Goal
My data consists of numerous points which would be too much to represent as a scatter plot. I would like to plot a point density.
Specifically, I am wondering if there is a way to obtain something similar to this with ggplot2:
Current code
pEPNSABobs1<-ggplot(dataE, aes(comp1,mod1obs, group=1))+
geom_smooth(aes(color="chartreuse"), se=F, linetype="longdash", size=1)+
stat_smooth(data=dataE, fill="chartreuse", color="chartreuse4", linetype="blank")+
geom_smooth(data=dataS, aes(comp1,mod1obs, group=1, color="lightpink"), se=F, linetype="longdash", size=1)+
stat_smooth(data=dataS, fill="lightpink",color="lightpink4", linetype="blank")+
scale_colour_manual(name = 'Legend',
values =c('lightpink'='lightpink4','chartreuse'='chartreuse4'), labels = c('PIM','ABB'))+
scale_size_area() +
xlab("CDD0.year") +
ylab(expression(f[CDD0.year.obs]))+
labs(title='(A)')+
theme(plot.title = element_text(hjust = 0, vjust=1),axis.title = element_text(size = rel(1.2)), title=element_text(size = rel(1.2)),axis.text=element_text(size = rel(1.2)),
legend.text=element_text(size = rel(1.2)))
Data
DataE <- structure(list(comp1 = c(1338.2461, 1721.8119, 1878.2578, 1781.8827, 1813.2432, 1711.5277, 2033.0855, 1636.394, 1580.0748, 1834.4927, 2150.4177, 1790.7859, 1980.2718, 1610.0624, 2064.5809, 2002.82, 1652.7442, 2143.8216, 2015.1028, 2201.7947, 1610.4855, 1983.2706, 1979.9317, 2282.4141, 1763.288, 2204.3358, 1781.4969, 2114.2082, 1567.7841, 2089.6192, 1653.2401, 1709.9662, 2118.7251, 1843.5898, 1561.9472, 1839.0119, 2441.8013, 1684.3595, 1862.4287, 2043.3588, 2043.1502, 1999.5591, 1929.3686, 1897.746, 2073.494, 1345.488, 1622.3962, 1692.8681, 1847.7492, 1863.1212, 1759.8359, 2092.2891, 1671.9526, 1646.3103, 1918.8867, 2187.7568, 1833.4847, 2031.483, 1653.4428, 2118.2413, 2049.7907, 1705.1815, 2191.5739, 2054.9909, 2253.6989, 1664.6036, 2038.5609, 2021.5454, 2380.9635, 1788.6053, 2225.5046, 1834.5804, 2104.5817, 1523.2706, 2150.1426, 1722.6452, 1750.2867, 2142.4975, 1871.6772, 1562.7973, 1865.9236, 2424.8774, 1700.2864, 1850.6267, 2059.4913, 2047.4193, 2002.2637, 1941.7118, 1916.4346, 2081.8719, 1357.3087, 1645.5375, 1739.0249, 1984.4754, 2500.5373, 2126.0111, 2067.2634, 2163.0708, 2149.2563, 1939.6116, 1872.462, 2024.5612, 2158.432, 1732.0504, 2287.9286, 1640.2811, 2332.7904, 2475.8456, 2097.2091, 1942.9509, 2121.2583, 1899.7503, 2060.2692, 2459.2143, 2395.0327, 2280.1373, 2628.2383, 2118.6924, 2209.724, 2228.5074, 2008.7249, 1819.8529, 2144.0186, 2466.9707, 2479.4277, 2483.6576, 2403.0477, 2025.4349, 2150.5789, 2332.0055, 2115.4415, 1981.608, 1912.8366, 2296.8201, 1985.4613, 1875.0743, 1969.649, 2048.9522, 1900.5933, 1921.7856, 2066.8277, 1859.8671, 1698.0369, 1493.0678, 1910.5082, 2102.3289, 2048.3883, 1949.4451, 1838.7137, 2257.4143, 1958.3303, 1836.1803, 2138.1416, 2194.0097, 1919.8365, 2200.6554, 1829.6413, 2290.396, 2156.0543, 1854.5949, 2240.8976, 2060.3596, 2362.8724, 1794.141, 2183.8272, 2129.4498, 2517.4392, 1901.8863, 2440.1299, 2059.9263, 2291.6513, 1642.4418, 2281.0632, 1888.9796, 1931.7574, 2232.7776, 1953.4144, 1613.9024, 2000.765, 2485.617, 1774.7963, 1900.3834, 2192.5563, 2149.8866, 2090.371, 2076.542, 2050.3292, 2152.2821, 1482.7591, 1674.3366, 1905.3904, 1971.8098, 1596.7659, 1899.0917, 2400.7906, 2048.1242, 1968.4794, 2057.2929, 2053.9162, 1837.3839),
