How to set the ranges of the values taken by ggplot2 stat_smooth() to fits lines?

Question

I would like to make stat_smooth to fit a line using only the data from specified ranges, in other words, I want stat_smooth to fit a line between x(0,99), x(100,199) and x(199,299).

I managed to get fairly close using facet_grid as follows:

ggplot(avtimes3, aes(x=trial, y=ttime, colour=factor(id))) +
facet_grid(. ~ brk, scales = "free") +
geom_vline(xintercept = short_bks, colour="red") +
geom_vline(xintercept = long_bks, colour="green") +
geom_point() + 
geom_point(shape=21, fill="white")+
opts(title=titl) +
ylab("Time taken (ms)") +
xlab("Trial No.")+
stat_smooth(method="loess") 

But it plots lots of empty space on each grid. I haven't been able to find a way of removing it.

The other partial solution I took from another post included creating a group for the ranges, but that doesn't seem to respect the factors passed to qqplot.

ggplot(avtimes3, aes(x=trial, y=ttime, colour=factor(id))) +
geom_vline(xintercept = short_bks, colour="red") +
geom_vline(xintercept = long_bks, colour="green") +
geom_point() + 
geom_point(shape=21, fill="white")+
opts(title=titl) +
ylab("Time taken (ms)") +
xlab("Trial No.")+
stat_smooth(method="loess", aes(group=brk)) 

Any help on how to get this to work? Thanks!

The data:

