Command & Control 
Perhaps surprisingly instructions to commanders-in-chief were not issued upon appointment, but rather, in lieu of a new set of orders, the new commander inherited the standing or unexecuted orders of his predecessor. 

Government & Parliament
As Britain was a constitutional monarchy, the king, George III, did not exercise absolute power and relied on the prime minister and cabinet to make executive decisions, to which he almost invariably gave his consent, and to Parliament for the passage of laws and the allocation of funds for the running of the affairs state. 
With respect to the management of the Navy, the cabinet contained the First Lord of the Admiralty, whose decisions were subject to a consensus reached in cabinet meetings. Once a decision was made, the Navy depended on the House of Commons to vote it funds. The Commons, and to an extent, the House of Lords, took an active interest in naval affairs and regularly debated issues connected with the cost of the service and its role in the war. Above all, it voted the annual estimates that supplied it with money. The naval estimates were divided into three categories The 'ordinary' funds covered the cost of the maintaining ships and dockyard facilities. During peacetime these costs were generally higher, for during wartime much of the burden of maintenance was paid for under other categories. The second estimate was known as the 'extra', which were funds allocated for the construction of new ships. Lastly, Parliament conducted a vote to cover the cost of a particular number of seamen and marines, which largely determined the naval force available for that year. 
The British Army was small as compared with Continental powers; the Royal Navy, on the other hand, exceeded 100,000 men and over 100 ships of the line, and had no comparable rival in the world, including France. Having said this, there were few checks to ensure that the money was used as intended, the number of men actually on service never quite reached the figures that Parliament pledged to fund, and there were no mechanisms to ensure that the money voted actually reached Navy coffers. More importantly, the money was never sufficient, so from year to year the Navy was chronically in debt. Contractors largely accepted this system, as payment eventually did reach them, so the Navy managed well enough from year to year, notwithstanding the fact that seamen's pay could fall into arrears for years at a time. 

 

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The Admiralty
Responsibility for organising the Royal Navy, planning and implementing its strategy and deploying its fleets and squadrons fell to, by modern standards, a remarkably small number of men at the Admiralty, who were responsible to the government. These seven men, the Lords Commissioners of the Admiralty, were not necessarily peers - indeed were often admirals - and answered to the First Lord of the Admiralty, who sat in the cabinet. As naval affairs were of such immense importance to the security of the nation, the Admiralty Board met on a daily basis in its offices in Whitehall, London, and determined the movement of ships as close as the Channel or as far away as the Indian Ocean and the Pacific. Supported by a working staff of 50 to 60, supervised by the First and Second Secretaries, the Admiralty performed various administrative functions, and saw to the commissioning and promotion of officers. These men exercised central control over the whole of the Navy, from determining the price the Navy would offer suppliers for food to deciding issues of great import such as the determination of a fleet in order to make contact with the enemy. Just as they exercised total control over the Navy, they also bore the burden of immense responsibility, for it through poor decision-making they contributed to major defeat, the security of the nation itself could be at stake. 
At the time, the Royal Navy was the most complex and expensive institution not merely in Britain, but in the world, and its dockyards represented the largest industrial undertakings anywhere. From London the Admiralty executed the government's instructions, major and minor, relaying orders by courier to the relevant ports, or using the telegraph system which, from 1796, connected London to Portsmouth, Chatham and Sheerness, and later to Deal.
Employment at the Admiralty Office was much sought after, for it was well paid and checks and officers often served for decades, with promotion available for those who acquired the requisite experience and demonstrated a high capacity for efficiency. Within the Office were four subsidiary boards: the Sick and Hurt Board, the Transport Board, and the Victualling Board, all of which were responsible to the Navy Board. The Admiralty was also responsible for the Royal Marines, the Fencibles and the Impress Service (who kidnapped or forced men into naval service), as well as for operating intelligence services. 
Each year the Admiralty commissioned ships with the funds provided for it by Parliament. The Admiralty was responsible for determining the basic specifications of a vessel before work began, with the details provided respecting tonnage, dimensions, and the numbers and calibres of guns on each deck. Once these were laid down, the Surveyors of the Navy, employed in the Navy Board, would design the vessels on paper, to include details of the decks, hatchways, masts and other significant parts of the ship. Beyond this, the more intricate details such as the fitting and decorations were usually left to those at the dockyards themselves, where vessels were constructed either by workers at a government-maintained establishment, or by civilian enterprise.