mod1obs = c(0.695830136555704, 1.06337206841913, 1.14861889402282, 1.02790421278896, 1.11775825622145, 1.43143032263757, 1.66436105688503, 1.79407632202943, 1.54246894155172, 1.47641083551176, 1.61115035184228, 1.68350958534902, 1.67052919588235, 1.86924870748066, 1.52139461422218, 1.7206336638354, 1.77255323580939, 1.67014367453142, 1.4828365451913, 1.30632542733184, 1.28066122419783, 1.36281355152317, 0.922105627695953, 0.485097355039981, 0.527121512464299, 0.810559323027329, 1.02715532531355, 1.14244699815587, 0.999551948498188, 0.951386076673739, 0.708742765512991, 0.591036273251615, 0.954269537513021, 1.33390119349384, 1.32340100204498, 1.48365670129187, 1.18354444471793, 1.17538278706292, 1.13658706470025, 1.09659824662134, 1.33968115088882, 0.97520848249232, 0.926838756160161, 0.916231908195398, 0.899325038616274, 1.16824595028327, 1.11899066863449, 1.11661928913426, 1.12284805168664, 1.05643303658747, 1.06710730526053, 1.22833157533542, 0.816937586646849, 1.00335563406519, 1.402274505934, 1.41743848783742, 1.14038690876476, 0.985366123273008, 0.843537703363177, 0.99753466530825, 0.956105174325841, 0.969042102699615, 1.0638789437522, 0.996797745632918, 0.941726356849215, 0.926215042532983, 1.03697021488655, 1.24561208170624, 0.903344544294698, 0.852585271143484, 1.14969403609893, 0.951461942556407, 0.969946352436395, 0.856006282102713, 1.11792476085488, 1.13412438712209, 1.15896430227978, 1.13984814117922, 1.26400232474479, 1.3157371290327, 1.10269366567886, 0.852330476973561, 1.06803837916353, 1.00555346861516, 1.07980330220743, 0.999413354748127, 0.835341074425715, 0.750343026273598, 0.750086242001393, 0.845059990359667, 1.01550610388101, 0.97183262908527, 1.02351377836664, 0.646201913922726, 0.832803589659996, 1.02112583534199, 1.05276036662667, 0.778087551043244, 1.04311980643046, 1.14374772863475, 1.26330982513545, 1.20248850820938, 1.03073057299644, 1.06049050327533, 0.834166914153454, 0.984789639654932, 1.08805486508421, 1.40007199005997, 1.33458208694833, 1.09447880143235, 1.32094094746787, 1.01033105751792, 1.15916733600421, 0.83814699368444, 0.922361964325012, 0.821150439904281, 0.757025921805821, 0.796454341025722, 0.753864630868797, 0.709679353471203, 0.947247272243527, 1.00883103860073, 0.954505648136825, 0.921522424138087, 0.845557836615405, 0.959332247443167, 0.726910705401073, 0.825894718073668, 0.849038625330317, 0.860196521211579, 0.88419468576954, 0.986401829980697, 0.844208566273473, 0.733125744746535, 0.718381697185048, 0.826648914954142, 0.787244473508777, 0.65512488225044, 0.752501264072651, 0.723469068584019, 0.743094728670719, 1.11846155736291, 1.08257557110011, 0.982979407982961, 0.885561974111481, 0.898359447667526, 0.770274340254794, 0.964105752093132, 1.419398413941, 1.06346164710011, 0.94787165982562, 1.21888848634176, 0.902929635142765, 0.924412982720593, 1.10282712434799, 0.899503164916735, 0.850644250882259, 1.01891899751745, 1.21897925575381, 1.26360292391086, 