> dput(avtimes3)
structure(list(trial = c(0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 
6, 6, 7, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 13, 13, 14, 14, 
15, 15, 16, 16, 17, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22, 
23, 23, 24, 24, 25, 25, 26, 26, 27, 27, 28, 28, 29, 29, 30, 30, 
31, 31, 32, 32, 33, 33, 34, 34, 35, 35, 36, 36, 37, 37, 38, 38, 
39, 39, 40, 40, 41, 41, 42, 42, 43, 43, 44, 44, 45, 45, 46, 46, 
47, 47, 48, 48, 49, 49, 50, 50, 51, 51, 52, 52, 53, 53, 54, 54, 
55, 55, 56, 56, 57, 57, 58, 58, 59, 59, 60, 60, 61, 61, 62, 62, 
63, 63, 64, 64, 65, 65, 66, 66, 67, 67, 68, 68, 69, 69, 70, 70, 
71, 71, 72, 72, 73, 73, 74, 74, 75, 75, 76, 76, 77, 77, 78, 78, 
79, 79, 80, 80, 81, 81, 82, 82, 83, 83, 84, 84, 85, 85, 86, 86, 
87, 87, 88, 88, 89, 89, 90, 90, 91, 91, 92, 92, 93, 93, 94, 94, 
95, 95, 96, 96, 97, 97, 98, 98, 99, 99, 100, 100, 101, 101, 102, 
102, 103, 103, 104, 104, 105, 105, 106, 106, 107, 107, 108, 108, 
109, 109, 110, 110, 111, 111, 112, 112, 113, 113, 114, 114, 115, 
115, 116, 116, 117, 117, 118, 118, 119, 119, 120, 120, 121, 121, 
122, 122, 123, 123, 124, 124, 125, 125, 126, 126, 127, 127, 128, 
128, 129, 129, 130, 130, 131, 131, 132, 132, 133, 133, 134, 134, 
135, 135, 136, 136, 137, 137, 138, 138, 139, 139, 140, 140, 141, 
141, 142, 142, 143, 143, 144, 144, 145, 145, 146, 146, 147, 147, 
148, 148, 149, 149, 150, 150, 151, 151, 152, 152, 153, 153, 154, 
154, 155, 155, 156, 156, 157, 157, 158, 158, 159, 159, 160, 160, 
161, 161, 162, 162, 163, 163, 164, 164, 165, 165, 166, 166, 167, 
167, 168, 168, 169, 169, 170, 170, 171, 171, 172, 172, 173, 173, 
174, 174, 175, 175, 176, 176, 177, 177, 178, 178, 179, 179, 180, 
180, 181, 181, 182, 182, 183, 183, 184, 184, 185, 185, 186, 186, 
187, 187, 188, 188, 189, 189, 190, 190, 191, 191, 192, 192, 193, 
193, 194, 194, 195, 195, 196, 196, 197, 197, 198, 198, 199, 199, 
200, 200, 201, 201, 202, 202, 203, 203, 204, 204, 205, 205, 206, 
206, 207, 207, 208, 208, 209, 209, 210, 210, 211, 211, 212, 212, 
213, 213, 214, 214, 215, 215, 216, 216, 217, 217, 218, 218, 219, 
219, 220, 220, 221, 221, 222, 222, 223, 223, 224, 224, 225, 225, 
226, 226, 227, 227, 228, 228, 229, 229, 230, 230, 231, 231, 232, 
232, 233, 233, 234, 234, 235, 235, 236, 236, 237, 237, 238, 238, 
239, 239, 240, 240, 241, 241, 242, 242, 243, 243, 244, 244, 245, 
245, 246, 246, 247, 247, 248, 248, 249, 249, 250, 250, 251, 251, 
252, 252, 253, 253, 254, 254, 255, 255, 256, 256, 257, 257, 258, 
258, 259, 259, 260, 260, 261, 261, 262, 262, 263, 263, 264, 264, 
265, 265, 266, 266, 267, 267, 268, 268, 269, 269, 270, 270, 271, 
271, 272, 272, 273, 273, 274, 274, 275, 275, 276, 276, 277, 277, 
278, 278, 279, 279, 280, 280, 281, 281, 282, 282, 283, 283, 284, 
284, 285, 285, 286, 286, 287, 287, 288, 288, 289, 289, 290, 290, 
291, 291, 292, 292, 293, 293, 294, 294, 295, 295, 296, 296, 297, 
297, 298, 298, 299, 299), id = c(1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 2, 1.5, 
2), ttime = c(2564, 2050.5, 2204.75, 2060.625, 2266.125, 1880.125, 
2224.25, 2067, 2215.375, 2199.25, 2333.375, 2434.625, 2278.875, 
2102, 2104.5, 2049, 2336.125, 2159.5, 2110.625, 2082.875, 2197.5, 
2136.5, 2107.375, 2025, 2342, 2289.875, 2106.25, 2146.75, 2187.25, 
2104.875, 2151.375, 2246.375, 2143.75, 2091.625, 2129.625, 2163.875, 
2132.5, 2265.25, 1959, 2054.25, 2205.5, 2033, 1992.875, 1965.625, 
1983.875, 1973.75, 1953.625, 1936.375, 2012.25, 2106.75, 2115, 
2195.375, 2210.875, 2097.625, 2016.25, 2084.375, 2005.25, 2250.875, 
2352.875, 2217.625, 2141.75, 2154.375, 2181.625, 2083.5, 2103.5, 
1959.5, 2020.75, 2255.25, 2039.125, 2144.125, 2216.125, 2216.125, 
2014.125, 2234.625, 1975.625, 2289, 2035.5, 2058.25, 2039.5, 
2222.5, 2013.125, 2156.375, 1896.375, 1990.875, 2014.125, 2030.625, 
1928.875, 2021, 2013, 2001.5, 1940.625, 2029.375, 2075.5, 2179.375, 
1991, 2292.25, 2020.375, 2065.375, 2007.375, 2192.5, 1954.25, 
2128.5, 1949.875, 2240.25, 2119.375, 2011.625, 1984.875, 2182, 
1955.375, 2010.5, 1924.5, 2043.25, 2033, 2183.375, 2075.75, 2011.375, 
1969.625, 2002.375, 1921.5, 2111.875, 1951, 2103, 1780.375, 1935.75, 
