon as possible, remarking that it had served its purpose, and in later years he concealed his lower official status from all but a few. 
A long winter's stay across from St. Louis, at River Dubois in Illinois, waiting for spring and for the transfer of Louisiana to the United States, enabled the captains to gather their men, evaluate and discipline them, and collect some additional information—notably the personal advice of James Mackay and the Missouri River maps of John Evans (Atlas maps 7–12). By the spring of 1804 they had eliminated a few less desirable recruits, had given the rest some idea of what was expected of them, and were ready to begin the great adventure.
Any government enterprise of comparable importance in the twentieth century would have a planning staff bigger than the Corps of Discovery of forty-odd men who set out from River Dubois on May 14, 1804. The planning staff for the expedition had consisted essentially of Jefferson and Lewis, with advice from Jefferson's friends in the American scientific community. Up to the date of setting out, it was essentially Jefferson's expedition; after that date, the captains were on their own. They faithfully carried out Jefferson's program, but success or failure now depended on them.
For the first stage of the journey, as far as the Mandan villages, they followed the footsteps of others. There were maps of the route, however sketchy, and the Indians had had some acquaintance with traders. In this period the captains devoted much time to informing the Indians of the change of sovereignty, to insuring as much as possible that the Indians transferred their nominal allegiance, and to alleviating intertribal conflicts. The journey was marred in this period by some disciplinary problems, by the death of Sergeant Charles Floyd—the only man of the Corps who died on the trip—near present Sioux City, Iowa, and by their nearly violent encounter with the Teton Sioux near present Pierre, South Dakota.
They passed the winter of 1804–5 at Fort Mandan, near the Mandan and Hidatsa villages in North Dakota; the wait for the Missouri to thaw allowed them to gather much information from the Indians on the geography as far as the Missouri headwaters. In April 1805, they sent back their heavy keelboat and some enlisted men and "proceeded on" up the Missouri in canoes and pirogues. With them now was the Shoshone woman Sacagawea, with her husband Toussaint Charbonneau and their infant son Jean Baptiste. More than four months of travel, including a month-long portage of the Great Falls of the Missouri, ended at the Continental Divide on the Montana-Idaho border, with the dawning realization that the portage to the waters of the Columbia would not be the simple matter they had hoped. 
Promises of guns and trade maintained the expedition's friendly relations with the Shoshones; in exchange, the captains secured horses and guides for the trip across the mountains. They could not have known it beforehand, but they had come to one of the most difficult places for crossing the Rockies, and they had barely enough time to make the trip before winter closed the trails. After a cold, hungry trek across what Sergeant Patrick Gass called "this horrible mountainous desert," they reached the country of the Nez Perces on the Clearwater River in Idaho; there they built canoes and hurried on down the Clearwater, the Snake, and the Columbia to the Pacific.  All the way from Fort Mandan they had journeyed through country known only to the native inhabitants, until they neared the mouth of the Columbia and reentered the world of known geography. Clark's note of November 7, 1805: "Ocian in view! O! the joy," though premature, expressed the emotions of them all.
They passed a dreary, damp winter at Fort Clatsop, on the Oregon side of the Columbia estuary, knowing that snow would delay their returning earlier. Nonetheless, they accomplished considerable scientific work there, and the journals are rich with ethnographic and natural history materials. Jefferson had considered the possibility of at least part of the party returning by sea, if they should meet any trading vessels on the coast. The captains had apparently abandoned this idea, and in any case they met no ships, though evidence of white contact with the local people was abundant.
On March 23, 1806, they began their return by canoe and horseback, delaying a month among the Nez Perces in Idaho waiting for the snow to melt in the Bitterroot Mountains. Having crossed the Bitterroots, they split the party. So confident were they now of their ability to survive that they separated in order to add to their geographical knowledge. Lewis crossed the Continental Divide to the northeast to find a shorter passage over the mountains and to explore the Marias River in present Montana, while Clark went southeast to travel down the Yellowstone. Lewis's trip led him to a tragic encounter on the Marias in which he and his men killed two Blackfeet, the only real violence of the trip. Clark's journey was relatively uneventful.
Reunited in North Dakota, Lewis and Clark again visited the Mandan and Hidatsa villages, left Sacagawea, Charbonneau, and young Jean Baptiste there, and hurried on down the Missouri to St. Louis. Traders along the way told them that virtually everyone had given them up as lost, rumor asserting that they were dead at the hands of Indians or that "the Spanyards had us in the mines &C.," in Sergeant John Ordway's words.  Only the president still retained some hope. They arrived at St. Louis on September 23, 1806; three days later Clark closed his journal on an anticlimactic note: "a fine morning we commenced wrighting &c."
Clark's last entry is a reminder that "wrighting &c." was one of the principal tasks of the captains, and one that they thoroughly fulfilled. As Donald Jackson has observed, Lewis and Clark were "the writingest explorers of their time. They wrote constantly and abundantly, afloat and ashore, legibly and illegibly, and always with an urgent sense of purpose."  They left us a remarkably full record of their enterprise, but questions about that record remain unanswered. One of the most vexing problems of the journals, as such, concerns a question whose answer might appear quite obvious: when and how were the journals written? The immediate and natural supposition of any reader is that the entries were written day by day on the dates placed at their heads by the authors. Examination of the journals now available, however, discredits that expectation. The existence of duplicate journals, mainly by Clark, for certain periods of the expedition, and internal evidence indicating that many entries cannot have been written on the days they cover, require greater consideration of the journal-keeping methods of the captains.
Nicholas Biddle, as a result of his collaboration with Clark in 1810 on the published history of the expedition, probably had more information about the two captains' methods of keeping a journal than anyone else who was not with the expedition, but he did not reveal it to his readers. By the time anyone again examined the journals at length, the authors were no longer available to provide what were no doubt simple explanations of many mysteries and apparent inconsistencies. When Elliott Coues examined the notebooks in the American Philosophical Society archives in 1892–93, he was struck by their good condition and concluded that the predominant red morocco-bound books, at least, could not have crossed the continent: "The covers are too fresh and bright, the paper too clean and sound. . . . The handwritings are too good, and too uniform. . . . The red books were certainly written after the return of the Expedition, and before Lewis's death in October, 1809—that is, in 1806–9." 
In opposition to Coues's belief that the journals might have been written, in part, as late as 1809 is Jefferson's statement that Lewis turned the notebooks over to him "on his return"—that is, on or soon after Lewis's arrival in Washington on December 28, 1806. Jefferson's understanding was that they had been written day by day, and that each notebook was sealed in a tin box when finished to protect it from the elements. Even assuming that Jefferson learned the exact procedure the captains followed, his description, written from memory nine years later, might not be precisely correct. However, he was hardly likely to have gained the impression that the volumes he specifically called "travelling pocket journals" were written on the trip if they were blank when he first saw them on Lewis's return. Nothing could have kept the president from poring over them, as he apparently did those sent back from Fort Mandan in 1805. His words strongly imply that the notebook journals were more or less complete by the time of Lewis's arrival in Washington. 
Of course, Coues never imagined that the captains wrote their journals from memory in the years after their homecoming. The red books he viewed at the American Philosophical Society did not include some other notebooks there that have different bindings; their condition convinced him that those could have been on the expedition, and he thought that true of some but not all the small, fragmentary items of a few sheets each that he examined. Those last he thought likely to be the remains of field journals made on the spot, day by day, their information later being transferred into the notebooks. 
When Reuben Gold Thwaites examined additional materials that he discovered a few years later, he found among them Clark's Elkskin-bound Journal, as he called it, covering the same period as some of the red books. This new volume, written on letter paper later sewn together and bound, undoubtedly in the field, seemed to fit exactly the description of field notes, later copied and expanded in the notebook journals. The Elkskin-bound Journal and some other new fragments made Thwaites confident that he understood the captains' basic procedures:
Thwaites did not attempt to say just when the field books were made, nor why some field notes and journals, notably the Elkskin-bound Journal, were preserved when so many others were "in large measure destroyed."
It was the daily custom of the captains to make rough notes, with rude outline maps, plans, and miscellaneous sketches, in field-books which they doubtless carried in their pockets. When encamped for a protracted period, these were developed into more formal records. In this development, each often borrowed freely from the other's notes—Lewis, the better scholar of the two generally rewriting in his own manner the material obtained from Clark; while the latter not infrequently copied Lewis practically verbatim, but with his own phonetic spelling. Upon returning to St. Louis, these individual journals were for the most part transcribed into neat blank books—bound in red morocco and gilt-edged—with the thought of preparing them for early publication. After this process, the original field-books must have been cast aside and in large measure destroyed; for but one of these [the Elkskin-bound Journal] is now known to exist. There have come down to us, however, several note-books which apparently were written up in the camps. 
Thwaites's explanation is broadly plausible, but again we confront Jefferson's statement that the red books turned over to him at the beginning of 1807 were written on the trip. If Jefferson was mistaken on this point, then Thwaites's theory requires the captains to have written the entire body of red notebook journals—fourteen notebooks containing several hundred thousand words—between the arrival in St. Louis on September 23, 1806, and late December 1806. Clark's last journal entry (September 26, 1806), apparently written in St. Louis, says that "we commenced wrighting &c," but as noted, there is no indication of what they were writing.
Following Thwaites's theory, the red books had to have been written in the course of some three months or a little more, during which the captains were traveling; visiting relatives; seeing to other business; and attending public ceremonies, welcoming celebrations, and banquets. During that period Lewis was also escorting the Mandan chief Big White (Sheheke) to the capital. Moreover, substantial parts of Clark's journals for the last part of the expedition are evidently copied from Lewis. On the journey to Washington the captains separated in mid-November and did not reunite until January 21, 1807, when Clark reached Washington. Unless Lewis left a great part of his journals with Clark, which seems most unlikely, the period during which the journal writing could have been done narrows to a period of less than two months after the expedition's arrival in St. Louis. If we add the fact that Clark's next to last notebook journal has a lengthy passage in Lewis's hand, inserted in the middle with no apparent gaps in the writing, the theory that the red books were wholly the product of the period after the return to St. Louis seems questionable.
There are other good reasons for doubting the postexpedition theory of composition. Eighteen red books are known, all having some connection with the expedition, though it is not known when the captains obtained them. One of them is Codex O, as labeled by Coues, which contains Lewis's astronomical observations for the first year of the expedition and his summary of creeks and rivers. It is generally believed that this book was among the materials sent back from Fort Mandan in April 1805; it has no data collected after that time. If so, then the captains had it with them from the start, and in all probability they had all eighteen identical books from the beginning, wherever they were purchased. No one can possibly imagine that they carried eighteen notebooks to the Pacific and back without having intended from the first to write in them along the way.