0.924187893834376, 0.930518507010402, 1.03052665863541, 1.15564902628815, 1.01660158016781, 0.904615715917612, 0.523182725557325, 0.625326640420025, 1.03256402151814, 1.19178281509474, 1.21239098183734, 1.00933857234806, 1.01170794284609, 1.02137919901009, 0.784528093252022, 0.97997559028248, 1.15073167836534, 1.09499252446889, 1.02629257850687, 0.865796462253095, 1.08500359034302, 1.14790809213261, 0.96317054146643, 1.1105434300635, 0.817447776121345, 0.888257155328381, 0.884423797252747, 0.935227482404514, 1.07740310874975, 1.02969991871418, 0.922959386699878, 0.642079018955661, 0.653388944491712, 0.597053974284795, 0.882728190259291, 0.918365607321804, 0.814327793136811, 1.00391967118938, 1.09246216046294, 1.07787732161824)),
row.names = c(2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L, 80L, 81L, 82L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L, 93L, 94L, 95L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L, 105L, 106L, 107L, 108L, 109L, 110L, 111L, 112L, 113L, 114L, 115L, 116L, 117L, 118L, 119L, 120L, 121L, 122L, 123L, 124L, 125L, 126L, 127L, 128L, 129L, 130L, 131L, 132L, 133L, 134L, 135L, 136L, 137L, 138L, 139L, 140L, 141L, 142L, 143L, 144L, 145L, 146L, 147L, 148L, 149L, 150L, 151L, 152L, 153L, 154L, 155L, 156L, 157L, 158L, 159L, 160L, 161L, 162L, 163L, 164L, 165L, 166L, 167L, 168L, 169L, 170L, 171L, 172L, 173L, 174L, 175L, 176L, 177L, 178L, 179L, 180L, 181L, 182L, 183L, 184L, 185L, 186L, 187L, 188L, 189L, 190L, 191L, 192L, 193L, 194L, 195L, 196L, 197L, 198L, 199L, 200L, 201L, 202L, 203L),
class = "data.frame")
and
DataS <- structure(list(comp1 = c(1800.2451, 1781.6087, 1737.2914, 1816.9749, 1643.348, 1438.5377, 1338.2461, 1721.8119, 1878.2578, 1781.8827, 1813.2432, 1711.5277, 2033.0855, 1636.394, 1580.0748, 1834.4927, 2150.4177, 1790.7859, 1980.2718, 1610.0624, 2064.5809, 2002.82, 1652.7442, 2143.8216, 2015.1028, 2201.7947, 1610.4855, 1983.2706, 1979.9317, 2282.4141, 1763.288, 2204.3358, 1781.4969, 2114.2082, 1567.7841, 2089.6192, 1653.2401, 1709.9662, 2118.7251, 1843.5898, 1561.9472, 1839.0119, 2441.8013, 1684.3595, 1862.4287, 2043.3588, 2043.1502, 1999.5591, 1929.3686, 1897.746, 2073.494, 1345.488, 1622.3962, 1692.8681, 1845.1739, 1661.4121, 1746.5679, 2225.7098, 1973.0317, 1877.0764, 1875.4714, 1996.5981, 1712.4015, 1715.2255, 2149.4741, 2303.7732, 1872.9362, 2279.4588, 1513.787, 2184.5552, 2361.3593, 2148.0699, 1978.381, 2008.029, 1955.9995, 1986.7266, 2079.5143, 1960.9757, 1809.0558, 2193.2401, 1729.3818, 1926.0217, 2157.6266, 1788.1556, 1475.6945, 1854.1782, 2090.9429, 2242.7276, 2120.1378, 1982.7239, 1860.3072, 1906.2126, 2115.5587, 1970.3582, 1809.3253, 1851.249, 2147.1908, 1774.673, 1816.4041, 1934.3119, 1901.6345, 1943.6281, 1793.2585, 1826.9192, 1727.9485, 1506.61, 1440.656, 1748.6882, 1956.9693, 1938.5561, 1850.1536, 1645.5995, 2086.7712, 1723.6074, 1805.0789, 2089.9296, 2139.9376, 1891.8347, 2158.9863, 1525.1479, 2132.2023, 2061.2398, 1707.3251, 2202.9106, 2017.0934, 2359.064, 1781.5352, 2081.9002, 2091.391, 2307.257, 1722.3419, 2200.4204, 1752.5609, 2110.2504, 1432.5841, 2121.8681, 1734.5244, 1912.6964, 2134.543, 1996.4716, 