1930.75, 2044.375, 1892.25, 2128.75, 1973.875, 1992.625, 1920.625, 
2093, 2047.875, 2285.625, 1968, 2208.375, 2021.25, 2079.375, 
1988.75, 2147.875, 1989, 2026.25, 1873.25, 2084.75, 2010.25, 
2163.25, 1960.125, 1987.125, 2043.75, 2154.875, 2188.25, 2402.625, 
2101.625, 2019.625, 2447.5, 1996.125, 2009.875, 2037.625, 2195.5, 
2123.875, 1986.625, 2093, 1793.125, 1858.125, 1862.625, 1895.5, 
1806, 1951.5, 1784.625, 2041.625, 1868.625, 2095.25, 1946.125, 
1930.75, 2010.5, 2179.375, 1903.875, 2049.25, 1958.125, 2053.75, 
2016.75, 2057.875, 1898.875, 2196.875, 1939.75, 2265.875, 2090.875, 
2187.875, 2082.75, 2089.125, 1904, 2303.25, 1982.125, 2094.375, 
2205.625, 2259.25, 2018.5, 1882.25, 1978.125, 1901.625, 1834.5, 
2019.375, 1802.125, 1929.875, 1700.75, 2019, 1691.125, 1959.375, 
1774.375, 2138.375, 1751.25, 2036.125, 1808.5, 2138, 1848, 2109.75, 
1823.125, 2001, 1923, 2057.125, 1827.5, 1877.375, 1823.125, 1860.25, 
1742.875, 2047.625, 2018.125, 2016.125, 1799, 2095.25, 1735.25, 
1951, 1776.625, 2057.125, 1726.125, 2068.5, 1806, 2107.875, 1774.375, 
1956, 1920.75, 1943.25, 1714.125, 1756.125, 1789.25, 1941.125, 
1734.125, 2195.375, 1788.375, 2005.375, 1832.5, 1861, 1830.25, 
2263.625, 1903.75, 2090.375, 2015.875, 2019.25, 1807.375, 2143.375, 
1882.5, 1901.75, 1897.125, 1866.75, 1943.125, 1943.875, 1818.75, 
2089.5, 1818, 1992.875, 1910.25, 1855.125, 1825.5, 1850.25, 1881.125, 
1953.625, 1840.25, 2119.25, 1745.25, 2045.5, 1767.625, 2019.875, 
1759.5, 1876.125, 1667.875, 1948, 1767.125, 2046.25, 1721, 1984.5, 
1842.875, 2300.125, 1726.625, 2252.875, 1718.75, 1983.625, 1842.375, 
2165.125, 1932, 2154.375, 1746.125, 1936.75, 1920.625, 2056.25, 
1854.375, 2022.125, 1973.625, 2064.25, 1883.5, 2077.375, 2117.25, 
2089, 1759, 2082.875, 1910.75, 1955.75, 1847.375, 1998.25, 1796.375, 
2028.5, 1804.5, 1920.625, 1793.25, 1841.125, 1778.625, 1929.25, 
1742.25, 1988.875, 1805.375, 1982.75, 1797.125, 1963.75, 1682.875, 
2028.25, 1664.375, 2109.5, 1747.625, 1992, 1767.125, 2064.125, 
1740.125, 2083.875, 1952.375, 2007.125, 1763.125, 2050, 1780.25, 
2181.25, 1810.5, 1990.25, 1706.875, 2029, 1715.125, 2211.375, 
1876.375, 2003.625, 1773.5, 1986.75, 1824, 2198.375, 1777.375, 
2075, 1761.25, 1873, 1725.125, 1917.75, 1773.875, 1860.25, 1788, 
1908.625, 1955.375, 1943.875, 1828.5, 1860.5, 1836.25, 2134.5, 
1829.75, 1949.375, 1762, 2058.75, 1736.75, 1908.625, 1816.375, 
2113.625, 1868.125, 2042.625, 1796.375, 2280.5, 1773, 1968.125, 
1885.75, 2136.375, 1784.5, 2103.875, 1785.875, 2296.875, 1782.625, 
1969.125, 1864.75, 2062.5, 1800.75, 2289.75, 1639.5, 2081.75, 
1735.125, 1947.375, 1617.875, 1871.125, 1676.375, 1998, 1685, 
1929.625, 1762.625, 2073.625, 1698.75, 1834.5, 1669, 1858.875, 
1705.625, 2164.625, 1750.125, 1835.875, 1836.25, 1992, 1741.625, 
1874.375, 1810.375, 2140.875, 1819.5, 2277.625, 1779.5, 2054.875, 
1703.375, 1978.125, 1754.625, 1964.875, 1749.875, 1959.625, 1932.875, 
1952.125, 1709.625, 2038.125, 1680.5, 1893, 1664.5, 1961.125, 
1700.25, 1871, 1753, 1889.75, 1724, 1878.875, 1827.375, 1849.25, 
1850.75, 1977.125, 1783.625, 1977.25, 1895.125, 2097.5, 1716.375, 
1985.5, 1675.375, 1845.25, 1764.5, 2089.375, 1766.75, 1848.125, 
1730.125, 1991.5, 1865.375, 2030.875, 1864.625, 1960.875, 1739.25, 
2204.375, 1758.125, 2175.375, 1871.5, 1994.25, 1739.25, 2028.875, 
1646.125, 1958.375, 1709.25, 1914.5, 1638.375, 1965.375, 1691.5, 
2154.375, 1833.75, 1892.375, 1891.625, 1999.25, 1752.75, 1952.5, 
1702.625, 1907.75, 1671.25, 1947.375, 1734.875, 2125.375, 1745.25, 
2145.25, 1756.125, 2095.25, 1707.5, 1939.375, 1738.25, 2102.875, 
1862.375, 2152.875, 1719, 2091.25, 1969.25, 2088.125, 1702.875, 
2231.625, 2007.5, 2087, 1732.625, 1866.625, 1675.875, 1971.625, 
1663.875, 2016.5, 1834, 1927.75, 1777.25, 1995, 2029.125, 2009.5, 
1778.5, 1868, 1711.5, 1820.375, 1706.625, 1911.375, 1850, 2001.625, 
1753.375, 2105.625, 1812.125, 2028.125, 1820.5, 2205.75, 1812.625, 
2238, 1812.125, 2236.25, 1713.375, 2482, 1844.25, 1951.25, 1995.125, 
2108.5, 1873.125, 1977, 1849, 2064.25, 1709.75, 1962, 1844, 1828.5, 