There is no specific reference to the red books in any of the preexpedition lists of supplies. Lewis listed "Books" and "Writing paper" among his requirements for the trip, and since he did not specify titles, the books may well mean notebooks. He drew "8 Rect. books" from the U.S. arsenal in Philadelphia and purchased six packing boxes for "Stationary &c." there, in the spring of 1803. An undated memorandum in Codex C, in an unknown hand, lists goods packed for the expedition at some point. The list includes four bales of goods, each containing "2 tin Boxes, with 2 mem. Books in Ea."; a recapitulation of the same goods in the memorandum gives "8 tin Boxes with memm. Books". This gives sixteen books. Among Lewis's personal effects inventoried after his death in 1809 were "Sixteen Note books bound in red morocco with clasps." The coincidence in number is striking; it would indeed be conclusive, except that there are eighteen red books extant, all having some connection with the expedition. There is no really satisfactory way to account for the two extra books. Since there is no certainty when the memorandum in Codex C was written, we cannot say which red books might have been in use and so not listed among those packed. For instance, Lewis used Codex O for his astronomical observations from the beginning of the expedition. If the Codex C list was made up just before setting out from Wood River, Codex O might not have been packed away in a relatively inaccessible box in a bale but could have been with Lewis or easily available.
It is, of course, entirely possible that the captains purchased two more identical books after the expedition, and it would be exceedingly difficult to say which of those now known would be the extra two, since all eighteen red notebooks contain or apparently did once contain material that could have been written during the expedition. Neither is there any clear indication of which two red books Lewis would not have included among the expeditionary materials he had with him on his last journey in 1809. The captains' practice of taking pages from one notebook and inserting them in another makes it impossible to be certain what material (particularly the fragmentary Lewis items) may have been in what book at the time of Lewis's death, or at any other time before the Clark-Biddle collaboration in 1810. 
Jefferson says the books were "cemented" up in tin boxes for protection when completed, but that they had been removed from the boxes before Lewis delivered them to him. Lewis or Clark must therefore have told him those details, which implies that they gave him some information about their methods of journal keeping. The captains could have kept the notebooks in boxes sealed in some manner to keep out moisture, taking them out for writing in relatively sheltered camps or when the weather was good, while rough field notes served for daily entries under less favorable conditions.
Writing in 1807, David McKeehan, Patrick Gass's editor, sought to establish the reliability of Gass's work by stating, "At the different resting places during the expedition, the several journals were brought together, compared, corrected, and the blanks which had been unavoidably left, filled up."  This information, vague and unspecific as it is, could only have come from Gass; the journals referred to could be field notes or notebook journals, or both. Certainly such resting places would have been the points at which the notebook journals were brought up to date, if they were not, in fact, the journals in which the entries were kept day by day.
The discovery in 1953 of rough, unbound notes by Clark, covering, besides the period at Camp Dubois, the first eleven months of the expedition—the same period as Clark's first three notebooks—complicates as much as it clarifies. One can easily believe that these scribbled, interlined entries, written on miscellaneous sizes of loose paper, often over sketch maps, arithmetical calculations, and addresses on used envelopes, were first-draft notes taken in the field on the journey up the Missouri. It is then easy to imagine Clark copying and expanding on them in the notebooks whenever time allowed, even as late as the winter at Fort Mandan. Once they reached Fort Mandan, however, the Field Notes become increasingly skimpy, with gaps sometimes weeks in length. For this period we must either imagine another full set of field notes, whose existence is both unproven and unnecessary, or suppose that in this period Clark wrote his entries daily into a bound journal. 
There is, however, material in the notebooks that is not in the Field Notes, indicating that Clark wrote into them when events were fairly fresh in his mind. In his Codex A entry for July 4, 1804, we find reflections on the Kansa Indians not in the Field Notes. On the other hand, in the Codex A entry for July 23, 1804, he names Camp White Catfish, although the fish for which the camp was named was not caught until the next day. Thus we must assume that the codex entry was written on or after July 24, or that he wrote the entry on the twenty-third, inserting the name of the camp later—which from the appearance of the page is entirely possible.
In the Field Notes for August 20, 1804, Clark records in the present tense that Sergeant Charles Floyd was seriously ill, then writes of Floyd's death. In Codex B for the same day, Clark repeats the description of Floyd's illness and death. One must suppose either that Clark wrote both the Field Notes and Codex B simultaneously, with considerable difference in wording, or that he wrote the codex entry later, without taking into account his knowledge that Floyd had died. This journalistic convention persists throughout the journals and, of course, complicates the problem of determining the time of writing of particular entries. In any case, in the notebook entry of August 20, Clark refers to Floyd as "our Decesed brother," a phrase not found in the Field Notes—perhaps evidence that he wrote the notebook entry when the emotion was still fairly fresh.
On October 13, 1804, a court-martial of party members tried Private John Newman for "mutinous expression." Clark's brief record of the episode in his Codex C entry for October 13 says that Newman was tried "last night." Apparently he wrote the codex entry the day after the trial. The paragraph on the trial, comes at the very end of the entry, so it is likely that the whole entry was composed on October 14, the day after its ostensible date. This is at a time when the Field Notes entries are still continuous and fairly extensive; the Codex C entry, however, includes much information not found in the Field Notes, apparently taken down by Clark at the time he received it. At this time he was obviously copying and expanding his first notes into the notebook journal quite promptly.
During the Fort Mandan winter, when Clark's notebook entries are quite full, entries in the Field Notes for widely separated dates follow one another without any evidence of missing pages. In fact, a single sheet, document 64 of Ernest Osgood's arrangement of the Field Notes, contains the entries for the period from November 19, 1804, to April 3, 1805; the entries follow one another with no indication of spaces for later insertion of material. Sheets in the Field Notes may have been lost, but it seems more likely that Clark wrote directly into his notebook journal. As further evidence, note that Lewis kept the bound book up to date when Clark was absent for ten days in February on a hunting trip; Clark then wrote a short summary of his excursion in the book on his return. From the appearance of the journal, Clark wrote this account immediately after his return, rather than inserting it later.
It does not seem wise to postulate the writing of field notes by either captain in cases where none have been found and there is no strong evidence of their having existed. Theories involving the existence of such notes are to be avoided unless the evidence clearly requires them. The sheer amount of labor involved in composing multiple sets of notes and journals argues against such suppositions. Considering the history of journal discoveries to date, however, no one would wish to assert positively that there are no lost notes or journals, or that none will ever be found. Certainly there are cases where notebook journal entries were clearly written weeks or months after the given date, and then it does not seem unreasonable to suppose that the writer kept notes of some sort.
The discovery of Clark's Field Notes consisting of the Dubois and River Journals, and other discoveries at various times and places, may seem to support the possibility of other such field journals. But the Dubois Journals relate to the period before the expedition proper and were not the basis, as far as we know, for a duplicate set of notebook journals. Obviously Clark kept both field notes and notebook journals for the journey up the Missouri to Fort Mandan, but it does not necessarily follow that he used the same procedure throughout the expedition, especially since he apparently did not follow this method at Fort Mandan and his field notes fall off sharply after his arrival there.
On April 7, 1805, the permanent party set out upriver from Fort Mandan; at the same time, the keelboat carrying the discharged members of the party headed down river with a load of dispatches, papers, and specimens for delivery to Jefferson. At this point we encounter more complex problems of journal-keeping procedures and missing notes.
The first question concerns just what journal materials were sent to Jefferson on the keelboat. At several points in the summer and fall the captains indicated that they intended to send back a pirogue with some of the soldiers and boatmen under Corporal Richard Warfington. Clark indicates more than once that they were preparing materials to be sent back with that party. As it happened, they did not dispatch the return party until the following spring, for reasons never stated. Both Clark and Lewis wrote letters to Jefferson indicating what they were sending, but neither was specific enough to spare us some puzzlement. Clark wrote on April 3, 1805, that he was sending the "notes which I have taken in the form of a journal in their original state," apologizing because "many parts are incorrect." Lewis wrote that they were sending the president "a part of Capt. Clark's private journal, the other part you will find inclosed in a separate tin box. The journal is in it's original state, and of course incorrect, but it will give you the daily detales of our progress, and transactions." A great deal hinges on the meaning of the expressions "private journal" and "original state," and on how we interpret the two parts of Clark's journal. 
Various interpretations are possible. We could take Clark's Field Notes to be a
"private" journal, and the notebook journals to be "public" or official; thus the
Field Notes constitute one part and the notebook journals—Codices A, B, and
C—the other. We might take the Dubois Journal and the River Journal, the two
parts of the Field Notes, as the two parts meant, but there is no evidence that the
Dubois Journal ever went to Jefferson, and the division into the Dubois Journal and the River journal is merely a modern convenience. The argument can be
made that the two parts were parts of the River Journal itself, on the basis of a
notation by Clark on document 56 of the Field Notes. One side contains journal
entries for September 20–23, 1804. The other side bears an address:
Sept 20 &
Genl. Jona. Clark of Kentucky
To the 22nd of Septr. 1804
To the care of Genl. Jona. Clark near Louisville Kty
To be opened by Capt. W. Clark or Capt. Meriwether Lewis. 
On the same document under the September 23 entry Clark wrote, "I must seal up all those scripts & draw from my Journal at some other time."
The address and the conclusion of entries on the same sheet seem to indicate that the captains still hoped to send a party back before winter, and that Clark intended to send the Field Notes to his oldest brother Jonathan, to be kept until his return. They had kept Warfington with them past the end of his enlistment in August so that he could head the return party. We might suppose that Clark made sure that his notebook journals were up-to-date at this point, since he could not use the Field Notes for this purpose after sending them back, and he may have brought the notebooks up-to-date similarly when they considered sending materials back from Camp White Catfish in July. On the other hand, if the notebooks were not up-to-date, this could be the reason why the return party did not set out before winter. This might even be the reason why Clark neglected the Field Notes at Fort Mandan and apparently wrote directly into his notebook journal, the earlier procedure having proved too time-consuming.
On document 58 of the Field Notes is a notation by Clark: "A Continuation of notes taken assending the Missourie in 1804—by W. Clark." It may be, then, that the two parts of Clark's "private journal" are the two parts of the Field Notes— the part sealed up to be sent to Jonathan Clark in September 1804, but not sent, and the notes taken after that time. The note about "A Continuation" could indicate that Clark thought of the Field Notes as being in two parts. 
Against the above interpretation, however, is another notation by Clark, written April 2, 1805, on document 64 in the Field Notes, during preparations to send off the keelboat and its cargo from Fort Mandan:
Here again is the phrase "in its original state," suggesting that the journal referred to is the same as mentioned in the captains' letters to Jefferson as Clark's "private journal." What journal was it?
I conclude to Send my journal to the President of the United States in its original State for his own perusial, untill I Call for it or Some friend if I Should not return, an this journal is from the 13th of May 1804 untill the 3rd of April 1805.