1720.3715, 1902.6841, 2402.3462, 1850.2001, 1919.6724, 2123.1945, 2177.1916, 2134.0072, 1969.5795, 1896.8108, 2132.3515, 1451.0973, 1612.5966, 1725.3021, 1581.0971, 2347.5604, 2483.6352, 2035.8553, 2426.3861, 1655.1293, 2382.9981, 2468.8676, 2256.6275, 2087.2235, 2124.0978, 2068.831, 2150.4903, 2262.8365, 2198.5672, 1968.5931, 2418.6407, 1953.0811, 2108.4554, 2361.584, 1979.866, 1741.6303, 2087.9856, 2286.7883, 2395.2738, 2270.3263, 2075.8854, 1874.2124, 2038.3772, 2245.1034, 2075.8632, 1946.548, 1955.202, 2355.13, 2011.3717, 1975.8039, 2099.3788, 2136.0128, 1909.835, 1965.8319, 1829.9619, 1630.4157, 1506.5606, 1897.0851, 2069.4124, 2024.9848),
mod1obs = c(1.13466310792768, 0.931923716274403, 1.48217365869915, 1.21838260146353, 1.79940276419435, 1.76643559356371, 2.45574670199418, 1.85759003858763, 1.52414873587958, 1.56924844587154, 1.75782289196183, 1.21854647206407, 1.67402271470746, 1.57661741696957, 1.54915950383801, 1.16767311295364, 1.51513098169545, 1.58721974127532, 1.48203349385421, 1.25150055063036, 1.55523168986921, 1.16757976105911, 1.06103912158879, 1.38682784393209, 1.26706181742404, 0.922200575100749, 1.15475122512565, 0.919460864722599, 0.622581998594566, 0.888857360932288, 0.561258461668506, 0.784221352878807, 1.05841796267749, 0.954913917366984, 0.864989456398651, 0.405901971360923, 0.437238711188011, 0.238832040897009, 0.398444779604082, 0.596968751447861, 0.780373761619182, 0.593964337126505, 0.674617006647725, 0.803014994811282, 0.914435218814932, 0.832419908437008, 0.870618364283852, 0.66205782789832, 0.668271801470194, 0.582218329504303, 0.551471500972662, 0.546862377936455, 0.782666777798501, 0.797397188682925, 0.233703554128143, 0.33078183414865, 0.477622787992685, 0.788352242940992, 0.655192745268702, 0.629025187982574, 0.606750329361944, 0.688876228035905, 0.811952779578203, 0.878151955673824, 0.666102340741867, 0.234485500963779, 0.377020837708222, 0.431015138976773, 0.599545478659815, 0.485341173599891, 0.54118137004067, 0.822700963102403, 0.680465320458669, 0.750819741408091, 0.914425077741122, 1.03163581838662, 0.750374660256944, 0.994337592683161, 1.00941746422589, 1.07118881485789, 1.2413361662074, 0.862210731330022, 0.807945428753615, 1.01206355371074, 1.1466781183792, 1.04520757430783, 0.906546865827641, 0.802138329712516, 0.927446849752543, 0.909606938810288, 0.726203964235328, 0.63174380758208, 0.827670510708034, 0.796140009519362, 0.908331184943455, 1.24437229369026, 1.01038032593664, 1.20106590210506, 1.47001915216196, 1.4216087908593, 1.19649249116061, 1.28729733432818, 1.050493946874, 0.490028901207541, 0.472897051757391, 0.474117219731324, 0.85500755809614, 1.16164758242536, 1.3257510136531, 1.28575789166575, 1.63477173725642, 2.45069111586777, 2.50502453325512, 1.70995863697504, 2.4729188484128, 2.65244156137921, 2.52288384634894, 2.91133218222026, 2.80631798084833, 2.85068631154525, 2.50623525545215, 2.39950652546403, 2.49930350794263, 2.47640980454363, 2.5743114316923, 2.27093700546959, 1.9784591153946, 1.794185941834, 1.59685624413893, 1.21577767933037, 1.1993875662254, 0.905547156548879, 0.791419465032495, 1.5777113878502, 