The Navy Board
The Navy Board, also responsible to the Admiralty, had to produce and deliver all the other needs of the Navy. This responsibility involved ensuring that ships were constructed, repaired and supplied with stores and equipment. The Board also controlled all the government's shipyards. Much of its work was contracted out to civilian companies which themselves employed a civilian workforce, and thus the Navy Board was sometimes thought of as the civilian branch of the Navy. The Navy Board had to ensure that the ships were adequately manned, and it was to it that feel the unpleasant task of gathering crews for the always expanding fleets and paying the men their wages. The offices of the Navy Board stored thousands of documents including contracts, lists, reports and letters, all filed and maintained by hundreds of officials and clerks, supported outside London by inspectors. 
The Navy Board was responsible for building and supplying the ships and managing the dockyards, as well as the purchase and manufacture of all the equipment and stores required by the Navy. It also appointed most of the warrant officers, many of whom it examined. This whole enterprise involved thousands of men. The Board was virtually independent of the Admiralty and was the only one of the four boards that kept accounts. The Navy Board consisted of ten members, a combination of naval officers and civilians, whom the Admiralty usually appointed for life. A commissioner from each royal dockyard had a seat on the Board, the whole institution led by the Controller of the Navy, who was invariably a senior officer. While the Admiralty commissioned ships, the Navy Board designed them, usually care of the Surveyors of the Navy and their assistants and draughtsmen. British ships were often considered superior to those of the British ships. After the Navy Board and Admiralty approved a design, the draughts were copied for the shipyards. In cases where ships were built in private yards, the Navy Board had to seek out builders and negotiate the cost from various competing firms. 
In the course of the wars the Navy Board built approximately 100 ships of the line and 700 smaller ships and craft, representing over half a million tonnes, plus other ships built overseas. The largest ships - the first and second rates - were constructed in the Royal dockyards, with the remainder built in private yards. The Board dispatched someone to monitor the construction of all the vessels, which were often built various sites along the Thames. Shipbuilding required the skills of 11 types of trade, above all that of shipwrights who reached this senior position only after seven years of apprenticeship in design and construction. Building a ship was a major enterprise: six months were required to build a sloop, between two and three years for a two-decked ship, and several years for a three-decker. Even then, once it was ceremonially launched, a ship still required several months for the process of fitting it out, including the erection of masts and placement of rigging, sails, stores, guns and other material. 
Three subsidiary boards worked under the Navy Board umbrella: the Victualling, Transport, and Sick & Hurt Boards, all of whose members were, like the Navy Board, appointed by the Admiralty. The Victualling Board supplied the Navy with food, drink and clothing, and appointed pursers to oversee the distribution of such articles aboard ship. It ran its own bakeries,  slaughterhouse and breweries to meet the needs of the sailors, and had its own ships to convey provisions to the Board's naval facilities at Gibraltar and elsewhere. The Sick & Hurt Board conducted examinations for surgeons supplied their equipment, and managed the Navy's hospitals. The Transport Board conveyed the Army and Navy personnel aboard a combination of privately hired merchant vessels and Navy ships . Transport Board was noted for its efficiency and ran between 40 and 50 storeships for the Navy alone, with many more used for the Army. In 1796 the task of managing prisoners of war passed into its hands from those of the Sick and Hurt Board. 