Clark says the journal began on May 13, 1804, which cannot apply to the Field Notes, unless he was in error. The last document of the Dubois Journal ends on May 14, and the River Journal's first sheet begins with the same date. The first notebook journal, Codex A, however, does begin on May 13. The journal to be sent back, Clark says, ends on April 3, 1805; that is true of the Field Notes and, in a sense, of the notebook journals. The April 3 entry in Codex C is followed by a list of items to be sent back on the keelboat, then the entries for April 4–7. Since the entry for April 3 in Clark's Field Notes shows that they expected to leave the next day, Clark could well have thought of the April 3 entry in Codex C as the last, adding a list of materials to be sent back for Jefferson's information. Thus, when he wrote in the Field Notes on April 2 that the journal went to April 3, that could also have been the case with the notebook journals. Since they did not, in fact, leave until April 7—due presumably to last-minute delays—it was natural for Clark to add entries for the extra days in Codex C.
With such an indication that Clark considered his notebook journals to be in their "original state," it seems reasonable that the two parts of his journal were the Field Notes and the notebook journals—Codices A, B, and C. That the notebook journals went to Jefferson is clear from Jefferson's letter to Benjamin Smith Barton in December 1805, referring to the feeding of cottonwood bark to horses by the Indians in terms very similar to those in Codex C but not in the Field Notes.  It seems most likely that the Field Notes also went to Jefferson, though there is no specific evidence proving this. Clark did note in a letter from Fort Mandan that he was sending "papers of considerable consequence" to his brother in Louisville, and the Field Notes would meet this description. It is likely, however, that those "papers" consisted of the Dubois Journal, not the River Journal. Document 65 bears the address of Jonathan Clark and the notation "notes at Wood River in 1803–4." Clark certainly did not send those notes—which surely must be the Dubois Journal—to Jonathan before the departure from St. Louis in 1804, for the other side of document 65 bears an entry for November 30, 1804, after they had reached Fort Mandan. From its appearance, document 65 could have been the wrapper in which the Wood River notes (Dubois Journal) were sealed for shipment to Jonathan Clark. If those notes were in a separate packet, it may have been because they were going to a different destination than the River Journal, sent to Jefferson. That Clark wrote a full entry for November 30 on document 65 may only mean that he thought of taking up regular keeping of the Field Notes after they had settled in at Fort Mandan, then abandoned the idea in favor of the notebook journals. 
Clark's journal-writing procedure, up to the departure from Fort Mandan, then, seems reasonably clear. On the upriver journey he kept daily field notes and copied and expanded them into his notebook journals as convenient, sometimes neglecting the Field Notes at Fort Mandan in favor of writing directly into Codex C. The daily continuity of the Field Notes ends with November 13, 1804, the entries becoming increasingly irregular; document 64 covers the entire period from that date to April 3, 1805, and appears to be the last sheet of the Field Notes. During the building of Fort Mandan in early November, the keeping of two journals may have seemed too much of a burden in the midst of other demanding work. If so, then Codex C was presumably up-to-date at that time, and perhaps Codices A and B were also. Codices B and C, however, overlap on October 1, 2, and 3, and the entries in Codex C for the first and second are skimpy in comparison to those in Codex B. Possibly Clark began writing in Codex C when Codex B was not yet up to date, on the first of October. The fuller entry for October 3 is in Codex C, and conceivably he had caught up and filled in Codex B by then.
More difficult to explain is Lewis's journal-keeping procedure and particularly the large gaps in his writing, which raise the possibility of missing manuscripts. The largest gap, and the one most curious to historians, is the long hiatus from the start of the expedition in May 1804, until the group set out from Fort Mandan in April 1805. That gap is particularly bewildering because we would expect Lewis to be more conscientious at the outset of the expedition, especially in light of Jefferson's explicit instructions about the keeping of multiple journals.  So incredulous have some observers been at this gap that they have speculated that Lewis was probably keeping either field drafts or standard journals of the party's activities that have since been lost. 
To say that Lewis's was keeping no journal from the outset is not precisely correct. There exist two small fragments, called Codices Aa and Ba by Coues, for the dates May 15 and 20, and September 16–17, 1804. Those sheets, apparently torn from one of the red books, suggest to some that Lewis was keeping a journal for the initial period, and that the remaining pages were so soiled, ruined, or unnecessary that they were discarded. Or perhaps the remaining pages are simply lost. Another explanation seems plausible and is presented here as part of a larger conception of Lewis's journal-keeping activities throughout the trip.
In Codex Aa it is noteworthy that the order of days is reversed; the entry for May 20 precedes the entry for May 15, with no break between the two. The entry for May 20 recounts Lewis's activities for that day as he set out by land from St. Louis for St. Charles where he was to rendezvous with Clark, who was leading the party upriver. The entry also reports the activities of Clark's party. Perhaps Lewis saw this entry as the beginning of his journal keeping since the captains had determined to set out the next day (May 21). Then why the addition of notes for May 15? That is a more detailed report of Clark's trip upriver, written as if Lewis had been present. Information in that entry exceeds the notes taken by Clark for that day in either of his two accounts (Field Notes and Codex A) and probably came directly from Clark. Perhaps Lewis thought he ought to add an entry for May 15 after his May 20 entry to give a more detailed account of the actual start of the expedition. Although Clark set out from River Dubois on May 14, the captains had earlier established May 15 as the date to begin, and perhaps Lewis still had that date in mind.
Codex Ba presents a different situation. On September 16 and 17, 1804, the group was encamped at "Corvus" Creek just above today's White River in South Dakota (see Atlas map 21). There the captains made the decision not to send back the pirogue with artifacts and other items representing their journey thus far. Perhaps Lewis had thought that their notes to that point would return to St. Louis with the other materials and eventually reach President Jefferson; thus, he may have considered that he was now beginning a journal, in a sense the first for him since he had apparently quit writing after his May 15 entry. Having made the decision not to send a boat and crew back, he may have ceased his journalizing (indeed, he stopped at midpage in midsentence) and perhaps delayed writing again until after the winter at Fort Mandan.
Even before those dates Lewis may have established a pattern of laxness in journal writing. He began a diary (here called the Eastern Journal) when he left Pittsburgh in August 1803, as he descended the Ohio River enroute to St. Louis, but from September 19 to November 11, he made no entries. He left thirty-nine pages blank in the notebook between those separated entries, however, perhaps with the intention of supplying the missing information later, but that hiatus was never filled. About October 26, Clark joined Lewis at Louisville, but Lewis did not turn over journal-keeping chores to his friend at that time. Had he done so, today we might have a more complete record of the remainder of the trip to Camp Dubois, for Clark was a more consistent recorder than his companion. Lewis returned to journalizing on November 11 and gave the journal to Clark on November 28, near Kaskaskia, as they separated while Lewis went ahead by land to St. Louis and Clark brought the boat party forward to establish Camp Dubois. From that point we have a nearly consistent record because of Clark's faithful journal keeping. 
Those writing gaps of Lewis's may be instances of a larger pattern of negligence. The gaps as a whole include the missing days from the Eastern Journal (September 19 to November 11, 1803); the lapse from May 14, 1804, to April 7, 1805 (with the exceptions noted); only spotty entries from August 26, 1805; to January 1, 1806; and the final hiatus from August 12, 1806, to the completion of the expedition. The last gap can be explained by Lewis's being partially disabled from a wound; in contrast to other stoppages, he noted that he was laying down his pen at that point. In all from May 1804, to September 1806, Lewis missed over four hundred days of journal entries. 
Some authorities have supposed that Lewis was keeping field notes during the period from Camp Dubois to Fort Mandan and intending to use that material to fill regular notebooks later, or that the fragments from a red book (the entries for May and September) were part of a complete set of notes that are now lost. Jackson has made the strongest case for Lewis having kept notes during the first leg of the journey, but he emphasizes the speculative nature of his conclusions. Briefly, Jackson believes that a mishap on May 14, 1805, may indicate a loss of journals. On that day one of the pirogues turned on its side and filled with water, and some of the papers and notebooks got wet. Jackson discovered that within a few days of the accident Clark began conscientiously to copy into his own journal Lewis's natural history notes, something he had not previously done. Jackson argues that the spoilages may have been greater than expected, convincing the captains that duplicating all records was necessary, not just keeping multiple diaries. He also conjectures that "perhaps Lewis's notes for the entire first leg of the expedition were either badly water-soaked or entirely lost." Thus, Jackson believes that the entries by Lewis for May and September 1804 may be fragments of a larger journal from that early period. Thwaites also thought that Lewis was a regular journal-keeper, but his reasoning is less plausible than Jackson's. He supposed that the journals may have been lost after Lewis's death in Tennessee. However, we would expect that Clark or Jefferson would have bemoaned such a loss at some time, but neither ever made reference to so serious a loss in any known source. Jackson's answer for a reason that there is no mention of the supposed loss of journals in May 1805 is that Lewis would tell Jefferson about the accident after his return but that there was no need to announce it to the world in his diary. 
Jackson and others who think Lewis kept a journal or field notes during the trip to Fort Mandan have found strong evidence in letters of Lewis and Clark to Jefferson just before the party set out from that post. The opening phrase of Clark's letter has been struck out and other words substituted by Lewis. Clark wrote, "As Capt. Lewis has not Leasure to Send 〈write〉 a correct Coppy journal of our proceedings &c." and Lewis substituted, "It being the wish of Capt. Lewis." There are several ways to read the excised parts: does Lewis not have time to send his journal, has he not had time to write it, or has he not had time to make a correct copy? Lewis's letter stated that he would send a canoe with some men back from the extreme navigable point of the Missouri River (a scheme later rejected) and with that boat "I shal send you my journal." Again, one can read the phrase variously: is Lewis to send a journal he has been keeping or one he intends to write? Rather than speculate on the hidden meaning of the letters, it is better to examine the totality of Lewis's journal keeping and to interpret from that perspective. 
Although extant daily entries by Lewis from St. Charles to Fort Mandan are lacking, there exists quite a bit of Lewis's writing from that period, and additional material is known to be missing. As the expedition's naturalist he kept fairly extensive notes on the flora and fauna of the region through which the party passed. In Codex R, he made a list of herbarium specimens that he was collecting. The descriptive writing is occasionally lengthy and shows not only Lewis's powers of observation but also his record-keeping activities. Observations of animals are almost as extensive and cover over fifty pages of Codex Q. The captain was also noting mineral deposits and geologic features along the Missouri and taking astronomical observations—both time-consuming tasks that included record-keeping. And, although Lewis cannot be credited directly, it is known that the captains were keeping lists of Indian vocabularies during this period, work that may have amounted to extensive note taking. The vocabularies are the missing material that might exhibit additional record keeping by Lewis.