1.46727507228871, 1.03812304747397, 1.04471285876448, 0.89791346550258, 1.00531560652384, 1.03963310517253, 1.55611837868102, 1.32499035130457, 1.32064172678175, 1.61378461617361, 1.77550053496517, 1.7444038412628, 1.88853641144745, 1.44554726136069, 1.52169806808946, 1.38482876983135, 1.50693746767208, 1.56467290333013, 1.55664813927757, 1.65044541980974, 1.50357779174674, 0.764054807030921, 0.495778285132959, 0.596411488294826, 0.693937433662632, 0.932011439769366, 1.10514738904478, 0.904927677550852, 0.969827490109055, 1.05101670841548, 1.12392075468322, 1.33509689588176, 1.20342821574007, 0.993967001310557, 1.20898145783709, 1.05447146612782, 0.744232955898758, 0.844458068128595, 0.780144262373508, 0.547168299748365, 2.83490197058459, 1.23839568773548, 1.10988758878693, 0.867733363063826, 0.73962833236251, 0.85416901457008, 0.784618799106827, 0.725934558423183, 0.834658973996715, 0.875948198454898, 0.881964176473614, 0.933974735332668, 0.870382237844421, 0.772181200080244, 0.829814527221943, 0.929018949289857, 0.892966747157662, 0.891484338497291, 0.942086202624782, 0.671953671900624, 0.788435092592626, 0.620007838797593, 0.87841213508972, 1.09789753017474, 0.917411139887858, 1.12120717286975)),
row.names = c(2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L, 80L, 81L, 82L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L, 93L, 94L, 95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L, 105L, 106L, 107L, 108L, 109L, 110L, 111L, 112L, 113L, 114L, 115L, 116L, 117L, 118L, 119L, 120L, 121L, 122L, 123L, 124L, 125L, 126L, 127L, 128L, 129L, 130L, 131L, 132L, 133L, 134L, 135L, 136L, 137L, 138L, 139L, 140L, 141L, 142L, 143L, 144L, 145L, 146L, 147L, 148L, 149L, 150L, 151L, 152L, 153L, 154L, 155L, 156L, 158L, 159L, 160L, 161L, 162L, 163L, 164L, 165L, 166L, 167L, 168L, 169L, 170L, 171L, 172L, 173L, 174L, 175L, 176L, 177L, 178L, 179L, 180L, 181L, 182L, 183L, 184L, 185L, 186L, 187L, 188L, 189L, 190L, 191L, 192L, 193L, 194L, 195L, 196L, 197L, 198L, 199L, 200L, 201L, 202L),
class = "data.frame")
Option 1: Density Polygons
ggplot(DataS, aes(comp1, mod1obs)) +
stat_density_2d(aes(fill = ..level..),
geom = "polygon",
bins = 10) +
scale_fill_gradientn(colors = c("#FFEDA0",
"#FEB24C",
"#F03B20"))
Option 2: Hexagon Bins
ggplot(DataS, aes(comp1, mod1obs)) +
geom_hex(bins = 10) +
scale_fill_gradientn(colors = c("#FFEDA0",
"#FEB24C",
"#F03B20"))
Data
DataS <- structure(list(comp1 = c(1800.2451, 1781.6087, 1737.2914, 1816.9749, 1643.348, 1438.5377, 1338.2461, 1721.8119, 1878.2578, 1781.8827, 1813.2432, 1711.5277, 2033.0855, 1636.394, 1580.0748, 1834.4927, 2150.4177, 1790.7859, 1980.2718, 1610.0624, 2064.5809, 2002.82, 1652.7442, 2143.8216, 2015.1028, 2201.7947, 1610.4855, 1983.2706, 1979.9317, 2282.4141, 1763.288, 2204.3358, 1781.4969, 2114.2082, 1567.7841, 2089.6192, 1653.2401, 1709.9662, 2118.7251, 1843.5898, 1561.9472, 1839.0119, 2441.8013, 1684.3595, 1862.4287, 2043.3588, 2043.1502, 1999.5591, 1929.3686, 1897.746, 2073.494, 1345.488, 1622.3962, 1692.8681, 1845.1739, 1661.4121, 1746.5679, 2225.7098, 1973.0317, 1877.0764, 1875.4714, 1996.5981, 1712.4015, 1715.2255, 2149.4741, 