1735.75, 1974.125, 1675, 2147, 1789.75, 2099.875, 1790.5, 2083, 
1713.5, 2250.125, 1930.25, 2321.75, 1742.5, 2189.875, 1840, 2070, 
1823.125, 2027.25, 1782.875, 2344, 1788.875, 2106.25, 1824.75, 
2251.625, 1902.5, 1961.375, 1873.5, 2158.75, 1855.125, 1933.75, 
1825.75, 2001.875, 1887.75, 2002.75, 1945.375, 2230.875), se = c(259.899705930686, 
137.567905310172, 228.087917729734, 172.114158284968, 234.074502600897, 
109.939827292024, 271.704918063696, 195.301781134443, 227.085803284951, 
169.989784356926, 257.363066052332, 353.735067201228, 231.204411529526, 
151.548082893092, 230.22527787241, 188.563933833745, 289.179037319443, 
130.584537478874, 250.616449800715, 90.5208021672367, 192.562883977454, 
178.968373103821, 225.736567192507, 157.087555204096, 222.259179466547, 
189.375330032716, 195.44269803266, 156.734278090568, 222.104443738912, 
155.254449844211, 229.124571350234, 234.785535687055, 214.213407443538, 
136.267454648675, 218.906693878922, 219.006069509826, 181.324098154185, 
198.187568984535, 160.006249877934, 152.706271505603, 280.670689090054, 
147.26276321111, 197.418648480474, 131.188242273133, 184.134989060821, 
117.833531184585, 177.697770857873, 95.0770246957697, 179.782482660098, 
149.204886697071, 143.619164061466, 171.956798717003, 225.56939362264, 
150.268680500248, 233.734415064864, 134.100833264163, 177.509833731623, 
179.588959004802, 302.633231433458, 256.399655776179, 261.114900132927, 
194.266379848099, 233.925960318034, 180.624314136117, 204.312523215923, 
147.377552080169, 190.48347791119, 143.664757334567, 184.82012853235, 
203.166050796949, 199.973965939498, 181.057847652148, 226.143478278409, 
219.701090567226, 192.715458040753, 161.770339856053, 161.292214850651, 
121.259130731316, 209.589053694537, 141.678080772675, 203.257616049542, 
158.180608516702, 146.132393189483, 151.949173539331, 171.350459324492, 
194.983967976491, 127.888265615509, 167.346091336829, 133.506152881217, 
141.716391833428, 110.950912167112, 128.343141825231, 135.5180536207, 
175.427125437561, 133.723194910767, 194.496120967562, 173.14114158892, 
142.659927487414, 199.71273454461, 219.278280469622, 135.405970273523, 
223.876480612477, 155.919786783828, 219.316531687487, 142.123178151409, 
132.259071725048, 131.867823095163, 192.080526268096, 97.3238220544472, 
154.800909004345, 143.230957348114, 172.257049409969, 113.881987789365, 
301.963629402852, 147.572228078321, 145.94690050788, 116.268306930258, 
103.901556687775, 123.388903182464, 217.304134920557, 106.773123959169, 
137.984730004032, 172.231876249516, 166.958479654588, 130.019607037884, 
182.871142914114, 142.971994010815, 203.262387603525, 68.1171358501557, 
215.99462108878, 142.521168540476, 236.726032125143, 124.067728839073, 
132.166282913933, 131.916369611313, 236.530271205249, 124.9966785273, 
159.275585240084, 89.4242995898925, 208.220816639794, 86.0348766489497, 
106.74431232757, 117.217708011326, 186.83259791283, 92.4279159283446, 
153.374745313562, 121.694646774505, 171.894115820093, 107.795731097559, 
127.720179284358, 272.201064734981, 364.814039590231, 155.784528103495, 
143.156624703255, 489.334059134015, 173.340544006382, 83.3367603462002, 
166.637431215627, 219.917679403648, 209.582530411224, 228.411747375843, 
189.848059548381, 139.321242034884, 107.117331780889, 112.04876768303, 
153.452994198782, 110.70181957467, 212.323287868826, 88.1538706507791, 
223.663885064493, 109.954525908928, 174.492810944831, 91.7725132947146, 
157.710715054042, 91.0863013065866, 274.394589277923, 98.7716409379303, 
171.341946119448, 134.708208136274, 186.973140737227, 120.51344767879, 
161.766303826141, 86.3732426945488, 199.796095834514, 104.603801829297, 
242.194169263011, 161.9110687891, 212.630332930518, 146.398032529715, 
205.110722494322, 115.358911972281, 240.223909687846, 120.004380500404, 
183.283731791138, 236.191503528992, 204.437359424767, 129.357340064534, 
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2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2)), .Names = c("trial", "id", 
"ttime", "se", "brk"), row.names = c(NA, -600L), class = "data.frame")