From January to May 1804, Lewis was keeping a weather diary. Those observations are repeated in Clark's Codex C, and it seems probable that Lewis was copying Clark's entries. After May 14 there is a gap of weather data in both captains' books until September 19; the notations are then resumed with hardly an interruption until April 3, 1805, when Lewis began placing weather data with the daily entries. The weather notes indicate a substantial amount of writing because they consist of two temperature readings for each day, the general state of the weather, the wind direction, and the rise and fall of the river. There are also comments on natural history including sightings of animals and the budding and fading of flora. It is uncertain whether Lewis made the notes along the way or at Fort Mandan, but it was a collaborative effort of the captains. 
Evidence that Lewis may have done more extensive writing exists in the form of a single loose sheet from Clark's Field Notes (Osgood's document 35). The sheet is entirely in Lewis's hand and contains on one side a draft for Lewis's description of the Platte River, which he later transferred into Codex O as his survey of rivers and creeks. Although there is a date of July 21 (1804) on the document, the reverse contains lunar observations (also in Lewis's hand) for February 23, 1805, while the party was at Fort Mandan. It could be that the draft describing the Platte was also written at Fort Mandan and there copied into Codex O. Because the draft from the Field Notes is an incomplete portion, it is certain that other pages are missing; whether they describe only the Platte or are a full draft of his summary may never be known. If Lewis was keeping thorough topographical notes throughout the first portion of the trip, it helps explain why no daily entry material has been found. It may simply have amounted to too much writing.
Taken together, Lewis's recording activities up to Fort Mandan add up to a large amount of writing and may represent a proportional share of the writing duties of the captains. What emerges is a picture of the two men sharing journal-keeping chores, though not following Jefferson's prescription to the letter. It is difficult to believe that all of Lewis's daily-entry journals (except for a few pages of writing for May and September 1804), from St. Charles to Fort Mandan and during the winter of 1804–5, could be lost. Clark during that period filled three notebooks of writing, and Lewis, the more verbose, would have written even more. Unless actual journals by Lewis or definite references to such writing are discovered, it seems likely that he kept no record of daily events for this period.
One incident on the way to Fort Mandan may corroborate the notion that Lewis kept no journal of daily events during that period. On July 14, 1804, a sudden storm hit the river, and great gusts of wind turned one boat on its side so that it began to fill with water. Cool heads and quick action saved the vessel from destruction, but Clark reported that his notes of the previous day had blown overboard during the accident. Clark mentioned that the loss "obliges me to refur to the 〈notes〉 Journals of Serjeants, and my own recollection [of] the accurences Courses Distance &. of that day." If Lewis had been keeping a journal of events during this time, why would Clark go to the journals of the sergeants or depend on his own recollection for the "accurences?" Certainly he would have trusted Lewis's notes over his memory or the notes of enlisted men if Lewis's journal had been available 
From the April 7, 1805, departure from Fort Mandan to late August 1805, complete notebook journals for both captains exist, with no fragmentary or parallel journals until August, although some copying was being done between the two men. There is no indication that either followed Clark's earlier practice of writing field notes and transferring them, with revisions, into notebook journals. Indeed, there is no reason to assume that the captains consistently followed any one plan or procedure throughout the expedition. Their responsibility was to keep as complete a record as possible of the many kinds of information that Jefferson wanted and to preserve that record from harm or loss. They could follow any procedure that suited their convenience and the conditions of the moment, in keeping with that mission. External conditions varied so much throughout the trip that there was every reason to change journal-keeping procedures to conform to the needs of the moment. When they were inconsistent in so much else, there is no reason to expect them to be consistent in this.
It is not necessary to believe, then, that for every finished journal there was a preliminary set of field notes nearly duplicating it, as in the case of the River Journal and Codices A and B. Without the known existence of field notes, or strong evidence requiring them, there is no need to assume that they were made. Duplication of journals would serve as insurance against loss or damage, but with both captains definitely keeping journals after April 7, 1805, there would be less need for keeping both field notes and notebook journals, which amounted to a time-consuming task. 
Field notes, however, would be of value in situations where there was an increased risk of damage or loss from weather or difficult travel conditions, when it seemed wise to seal up the notebooks in tin boxes (described by Jefferson) and keep field notes easily accessible or carried on the person. Such precautions could also be taken when one of the captains was scouting ahead on foot, accompanied by only a few men; he might leave his notebook journals with the main body, for convenience or in case something happened to him and he did not return. After such separations, one might copy the experiences of the other into his own journal, to insure the preservation of a complete record.
As they moved up the Missouri around the Great Falls, the captains were separated at various times in June, July, and August 1805, as one or the other was ahead, portaging the falls or later looking for the Shoshone Indians. In these intervals, Lewis sometimes copied Clark's journal for the days of separation under the date of their reunion, suggesting that he was keeping the notebook journal day by day. At other times, Lewis gave an account of Clark's activities in his own entries for each day, indicating that those entries must have been written after they were reunited. Clark in this period did not ordinarily copy Lewis's record of daily events while they were separated. 
In some of Clark's red notebooks are extra pages he apparently inserted, sometimes torn from other red books but at least once cut to fit from letter paper. The handwriting on the inserted sheets is neater and more legible than Clark's usual bold but rather careless hand, but it is definitely Clark's, and the need for legibility is the likely reason for many of the insertions. This circumstance strengthens the likelihood that the ordinary handwriting represents daily entries written on the trail, during the day or in camp. A notable example is Clark's insertion of pages to recopy his survey notes of the Great Falls portage, already written in his rougher hand in the middle of his June 17, 1805, entry, probably during the course of the day. He decided to copy the notes over for greater legibility and in fact inserted more sheets than he needed. The inserted sheets are in the middle of the original rough notes. 
There are four fragmentary journals by Lewis from August and September 1805, designated Codices Fa, Fb, Fc, and Fd by Coues. Each consists of a few loose sheets covering periods of two to five days. Codex Fa describes events also related in more detail in Lewis's Codex F; the others are all from periods after the end of Codex F, during a hiatus of over four months for which there are no other known Lewis journals, except for a later fragment, Codex Ia.  It is tempting to regard them as being literally "fragments," that is, portions of a lost body of field notes by Lewis covering perhaps the entire gap in his journal from late August 1805, to January 1, 1806. But the fragments themselves provide no evidence for this hypothesis. If they had portions of a previous day's entry at the beginning, or of the next day's entry at the end, there would be good reason to regard them as portions of a larger body of notes now lost. On the contrary, however, they appear to be complete in themselves. Codex Fa has a dated heading for an entry at the end that was never written, since only a blank space follows the date on the last sheet of the codex. Moreover, all of the fragments except Fc relate to periods when the captains were separated; Fa chronicles a scouting excursion ahead of the main body when Lewis might have preferred not to risk his notebook journal, and the other two describe periods when Clark scouted ahead and Lewis had to keep a record of the movements of the main party. Codex Fc derives from two days of relative leisure at Travelers' Rest in western Montana when Lewis may have intended to resume journal keeping after a lapse of about two weeks.  Lewis's later Codex Ia (November 29–December 1, 1805) also covers part of a period of separation and gives no indication of being part of a larger whole. 
In Codex G, Clark sometimes groups courses and distances for several days in one place, suggesting that he may have kept this information in separate notes and transferred it to his notebooks when time allowed. It may be that he kept course and distance notes on the same sheets with sketch maps, as he did with Atlas maps 33–42, although no such maps have been found for the route from the Great Falls to Travelers' Rest in western Montana, traversed during the period covered in Codex G.
On September 11 the Corps left Travelers' Rest on the Lolo Trail; this is the day on which Clark's Elkskin-bound Journal begins, continuing until December 31, 1805. It thus overlaps his red notebook journals Codex G (to October 10), Codex H (October 11–November 19), and Codex I (to December 31). This journal consists of sheets of letter paper sewn together and crudely bound in elkskin, presumably in the field. While we cannot be certain whether it was bound before or after writing, the fact that it ends precisely on the last day of 1805, the day before Lewis's known journal-writing again resumes, strongly suggests the latter.
From September 11 to 20, the Elkskin-bound Journal consists of courses and distances, with sketch maps of the Lolo Trail route. The courses and distances become progressively more detailed, briefly mentioning daily incidents; by September 13 they are in effect short journal entries in themselves. After September 21, the book becomes a regular journal of daily events. Here some speculation seems warranted. The Lolo Trail was one of the roughest parts of the trip, the trail hazardous and the weather terrible; the horse carrying Clark's writing desk slipped down a mountainside on the fifteenth, smashing the desk. These were conditions under which it would be prudent to seal up the notebook journals in tin boxes for protection and keep rough field notes along the trail. The sketch maps and courses and distances suggest that the elkskin book started out as the sort of route notes Clark kept at other times, such as those with Atlas maps 33–42. Their becoming progressively more extensive from September 11 to 20 suggests that Clark did indeed seal up Codex G at some point during this period, the Elkskin-bound Journal becoming the preliminary journal, the first draft for the notebooks. Clark went ahead with a few men, looking for game, on September 18, and the courses and distances in the elkskin book become particularly extensive from that date. There can be no certainty, however, that was the date when Codex G was sealed up.
From September 21, the elkskin book consists of regular daily entries in the conventional form, not in the form of courses and distances. September 20 was the day Clark met the Nez Perces at Weippe Prairie, Idaho, a meeting described in some detail in the elkskin notebook courses and distances. Lewis and the main party did not catch up until September 22. If Codex G was in a tin box on a packhorse with Lewis's group, we can understand why Clark wrote his regular September 21 entry in the elkskin book. He traveled a few miles that day but gave no courses and distances until the next day, September 22, when he wrote, "our first course of yesterday was nearly. . .," as if he had not written it down anywhere else and was going by memory. There may have been no notes other than those in the elkskin book.
Clark's courses and distances for September 11–21 and September 25 are together in Codex G after the September 30 entry; he may have taken the notebook out on that day and brought it up to date, or he may have been keeping entries in it and simply have delayed copying the courses and distances because he was busy. In any case, he continued to keep journal entries in the elkskin book until December 31, paralleling notebook journal entries in Codices G, H, and I. That the Elkskin-bound Journal entries were the first draft and the codices the second seems probable. For much of the period from early October to early December the expedition was going downriver in small dugout canoes, and when they neared the Pacific Coast they entered an area of almost constant rain and storms. It may have seemed wise to keep the red books in their waterproof boxes much of the time and continue to use the sheets that became the Elkskin-bound Journal.