The Board of Ordnance
The Board of Ordnance, a government department separate from the Admiralty and based in the Tower of London and at Woolwich, held responsibility for supplying all the Navy's (and Army's) armaments - everything from pistols and dirks to cannon. The Board ran the factories that manufactured powder and guns; it provided the transport to convey the munitions and arranged contracts for work through civilian firms. It also experimented with new types of guns and powders and made studies of existing weaponry. The Board of Ordnance not only maintained supplies, it also had responsibility for equipment already aboard vessels and in dockyards. This meant liaising with ship's captains to determine the condition of every weapon on his ship and the amount of shot and powder used, both during practice and in action. Guns and powder captured from the enemy had to be logged by captains, with the list of items sent on to London. 
Proper functioning of this organisation would not have been possible without a large number of officials and clerks, and the offices of the Board of Ordnance were lined with pigeon holes and boxes containing information in the form of lists and correspondence received from ships around the world concerning all the ordnance aboard ship in the Navy. Every captain was required to account for the expenditure of all ammunition and shit, barring which he received a reprimand from the Board, wherever in the world he might happen to be. 


Royal Navy dockyards and bases
At the beginning of the wars Britain maintained six dockyards, all run by the Navy Board. By 1815 these had launched 41 ships of the line and 78 other ships. About 60 private yards constructed another 60 ships of the line and over 600 other ships, some produced according to Admiralty design, others of the merchant yard's design with the intention of selling the vessels to the Admiralty. Private yards of course also produced merchant ships, some of which the Admiralty chose to buy and convert for its own needs. In addition to ship construction, the Royal yards also had to provide workmen for the Navy and repair and maintain its ships. Royal dockyards were situated at Portsmouth - largest in the country - Plymouth and Chatham. A naval hospital stood at Haslar, near Portsmouth, together with an ordnance depot, a gunwharf and a marine barracks. Chatham and Plymouth had similar facilities. Portsmouth, Chatham, Sheerness and Plymouth were all fortified and were situated near the main anchorages. Ships in service only docked in port for refitting or to allow their crews, leave; otherwise they remained at their respective anchorages, offshore, from where they could put to sea with little delay. Ships operating out of the Nore watched the Dutch coast; those in the Downs covered the North Sea and the southern coast of Holland; the anchorages at Spithead and St Helens were bases for ships monitoring the Channel; and Torbay served as the station from which to watch Brest, Spain and the Atlantic. Ships based at Plymouth operated in the Atlantic and beyond. 
Dockyards in home ports could provide most of the needs of the Navy, but with its world-wide responsibilities the Royal Navy had to maintain bases across the globe. These facilities contained stores, food, depots for munitions, and equipment and materials for repairing ships afloat. In some cases medical care was provided, such as at Gibraltar. A civilian representative of the Navy Board oversaw the bases. 
At the beginning of the wars in 1793 the Navy's overseas bases were located at Gibraltar, Halifax in Nova Scotia, and Jamaica and Antigua in the West Indies, but these were added to throughout the conflict so that by 1815 British ships could defend all the nations principal trade routes. To Supply the bases, the Admiralty bought naval stores in Britain and left their conveyance abroad to the ships of the Transport Board. The Victualling Board purchased food and drink for the use of the Navy, though supplies could be acquired locally when ships docked in foreign ports. As at home ports, the Board of Ordnance provided ordnance to British ports overseas, where ships repaired and replaced damaged weaponry. 
Various new ports were acquired during the course of the wars, two of the most important being in European waters. In the Mediterranean, the Army captured Minorca in 1798, thus enabling the Navy to use Port Mahon thereafter. When, however, peace with Spain was renewed in 1802 by the Treaty of Amiens, Britain restored the island to her erstwhile enemy. Port Mahon was of particular importance to enabling a fleet to watch the main French Mediterranean port at Toulon. Malta fell to British forces in 1800 after a two-year siege, providing the Navy with the invaluable port at Valetta, which was retained throughout the wars and formally acquired by Britain in 1814. The value of Malta as a base was recognised by many, including Admiral Lord Keith:


Malta has the advantage over all the other ports.....that the whole harbour is covered by its wonderful fortifications, and that in the hands of Great Britain no enemy would presume to land upon it, because the number of men required to besiege it could not be maintained by the island....At Malta all the arsenals, hospitals, storehouses, etc, are on a grand scale. The harbour has more room than Mahon and the entrance is considerably wider. 
 

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