Answer 1

If you are talking about the space between facets, you can try this (also note that we do not have short_brks and long_brks so I removed those from your example code). grid is required for the unit function.

require(ggplot2)
require(grid)

avtimes3$id <- factor(avtimes3$id)
## create and store plot
p <- ggplot(avtimes3, aes(x=trial, y=ttime, colour=id)) + 
  facet_grid(. ~ brk, scales = "free") + 
  geom_point(shape=21, fill="white") +
  ## remove space between panels    
  opts(panel.margin = unit(0, "lines")) + 
  ylab("Time taken (ms)") + 
  xlab("Trial No.")


## as you had
p + stat_smooth(method="loess")

## only one line per facet
p + stat_smooth(method="loess", aes(colour=NULL))

Edit: Rereading what you wrote and tried, I think you may want this:

## setup plot
p <- ggplot(avtimes3, aes(x=trial, y=ttime, colour=id)) +  
  geom_point(shape=21, fill="white") + 
  ylab("Time taken (ms)") +  
  xlab("Trial No.")

p + stat_smooth(aes(group = brk), method="loess")

The here that differs from what you had before is that the first argument to stat_smooth is mapping, the fifth is method. In R you have two options (maybe more). Either give the arguments in order or explicitly name the arguments. In your second example, you gave the arguments out of order and did not name explicitly like:

p + stat_smooth(method = "loess", mapping = aes(group = brk))

To get separate lines for each id and grouping by brk is a bit trickier (conceptually). We need the interaction of brk and id. Colouring alone does not work, as it would with most geoms.

p + stat_smooth(method = "loess", mapping = aes(group = interaction(brk, id)))