The elkskin book begins on the exact date of starting on the Lolo Trail, which may indicate that Clark had not kept detailed field notes for some time before that but had written daily information directly into his notebook journals. He could well have been keeping course and distance notes, with sketch maps of the route, as he had earlier, notes such as the pages in the elkskin book apparently started out to be. But why were those bound notes preserved if similar ones for an earlier period (the summer and fall of 1805) were not saved also? We must, of course, allow something for sheer chance, but the special care taken to bind the notes suggests a particular need to preserve material covering that period. One reason for preserving them might be the exceptionally large number of maps (nineteen) along with the journal material; none of the maps of the Elkskin-bound Journal are repeated in the codices for the same period. Again note that there are, to our present knowledge, no notebook journals by Lewis from late August 1805, to January 1, 1806; only fragmentary loose sheets are known, and all except one (Codex Fc) cover periods when the captains were separated.
The Elkskin-bound Journal ends the day before Lewis is known to have resumed his journal-keeping, the first day of 1806. It would be a remarkable coincidence if Clark just happened to run out of paper in the book on that day. Internal evidence indicates that large portions of Clark's notebook journals after early November 1805 were probably written months later. If the sheets in the elkskin book were the only continuous record by either captain for a period of over three and one-half months, then we can readily understand why they took special care to preserve them. If Clark's red books were sealed up and packed away for much of that time, we can also understand why what started out as rough notes and sketch maps became a journal of events as well. 
What was Clark doing with his notebook journals during the period (September 11–December 31, 1805) covered by the Elkskin-bound Journal? Entries in late September and early October 1805 in Codex G are generally more extensive than those in the Elkskin-bound Journal; both are brief during periods when Clark was ill or particularly busy. After the party set out down the Clearwater River in canoes on October 7, the Elkskin-bound Journal again becomes primarily expanded courses and distances. Codex H, however, begins on October 11, and from this point the elkskin book entries again become progressively more detailed and lengthy, as if it were again the record actually kept on the given dates. On November 7, 1805, the day the party arrived, or so they thought, in sight of the Pacific, Clark records the event in both journals in terms suggesting immediate emotion.
The Codex H entry for November 7, however, also contains a passage in quotes describing the dress of the local Indian women, noting that it was so skimpy that the "battery of venus is not altogether impervious to the penetrating eye of the amorite." Not only is the language most unlike Clark's, but the whole paragraph is placed in quotation marks to indicate that it was not Clark's. In fact, the whole paragraph occurs verbatim in Lewis's Codex J entry for March 19, 1806—over four months after the ostensible date of Clark's entry. This forces us to conclude that Clark wrote the November 7, 1805, entry in Codex H on or after March 19, 1806. Lacking any indication that the page with the quoted paragraph was inserted later, we must assume that the remainder of Codex H after that date—and Clark's subsequent notebook journals, largely copied from Lewis's—were written on or after March 19, 1806—an assumption that creates some intriguing problems. 
There is some evidence, moreover, that much of Codex H before November 7, 1805, was not written until months after the given dates. In the entry in that journal for October 18, Clark notes how "the Great Chief and one of the Chim-nâ-pum nation" on the Columbia drew for him a sketch of the upper Columbia and its inhabitants and tributaries. Clark's copy of the sketch appears in the middle of the journal entry as if done at the same time as the entry itself. Yet the map labels as "Clark's River" the Pend Oreille River where it enters the Columbia. There is good reason to believe that the captains did not decide to give the name Clark's River to the combined Bitterroot-Clark Fork-Pend Oreille rivers until between April 17 and May 6, 1806 (see Atlas, pp. 10–11). An almost exact duplicate of the map in another notebook not containing daily entries shows the same stream as the "Flathead River," the name they used earlier. It may be, then, that Clark did not write the October 18 entry until late April or early May of 1806, inserting the sketch the Indians had given him under the appropriate date by copying from an earlier version. Codex H begins only a few days before that date, on October 11, 1805, so it might well be that, on finishing Codex G on October 10, Clark decided that since they were traveling downstream in canoes, it would be wise to use the Elkskin-bound Journal for daily journal keeping and keep his notebooks safely sealed away in boxes. As noted, the elkskin book's entries become increasingly extensive about this time.
Codex H ends on November 19 with a brief entry and Clark's words "See another book for perticulars." Codex I takes up with a longer entry for the same date, but only after thirty-four pages of introductory miscellaneous material—courses and distances from Fort Mandan to the Pacific, including some for a trip down the coast that Clark made in January 1806. That Codex I then takes up the narrative on November 19, 1805, immediately after this collection of data, suggests that Codex H was finished and the daily entries in Codex I begun in sequence. If so, then Clark also wrote Codex I after March 19, 1806, when Lewis wrote the "battery of venus" passage, which Clark copied under the date of November 7, 1805, in Codex H.
Why, then, did Clark wait so long to write this material in the red books? Up to December 31, 1805, he was writing in the sheets bound in elkskin and may not have seen any reason to start another journal, or he may not have gotten around to it. There is no clear evidence of such notes continuing after the first day of 1806. But Clark's Codex I has three short entries for January 1, 2, and 3 at one end of the book, upside down to all the rest of the writing in that book, which starts at the other end. It would seem that Clark began Codex I as a continuation of the Elkskin-bound Journal (ending December 31), then decided to do something else. It appears that he again took up Codex H, filled it up with entries paralleling the elkskin book through November 19, then continued in sequence in Codex I; if so, then he evidently did so after March 19, the date of Lewis's observations about the visibility of the "battery of venus." Apparently Clark wrote no journals of which we have knowledge for nearly three months, and this at Fort Clatsop, where he would have had relative leisure for writing. Codex I does contain a detailed record of Clark's trip down the Oregon coast on January 6–10, taken from notes (here called First Draft, January 6–10, 1806) of the kind the captains kept on other occasions when separated. Lewis's synopsis of Clark's trip is in his Codex J for January 10, the day of Clark's return, and was likely written at that time from Clark's verbal account and First Draft notes.
Lewis began a new journal (Codex J) on January 1, 1806, and continued a consistent writing until August 12 when he laid his pen down, ending his record of the expedition. That is the first journal writing by him, as far as we know, since August 1805, except for scattered fragments. Perhaps the new journal is another point of beginning as has been conjectured with Codices Aa, Ba, and Fc, and here his good intentions of journal keeping (combined perhaps with a New Year's resolution) were fulfilled. Codex J is a detailed record, to March 20, of life at Fort Clatsop, and contains extensive descriptions of local flora and fauna and the life of the nearby Indians, with numerous illustrations. Nowhere else did Lewis devote more time to fulfilling the scientific objectives of the expedition by recording so much. All of the observations are incorporated in the daily entries, generally after the record of the day's events. In what was evidently an additional measure to insure the preservation of this material, Clark copied most of it into his journals almost verbatim. For some reason Clark did not always copy material under the same date as Lewis and sometimes placed it under an entry several days earlier than that of Lewis's. Clearly he was not copying Lewis's day by day.
Clark's copying of Lewis for the period after January 1, 1806, is in a more careful, neater hand. There is no way of knowing whether Clark's neater hand was something he could do at any time he chose to make the effort, or whether it represents writing at leisure and in comfort after the return from the voyage. But if the reason for copying from Lewis was insurance against loss, it would make more sense to complete it as soon as possible during the journey.
Lewis's Codex J also includes natural history material appropriate to the Rocky Mountains and Interior Basin, notes additional to the few fragments extant for that period. If Lewis had kept a journal for that period (August-December 1805), why did he copy it into daily entries for the time at Fort Clatsop? Why not copy it into a separate journal covering the actual dates? That question must remain a mystery. There must have been some sort of natural history field notes or other journals for that period that are now lost. If Lewis did have notes in daily journal form covering the August-December gap, why did he not copy them into his own journal at Fort Clatsop when he would have had time? One answer might be that the notes he had were mainly natural history and ethnographic material, and that he did copy them into Codex J, under current dates. If both Lewis and Clark were copying from supposed notes made by Lewis before arriving at Fort Clatsop, then it might be clear why Clark's version of the scientific material comes under different dates than in Lewis's journals, while his daily record of events follows Lewis verbatim on the same dates. But Clark's duplication of Lewis's natural history notes in the codices (particularly Codex J) is so exact that the hypothetical notes must themselves have been as elaborate as those in Lewis's notebooks. 
As noted, Clark apparently did not write his November 7, 1805 entry in Codex H until on or after March 19, 1806, when he copied the "battery of venus" passage into that entry. March 19, when Lewis evidently wrote the paragraph, was just four days before the expedition left Fort Clatsop on the return trip. We can hardly imagine Clark writing over four months' worth of notebook journals, including extensive natural history notes, in that period of time, which surely was crowded with preparations for leaving. If he was copying from Lewis after the departure from Fort Clatsop, when did he do it—along the trail, during the lengthy stopover at Camp Chopunnish in Idaho, or after the arrival in St. Louis? And what did he do about his own daily journalizing during the homeward journey?
Clark's copying of Lewis continues during the first few days of the party's journey up the Columbia; he was still writing in the same book (Voorhis No. 2 in Thwaites's numbering system) and the entries could have been written some time later. The last two days of Voorhis No. 2, April 2 and 3, describe Clark's trip up the Willamette River on those days and could easily have been taken from field notes.  Lewis copied that narrative under his April 6 entry, with some changes in wording. Clark's Voorhis No. 3 begins on April 4 and is more a record of daily events without the extended descriptions copied from Lewis.
Since Voorhis No. 3 takes up immediately where No. 2 leaves off, however, it is logical to think that Clark did not start No. 3 until the other was finished—perhaps some time after the given date. Under April 6, Clark again has some natural history data copied from Lewis's entry of April 7. Clark may have been keeping some sort of field notes at this time. There are such notes made by him for the period of April 16–21, but for most of that time the captains were separated, with Clark trading for food at various Indian villages near the Great Falls of the Columbia. He might well have not wanted to be troubled with carrying a notebook journal at that time, but perhaps he was not keeping a journal at all in the period of the journey upriver. We have no idea when the two decided that Clark should copy Lewis's Fort Clatsop journals, perhaps doing no journalizing himself in the meantime, although the short entries for January 1–3 in his Codex I suggest the decision was taken in early January 1806. Nor is it clear how long after March 19 Clark waited to begin his copying.
From May 14 to June 10, 1806, the expedition was at rest at Camp Chopunnish, on the north bank of the Clearwater River in the Nez Perce country of Idaho, waiting for the snow to melt sufficiently on the Lolo Trail for their passage east. In this extended period of relative leisure Clark might have done some of the extensive copying from Lewis's journals. As noted, the use of the name "Clark's Fork" in a map placed with the October 18, 1805, entry in Codex H suggests that much of that notebook journal was not written until late April or early May of 1806, or later. That possibility would fit well with the hypothesis that much of Clark's catching up in his notebook journals and his copying from Lewis took place at Camp Chopunnish in May and June of 1806. Voorhis No. 3 has on its flyleaf a list of Chopunnish (Nez Perce) names for rivers; that fact suggests that the book, covering April 4–June 6, 1806, was out of its box and readily available during the period to record the information. Perhaps Clark finished his copying at Camp Chopunnish, although it would have been a substantial task. Clark records events of the period in words very similar to Lewis's, but daily events could obviously have been copied the day they happened. It is notable, however, that after the end of May we no longer have passages in Clark's journal that are clearly copied from Lewis, placed by Clark under dates earlier than in Lewis's journal. 
At the beginning of Codex M is a map of the Rockies based on a sketch given by "Sundary Indians of the Chopunnish Nation on the 29th 30th and 31st of May 1806." Clark may not have copied the sketch until several days later, but its presence in Codex M, which begins on June 6, near the end of the Camp Chopunnish sojourn, suggests that the book was unpacked and available at that time. It is therefore possible that Clark's copying from Lewis was complete to June 6 and he was able to start Codex M on the actual date.
Having returned to Travelers' Rest, the captains split the party on July 3, Lewis going northeast to seek a shorter route to the Missouri, Clark southeast to explore the Yellowstone. By all previous experience they should each have kept a journal during the period of separation, especially since they would be covering territory they had not previously explored.  Did they keep field notes on the trail or write in their notebook journals?
Lewis's Codex L runs to July 4, then resumes after eighteen blank pages with an entry for July 15; that is the only such unfilled gap in time in a notebook journal. The fragmentary Codex La (July 3–15) covers that period, and Lewis probably intended it as the first draft. He probably packed away the notebook Codex L for safekeeping while traveling through the mountains, then resumed writing in it on July 15, leaving the blank pages to fill in later from the material in Codex La. In fact he never got around to that, probably because he quit writing entirely on August 12, by which date all the writing in Codex L was probably complete. He probably wrote his account of the violent encounter with the Blackfeet on July 27–28 at least a few days later, after rejoining his party following a hurried ride across country. He continued Codex L to August 8, after which the fragmentary Codex Lb covers August 9–12; on the twelfth Lewis stopped writing entirely because of discomfort from the accidental gunshot wound inflicted by Pierre Cruzatte on August 11. He had rejoined Clark on August 12, and the latter could now keep a record for the whole party.
The loose pages constituting Codex Lb were evidently once part of a red notebook found among Clark's papers, which bears on its cover the notation "9 to 12 Augt. 1806"; it now contains no expeditionary material. Lewis evidently began writing in the book after finishing Codex L, then stopped after a few days because of the pain of his wound. In later years Clark removed those few pages to use the book for other purposes. Considering the unfilled gap in Codex L, it appears that Lewis's journal keeping ceased entirely on August 12, 1806, and was then complete as it now stands.
Clark's travels after leaving Lewis involved several shifts from horseback to canoes and back to horses, but there is little indication that he did not write entries directly into his notebook journal (Codex M) for much of the period. A fragment for this period, covering the days July 13–19 and July 24–August 3, consists of courses and distances for his Yellowstone exploration—July 13 was the day he left the Three Forks of the Missouri headed for the Yellowstone. The Codex M entries for those days are much more extensive than the material in the fragment. The gap in the fragment represents the period when Clark's party stopped to build canoes, when there were no courses and distances to be recorded. Codex M has fairly extensive entries for those days. The Codex M entries through July 23 are in sequence, with no large gaps or crowding; as far as we can tell, Clark could either have been keeping that journal day by day, or he could have brought it up to date to the twenty-third while encamped.
Clark reached the Missouri, at the mouth of the Yellowstone, on August 3. At the end of his August 3 entry in Codex M is a passage, over two pages in Lewis's hand, describing the Yellowstone, which obviously Lewis could not have written before the captains' reunion on August 12. Clark's August 4 entry then follows on the next page without any gap. Unless Lewis managed to fit his passage neatly into a gap left by Clark, then the subsequent entries by Clark must also have been written after August 12. Lewis may have written the passage on August 12 before he stopped writing, but he could also have written it weeks later, after he had largely recovered from his gunshot wound, even after the arrival in St. Louis.
In his August 10 entry in Codex M, Clark gives a description of a cherry in Lewis's characteristic technical vocabulary, which is in fact copied from Lewis's description in Codex Lb for August 12; Clark could not have copied it before August 12, the date of their reunion.  Clark has a lengthy description of Lewis's experiences after their parting, with courses and distances, in his August 12 entry. The day of their reunion was the logical place for that information, but there is no proof that he actually wrote it on the twelfth. After that narration, however, Clark finishes the entry with the remaining events of August 12, the natural sequence if he had written the entry on that date.
The last daily entry in Codex M is that of August 14; it breaks off in the middle and is taken up in Codex N, an unusual procedure for Lewis and Clark. The entry in Codex M runs into the bottom of a weather table for the month of August 1806, which is complete to the end of the month. It is not clear which was written first, since Clark might have broken off the August 14 entry to leave space for finishing the weather table already started. Otherwise, we would have to assume he wrote the August 14 entry after the end of August. Codex N takes up under the heading of August 15, yet it clearly describes the same Indian council as that of August 14, in Codex M; the transition from one day to the next is never clear. Hurried copying at a later date might be the explanation of the unusual confusion of dates.
At the end of Codex M, Clark wrote an undated "Memorandom" to himself about some things that needed to be done; among them was to "Copy a Sketch of the rochjhone [Yellowstone]." Under the date of August 10, Clark notes that he "finished a copy of my Sketches of the River Rochejhone," which may mean the memorandum was written before that date. He also notes that he must make "a copy of the courses and distances," perhaps meaning to copy the fragment giving courses and distances for July 13–19 and July 24–August 3. The last item is "to fill up [vacinces?] in my book." Those "vacancies" could be merely the various blanks left in the journals for names of streams decided on later; they could be portions of pages left blank for insertion of material; or they could be more extensive blank spaces in the notebooks. At any rate, the note emphasizes the uncertainty for scholars of determining when any particular entry or portion of one was written.
Clark's Codex N has several blank spaces at the end of entries, perhaps left for insertion of extra information in case of need; that provides no satisfactory indication of when the writing was done. Codex N also contains miscellaneous notes that could have been made at various dates. The first two pages (including one side of the front flyleaf) are lists of goods shipped from St. Louis after the expedition's return, written in the same direction as the journal entries that follow. It is possible, then, that Clark wrote the whole of the daily entries in the book (August 15–September 26) after the latter date. The use of the flyleaf, however, might be taken as an indication that the list was written after the journal entries. The confusion of dates at the beginning of Codex N, the gaps perhaps left for later insertions, and one instance (August 16–17) where one day's entry runs over into the beginning of the next, could all be taken as indications of haste. Such haste, however, could belong either to the period of the final rush downriver by the homesick explorers, or to the period after the return, when Clark was trying to finish his task. Codex N ends on September 26, three days after the arrival in St. Louis; the entries are progressively shorter the last few days, the last two notably so. There is no discernible reason why Clark chose to end at this particular point rather than on the day of arrival; that would be especially odd if he were copying the material from notes later.
There is still doubt, then, as to when Clark finished his writing. Jefferson's statement that "ten or twelve" red books were turned over to him on Lewis's return is too vague to support any precise conclusions. If Lewis showed the president all his own and Clark's daily notebook journals—Codices D through N and Voorhis Nos. 1, 2, and 3, there would be fourteen red books.  That leaves room for some unfinished journal keeping by Clark, consisting most probably of Codex N and part of Codex M if there was any such unfinished work. If Clark had delivered the remaining material on or soon after his own arrival in Washington on January 21, 1807, Jefferson might not have considered the circumstance memorable or worth mentioning years later, especially since he always tended to think and write of the expedition and the journals as essentially Lewis's.
The reader may not think the above a substantial advance beyond David McKeehan's statement of 1807 that "the several journals were brought together . . . and the blanks . . . filled up . . . at the different resting places." That is the procedure common sense would suggest, and it accords with the evidence available. In all probability, the bulk of the journals were complete when Jefferson saw them, some three months after the end of the expedition. Neither Jefferson nor McKeehan made any specific mention of field notes, but they were certainly made because some still exist. The possibility remains that the captains made other field notes and that some of those may yet be found. The evidence, however, does not require us to assume extensive sets of field notes amounting to duplicate journals covering the whole journey and copied into notebooks during or after the expedition.
Neither does the evidence indicate a uniform journal-keeping procedure followed consistently throughout the expedition. The captains followed their own convenience so far as consistent with making a complete record and with the safety of the documents themselves. If they had any fixed procedure in mind when they started out, they were certainly flexible enough to change it in the light of experience. Clark's full and extensive Field Notes for the journey up to Fort Mandan do not prove the existence of such notes for periods when none have been found. There are good reasons for believing that both captains wrote parts of their notebook journals later than their given dates, in the case of some of Clark's journals months later. At other times the evidence suggests that they kept the notebook journals day by day or soon after the given dates. They may have written in the notebook journals daily when the going was fairly smooth and the books were easily transported and protected. Under bad conditions they probably sealed up the notebooks in tin boxes for safety, using more or less extensive rough notes to keep a daily record.
The most significant criterion for the use of field notes would be the risk factor. In the beginning, when they were still gaining experience and testing procedures (on the journey to Fort Mandan), when travel and weather conditions were particularly bad (on the Lolo Trail), or during separations (the trip to the whale site on the Oregon coast), we can expect to find field notes with the finished journals.
The presence of several fragmentary, unbound codices naturally suggests a comparison with Clark's Field Notes of the first year; could they be the remains of a similar comprehensive set of preliminary journals, the basis of the notebook journals? The majority of them represent periods when the captains were separated; does this mean that the authors wrote them only because of that circumstance, or was that the reason those notes were preserved while many others were discarded? None of the fragments gives a clear indication of being part of a more extensive body of notes. There are no parts of a previous day's entry at the beginning, nor the beginning of another entry cut off at the bottom of the last page. In one or two cases the author may have intended to continue but left blank space indicating he never got around to it. The same appears to be the case with the Elkskin-bound Journal. The "fragments," as far as the evidence goes, are complete in themselves and not the remains of something larger. There was nothing, after all, to prevent the author of each fragment from copying it into his notebook and then discarding it with the rest of his hypothetical field notes. The preservation of these scattered pieces is more likely to have been the result of the captains' desire to preserve everything that could possibly be useful and relevant. Because so many of the fragments are Lewis's, they are part of the mysteries surrounding his journal keeping.
Nine of Lewis's fragmentary codices (Aa, Ba, Fa, Fb, Fc, Fd, Fe, Ia, and Lb) are apparently pages taken from notebooks, all but one (Ia) from red books. It is possible that Lewis removed the pages before writing on them, but it is equally possible that the writing was done in the books and the pages removed at some later period. Codex Fc, for instance, came from Codex P, and there is some reason to believe that those pages were not removed until 1810, when the book was used to copy natural history notes for Benjamin Smith Barton. As noted, many of the fragments represent periods when the captains were separated or when weather and travel conditions posed a special risk to the journals. On such occasions Lewis may have used a book that was largely blank, containing perhaps some relatively unimportant or duplicated data. Thus if the book he was carrying with him was damaged by weather or a dip in a river, or if he failed to return from a scouting mission, important material would not be lost, as would be the case if a regular daily journal suffered. This possibility may strengthen the likelihood that the so-called fragments are complete in themselves and not part of a body of lost field notes. Jefferson's reference to the red books as "travelling pocket journals," although he was not present when they were written, at least suggests that some of them were at some times carried on the person. Their size renders this quite possible. The "fragment" pages could have been removed from the books during the expedition, after the return, or when Clark and Biddle were working on the journals in 1810. If Lewis did have daily field notes and did not get them copied, what happened to them? When they saved so much else—so many fragments, scraps, and sketches—why not save material by the expedition leader covering periods when there is no other writing by him? Once again we have hypothetical lost journals, for whose existence there is no real evidence.
When Clark gave Nicholas Biddle custody of the notebook journals in 1810, Clark retained some of his own notebooks, which became part of Thwaites's discovery of material from the Voorhis family. The ones he retained covered periods for which there are known Lewis journals. The ones turned over to Biddle cover the periods where no Lewis journals are known to exist and the long separation in the summer of 1806. It certainly appears that the basis of Clark's choice of which of his own books to give Biddle was the existence or nonexistence of journals by Lewis covering the same period. If so, then the present gaps in Lewis's journals apparently existed by 1810 at the latest, and as noted no letters are known that lament the loss of daily journals by Lewis, either at the time of his death or earlier.
Clark's Elkskin-bound Journal represents a special case where extra care was taken to preserve a lengthy body of what evidently started out as rough course and distance notes with sketch maps made on the spot. But for most of the period covered by that journal there is no known writing by Lewis, and it seems that Clark did not write his notebook journals for at least half the period until months later. Moreover, conditions during the period were often such that the notebooks would have been safer in their sealed boxes. The Elkskin-bound Journal ends at the very point where Lewis's known journalizing resumes.
From the evidence it appears that Clark kept no regular journal for almost three months at Fort Clatsop (January, February, and March 1806), while Lewis was keeping his journal with its extensive notes on natural history and ethnology. Either they planned all along for Clark to copy those notes or decided on this precaution at some later point for safety's sake. It is unclear when Clark completed the copying of Lewis's Fort Clatsop journals or when he wrote the remainder of his notebook journals—how much he completed on the trail or how much, if any, after reaching St. Louis. We can only guess how long it took him to copy from Lewis or to compose his own entries. He introduced many of his own characteristic spellings into copied material, indicating that he was not trying to achieve literal faithfulness, and he sometimes changed the wording and included material from his own experiences where it seemed relevant.
At points where a notebook journal appears from good evidence to have been written weeks or months after the given date, it is not unreasonable to suppose the existence of some sort of field notes to assist memory. The clearest and most extreme case of the sort, Clark's notebook journals of fall 1805 to spring 1806 (Codices H and I and Voorhis No. 2), is explained by the existing Elkskin-bound Journal (from November 1805 to December 31, 1805), and after January 1, Clark copied from Lewis's journals. In cases where the interval between the given date and the actual writing of the entry was shorter, the notes could have been as extensive as the existing field notes of Clark's from the first year, or they might have been in the nature of expanded course and distance notes with sketch maps, of which various examples remain.
There is little reason to accept the theory that the red notebook journals were all written after the return from subsequently discarded field notes. Considering the great amount of extant material and the labor involved in writing it, we need not imagine extensive sets of field notes paralleling the notebooks when the existence of such notes is neither known nor required by the evidence. Whatever Clark's "we commenced wrighting" in his last journal entry refers to, it was probably not the task of writing all the red books covering a year and a half of travel. Most of the material we now have was written by the captains in the course of the expedition. In reading it, we are in a sense traveling with them and sharing their day-by-day experiences and uncertainties.
Whatever the nature of the "wrighting" mentioned in Clark's last journal entry, the captains were in no doubt about the importance of their written record. Much of Jefferson's instructions to Lewis consisted of either detailed lists of the sort of information they were to record or admonitions about the importance of making duplicates and preserving their notes against loss. If they could make contact with some American ship on the Pacific coast, even if they did not choose to return by sea, they were to send some trustworthy member of the Corps of Discovery home by that route with a copy of their journals to date. Jefferson wanted a full record of their findings to present to the world as soon as possible in a multivolume work, including a narrative of the journey and a full exposition of their scientific and geographic discoveries, with appropriate maps and illustrations. The published accounts of Captain Cook's voyages and the journals of American naturalist William Bartram probably provided models of what Jefferson had in mind. Certainly he did not intend to have the journals published in their original, rough form; the convention of the time demanded that someone should produce a polished, literary version. Jefferson intended that Lewis, who had the sort of literary style admired at the time, should do the writing. 
Jefferson and everyone else associated with the work would meet repeated delays and frustrations; indeed, no one alive at the time would see the full record presented to the world. For all his good intentions, Jefferson himself was responsible for many of the initial delays, for he promptly appointed Lewis and Clark to official positions that prevented their devoting their time to preparing the journals for publication. Lewis he nominated as governor of the upper portion of Louisiana, with its capital at St. Louis, and Clark was to be superintendent of Indian affairs for the same region. The country needed men of knowledge and ability in those positions, and on the face of it no two were better qualified. Yet Lewis's appointment would prove disastrous for him.
Before leaving for St. Louis, Lewis made arrangements for publication with a Philadelphia publisher, John Conrad, and published a prospectus for a three-volume work to be financed, like many books of the time, by the subscriptions of prospective readers. According to the prospectus issued in April 1807, the first volume would be a narrative of the journey, the second would present the geography and "a view of the Indian Nations," and the third would give the scientific results. "Lewis & Clark's map of North America" was to be published separately "on a large scale." Jefferson and Lewis hoped to have the first volume out by the end of 1807. 
Not only did Lewis's duties as governor prevent his working on the narrative but the frustrations and pressures he met also tragically disrupted his personal life. Financial difficulties, political opposition, and probably alcoholism brought him to despair. In October 1809, on a journey to Washington to straighten out his tangled official accounts, he died of gunshot wounds by his own hand in a lonely cabin in Tennessee. Jefferson and Clark, who must have known him as well as anyone, seem to have had no doubt that he committed suicide, but various later historians have sought to prove that he was murdered. At the time of his death he had done nothing to prepare the narrative of the expedition for publication, but fortunately, the journals were found in his personal belongings. The task now fell to Clark, who was only too conscious of his deficiencies as a literary man. 
In the meantime, Sergeant Gass had published a heavily revised version of his journal in 1807. To supplement their own records, the captains had required the sergeants to keep journals, and others kept records as well; those journals will be discussed in another part of this volume, and existing journals will appear in this edition. Gass had no permission to publish, and Lewis was somewhat vexed at the sergeant's enterprise. Lacking any literary pretensions, Gass had his journal worked over by David McKeehan, who produced a heavily edited volume, probably quite unlike the original. Gass could add little to the scientific results, and the McKeehan text scrupulously avoids mentioning personal names and many other matters that would have added to the history of the journey. Gass does give a few pieces of information not found elsewhere, such as the dimensions of Fort Mandan (November 3, 1804); because he was a carpenter, he may have supervised the building. 
Jefferson had always thought of the journey as essentially Lewis's; Clark's function was to second the commander and take over if anything happened to Lewis. No such necessity arose during the expedition, but after Lewis's personal disaster, Clark did indeed have to take over and finish their joint task, now in a phase for which he considered himself little qualified. We might have expected that Jefferson, having left the presidency in 1809, would have had the time, as he certainly had the qualifications, to prepare the work for publication himself, but there is no evidence that he ever considered it, although he maintained his interest in its progress.
With Lewis's death, Clark became custodian of the captains' journals, and to him fell the duty of preparing the narrative account of the expedition. Unsure of his own literary abilities, he turned to Nicholas Biddle, a literary figure of Philadelphia. Reluctant at first to accept the task, Biddle eventually acquiesced and agreed to visit Clark at Fincastle, Virginia, the family home of Julia Hancock Clark, the captain's first wife. There Biddle spent about three weeks in the spring of 1810, learning about the expedition and poring over the journals. Biddle took copious notes in partially filled and unused notebooks from the expedition. His task was to write an account of the trip while leaving scientific matters to others. Biddle had full use of the captains' journals at that time and Sergeant John Ordway's journal as well, and took most of them with him. Later in Philadelphia he had the personal assistance of George Shannon, a private in the party. 
After Clark's return to the West, he and Biddle corresponded about the problems of publication and further questions that occurred to Biddle. The failure of John Conrad's publishing business in 1812 further delayed publication. In 1813, Biddle made arrangements with another Philadelphia firm, Bradford and Inskeep, and also turned the work over to Paul Allen for final revision. Although Allen's contribution was secondary, his name was the only one to appear on the title page as author. Biddle probably followed a literary convention of the time that a gentleman did not publish under his own name, if he did not earn a living by writing. Indeed, Biddle received not a cent for his work; neither did Clark, for Bradford and Inskeep also went into bankruptcy in 1814, the year of publication of History of the Expedition under the Command of Captains Lewis and Clark. Only 2,000 sets were printed. Two years after publication, Clark himself was still trying to obtain a copy. 
For nearly eighty years Biddle's work, except for the Gass volume, would stand as the sole literary product of the Lewis and Clark expedition. Many readers believed that in it they were reading the actual journals of the captains. Biddle was scrupulous about accuracy, taking care to question Clark on innumerable points. He had not traveled in the West, and he could not have known the country as the captains did. Because of a personal interest in ethnology, he included much of the wealth of information to be gleaned from the journals about native peoples. Certainly his care, together with Clark's map of the West published with it (Atlas map 126), helped make the work a valuable source of information on the country and its people.
Very few of Lewis's impressive notes on natural history appear in Biddle's work, for the planned scientific portion of the History was left in the hands of Benjamin Smith Barton, a leading naturalist of Philadelphia. Before his death, Lewis had discussed his intended publication with Barton and had perhaps asked him to write the scientific volume—chiefly those parts concerned with natural history. Clark made a similar arrangement with Barton in 1810 and had the natural history notes in the daily-entry journals copied into other notebooks for the naturalist. Because of Barton's age and failing health, and perhaps his procrastination, no volume on the scientific achievements of the expedition ever appeared. 
After Jefferson and Biddle had deposited the journals with the American Philosophical Society in 1817 and 1818, the volumes rested virtually untouched for some seventy-five years, and Biddle's history remained their only representation to the world. Yet the Biddle paraphrase was by no means all that Jefferson had hoped; in particular, the omission of the scientific findings helped establish a view of the expedition, common to this day, as primarily a romantic adventure. That conception was altered largely through the work of one man of large scientific achievements and with an unassailable conviction of the correctness of his own views. Elliott Coues became the next editor of the Lewis and Clark documents and in his work illuminated the numerous scientific discoveries of the captains. Moreover, he codified the society's expedition documents under a reference system that is in use to this day. Although Coues was to become one of the most notable editors of western historical documents, his professional training was in quite different fields. He had served for eighteen years as an army surgeon, but his great interest was in birds, and he had become the leading American ornithologist of his day. His military duties took him to various regions traversed by Lewis and Clark, so that, unlike Biddle, he had firsthand knowledge of the West. He came to the editing task in 1891 when publisher Francis P. Harper sought someone to prepare a new edition of Biddle history. 
In a sense, Coues rediscovered the Lewis and Clark manuscripts that had been deposited by Biddle and Jefferson with the American Philosophical Society in 1817 and 1818. Since that time the journals had hardly been touched, and although they were not lost, they were certainly little known. Society records demonstrate that while the journals rested securely in the archives between Biddle's and Coues's time there were a number of applications for their use. In 1837, Secretary of War Joel Poinsett asked the society to loan the journals to John James Audubon, who wished to prepare a natural history of the expedition. Audubon was then in Europe, and it was decided not to risk the journals to an ocean voyage, but the society offered full use of them at Philadelphia. In 1884, the society published its minutes up to 1838, which revealed to readers that the journals were in its keeping. During the next few years, ethnologists Daniel G. Brinton and Henry Henshaw and geographer Alfred J. Hill inquired about the manuscripts. But it was Coues who rekindled the nation's interest in Lewis and Clark. 
During the Christmas season of 1892, Coues began to examine the manuscript journals in the study of his home at 1726 N Street, Washington, D.C., having been loaned the documents to prepare his edition of Biddle's work. Coues was unawed by these original notebooks, for he quickly began to set them in order for easy reference and to tamper with them in a shameless fashion. He removed their brass holding clasps; he reordered and covered loose pages and set them in chronological sequence; and he labeled each notebook and paginated the lot. He even made a secret copy of the whole without the knowledge or consent of the society. Moreover, he added numerous and sometimes long interlinear notations and trimmed several ragged pages. For those reasons, despite their admiration for Coues's edition (his annotation was a magnificent addition to Biddle's work), scholars have been critical of the doctor. 
Not all that Coues did to the journals, however, should be considered detrimental. His labeling, reordering, and paging of the notebooks and loose papers provide a practical way of cataloging and referring to the journals. Besides designating the notebooks as codices and setting them in chronological order, Coues wrote out a lengthy description of the journals' contents—noting maps, drawings, figures, and tables—and discussed the authorship and disposition of each journal. All that work is very helpful, although it does not excuse his defacing of the manuscripts. 
Coues's 1893 edition of Biddle's History was in many ways a masterly work. He was able to identify many of the plants and animals mentioned and to locate many geographical points. With the aid of the journals, he elucidated many of Biddle's obscure passages, adding extensive supplementary quotes from the journals. Coues was a champion of the footnote, undaunted by problems of space; his notes come close to outrunning Biddle's text, and he was willing to alter Lewis's and Clark's language when quoting from the journals. He seldom hesitated to interject his own opinions or information, whether or not it was relevant to the subject; in particular, he could not refrain from mentioning if he had visited points passed by Lewis and Clark, and he seldom admitted doubt on any point if he could possibly avoid it. Nonetheless, his editorial work was a major contribution to the knowledge of the expedition. 
Coues evidently made his secret copy of the journals in anticipation of editing them for publication himself, but other work and his early death in 1899 prevented this.  Instead, the job fell to Reuben Gold Thwaites, who undertook the task for the publishing firm of Dodd, Mead and Company in 1901. Thwaites, head of the State Historical Society of Wisconsin, was already an experienced editor of several western historical documents. In the course of his Lewis and Clark research he discovered a number of new documents that greatly enhanced his edition. He included everything from the expedition that had been deposited at the American Philosophical Society by Jefferson and Biddle but decided against including Gass's journal because he considered it easily available elsewhere. Among his discoveries were the journals of Sergeant Charles Floyd and Private Joseph Whitehouse and, even more important, a number of daily journals and other documents by Clark that the latter had retained instead of giving them to Biddle in 1810. Those were in the possession of Clark's granddaughter and great-granddaughter, Julia Clark Voorhis and Eleanor Glasgow Voorhis, and now constitute the Voorhis Collection at the Missouri Historical Society, St. Louis. (See Appendixes B and C.) 
Thwaites's work would surely have satisfied Jefferson. All scientific material was included as well as the maps found in the Voorhis Collection. He also printed a number of the letters from the collection in an appendix. Yet Thwaites labored under certain handicaps of space and time and lacked the broad geographic and scientific knowledge that Coues brought to his work. Errors of transcription slipped by, and his organization of materials is open to criticism in some respects. By the standards of a later generation, his annotation was meager and somewhat erratic; he borrowed from Coues's footnotes and supplemented them with help from other scientists and his own knowledge of western history. The deficiencies of his work demonstrate both the increasing intellectual specialization and the amount of scholarship that remained to be done on the expedition. Nonetheless, Thwaites made available to the world for the first time the bulk of the captains' and their subordinates' journals, more or less as the authors had prepared them. It was his work that made possible the subsequent generations of Lewis and Clark scholarship that have finally rendered a new edition necessary. 
Thwaites thought he had probably uncovered all the Lewis and Clark material still in existence, but within a decade of his edition, new documents became available. Among expedition papers discovered by Biddle's grandsons in their grandfather's papers in 1913 were the three-volume journal of Sergeant John Ordway and a journal kept by Lewis and later Clark of the preliminary trip from Pittsburgh to Camp Dubois, from August 30 to December 12, 1803. Thwaites had known that Ordway had kept a journal and had been searching for it when he discovered the Voorhis journals, but the Lewis and Clark document—here called the Eastern Journal—was a totally unexpected discovery, for no one had suspected that any notes were kept on this initial phase of the trip. The editorial work on Ordway's journal and the Eastern Journal went to Milo Milton Quaife, Thwaites's successor at the State Historical Society of Wisconsin. Quaife was a professional historian, though at the time he took the job he lacked the editorial experience of both Coues and Thwaites, and the scientific and geographic knowledge of Coues. He carefully compared Ordway's account with those of Lewis, Clark, Floyd, and Whitehouse. He restrained himself in annotation, unlike Coues, and most of his notes relate to geography; however, he has been criticized for his dearth of annotation. 
The rediscoveries of Lewis and Clark documents described thus far, while pleasant surprises to scholars, were in places where such materials might reasonably have been expected, if they were in existence. In 1953, however, a major find came to light under totally unexpected circumstances. In St. Paul, Minnesota, Lucile M. Kane, curator of manuscripts for the Minnesota Historical Society, inspected the papers stored in an old desk of General John Henry Hammond, who had died in 1890. One bundle of papers, wrapped in a Washington, D.C. newspaper, proved to be sixty-seven sheets of field notes written by William Clark in 1804 and 1805, with some interpolations by Lewis. Portions of them cover the winter at River Dubois, about which little was previously known. The rest consist of preliminary notes for the period May 14, 1804–April 13, 1805, though entries are less frequent after November 1804. The first group of papers has been called the Dubois Journal while the second set has been labeled the River Journal. Thwaites had suspected that such notes were made, then copied and expanded in the regular notebooks at some subsequent time that he could not determine, and the new find confirmed his surmise, at least for the period of the River Journal. 
Ernest Staples Osgood, an experienced historian of the West, became editor of the Field Notes, but litigation over the ownership of the documents interrupted his work. The heirs of Hammond's estate eventually regained control of the papers from the Minnesota Historical Society and sold them. The final private owners, Frederick W. Beinecke and family, ultimately donated them to Yale University where they remain today. Osgood then concluded his editing of the papers and his book was published in 1964 by Yale University Press. Osgood's work is in many ways the best in the Lewis and Clark story to date. In annotating the Dubois Journal, he was able to illuminate a period hitherto largely obscure; the portions dealing with the actual journey to Fort Mandan, though covering more familiar events, provided much useful supplementary knowledge. Osgood devoted a lengthy introduction to the many problems of the origin and history of the documents and provided facsimiles so that readers could make their own comparisons. 
The need for a new edition of the journals has been apparent for some time. The number of discoveries of new journals and the nature of modern editorial techniques have made Thwaites's edition somewhat obsolete. In fact, Thwaites did not publish everything that was available in his day, for he omitted some miscellaneous material in the Voorhis Collection, and he did not include Gass's journal in his volumes since it was accessible at the time. Quaife also neglected to publish everything that came in with the Biddle family deposit but concentrated instead on the two outstanding finds, the Eastern Journal and Ordway's Journal. Those items and other overlooked material will be in this edition. More recently discovered material is also available here for the first time, most important, Joseph Whitehouse's paraphrased journal, discovered in 1966, which extends the available portion of the original. Moreover, the difficulty of obtaining some published material today (especially Quaife's and Osgood's works) has increased the need for this edition. Considering Thwaites's gaps, slight as they are, we can say that this is the first comprehensive, collated edition of all known journals.
The principal goal of the new edition is to present users with a reliable, definitive text. The aim is to approach Coues's unfulfilled ambition of creating a text that is "verbatim et literatim et punctuatim." Earlier editors, pressed for time and working virtually alone, were not so fortunate as to have several reviews by different persons of their transcriptions. Every effort is being made here to present a transcript that is nearly identical to the original.
The new edition will also give readers a thorough, uniform annotation of the journals. Previous editors, at least until Osgood, have relied largely on the work of Coues in his annotation of Biddle's paraphrased edition of 1814 or have not annotated as thoroughly as present users wish. Scholars have been particularly struck by the paucity of notes in Thwaites's edition. With the publication of Osgood's work in 1964, it became clear how antiquated previous editions were. Osgood had considerable editing skills, but he also benefited from the great amount of twentieth-century scholarship on Lewis and Clark. He was especially aided by the publication in 1962 of Jackson's edition of expeditionary correspondence, which had actually created a surge of new scholarship. Since Osgood's work covers only a portion of the trip (through the winter of 1804–5) and only a small part of the writing for that time (Clark's Field Notes), the additional writing and the long, interesting segment from April 1805 to September 1806 is largely fallow ground, to be worked here for the first time with modern annotation. A full discussion of the transcribing policies and the annotating guidelines adopted for this edition is given in the following section, Editorial Procedures. We hope that the new edition will foster a broader knowledge and spark a new enthusiasm for the expedition, its courageous members, and its accomplishments.