2303.7732, 1872.9362, 2279.4588, 1513.787, 2184.5552, 2361.3593, 2148.0699, 1978.381, 2008.029, 1955.9995, 1986.7266, 2079.5143, 1960.9757, 1809.0558, 2193.2401, 1729.3818, 1926.0217, 2157.6266, 1788.1556, 1475.6945, 1854.1782, 2090.9429, 2242.7276, 2120.1378, 1982.7239, 1860.3072, 1906.2126, 2115.5587, 1970.3582, 1809.3253, 1851.249, 2147.1908, 1774.673, 1816.4041, 1934.3119, 1901.6345, 1943.6281, 1793.2585, 1826.9192, 1727.9485, 1506.61, 1440.656, 1748.6882, 1956.9693, 1938.5561, 1850.1536, 1645.5995, 2086.7712, 1723.6074, 1805.0789, 2089.9296, 2139.9376, 1891.8347, 2158.9863, 1525.1479, 2132.2023, 2061.2398, 1707.3251, 2202.9106, 2017.0934, 2359.064, 1781.5352, 2081.9002, 2091.391, 2307.257, 1722.3419, 2200.4204, 1752.5609, 2110.2504, 1432.5841, 2121.8681, 1734.5244, 1912.6964, 2134.543, 1996.4716, 1720.3715, 1902.6841, 2402.3462, 1850.2001, 1919.6724, 2123.1945, 2177.1916, 2134.0072, 1969.5795, 1896.8108, 2132.3515, 1451.0973, 1612.5966, 1725.3021, 1581.0971, 2347.5604, 2483.6352, 2035.8553, 2426.3861, 1655.1293, 2382.9981, 2468.8676, 2256.6275, 2087.2235, 2124.0978, 2068.831, 2150.4903, 2262.8365, 2198.5672, 1968.5931, 2418.6407, 1953.0811, 2108.4554, 2361.584, 1979.866, 1741.6303, 2087.9856, 2286.7883, 2395.2738, 2270.3263, 2075.8854, 1874.2124, 2038.3772, 2245.1034, 2075.8632, 1946.548, 1955.202, 2355.13, 2011.3717, 1975.8039, 2099.3788, 2136.0128, 1909.835, 1965.8319, 1829.9619, 1630.4157, 1506.5606, 1897.0851, 2069.4124, 2024.9848),
mod1obs = c(1.13466310792768, 0.931923716274403, 1.48217365869915, 1.21838260146353, 1.79940276419435, 1.76643559356371, 2.45574670199418, 1.85759003858763, 1.52414873587958, 1.56924844587154, 1.75782289196183, 1.21854647206407, 1.67402271470746, 1.57661741696957, 1.54915950383801, 1.16767311295364, 1.51513098169545, 1.58721974127532, 1.48203349385421, 1.25150055063036, 1.55523168986921, 1.16757976105911, 1.06103912158879, 1.38682784393209, 1.26706181742404, 0.922200575100749, 1.15475122512565, 0.919460864722599, 0.622581998594566, 0.888857360932288, 0.561258461668506, 0.784221352878807, 1.05841796267749, 0.954913917366984, 0.864989456398651, 0.405901971360923, 0.437238711188011, 0.238832040897009, 0.398444779604082, 0.596968751447861, 0.780373761619182, 0.593964337126505, 0.674617006647725, 0.803014994811282, 0.914435218814932, 0.832419908437008, 0.870618364283852, 0.66205782789832, 0.668271801470194, 0.582218329504303, 0.551471500972662, 0.546862377936455, 0.782666777798501, 0.797397188682925, 0.233703554128143, 0.33078183414865, 0.477622787992685, 0.788352242940992, 0.655192745268702, 0.629025187982574, 0.606750329361944, 0.688876228035905, 0.811952779578203, 0.878151955673824, 0.666102340741867, 0.234485500963779, 0.377020837708222, 0.431015138976773, 0.599545478659815, 0.485341173599891, 0.54118137004067, 0.822700963102403, 0.680465320458669, 0.750819741408091, 0.914425077741122, 1.03163581838662, 0.750374660256944, 0.994337592683161, 1.00941746422589, 1.07118881485789, 1.2413361662074, 0.862210731330022, 0.807945428753615, 1.01206355371074, 1.1466781183792, 1.04520757430783, 0.906546865827641, 0.802138329712516, 0.927446849752543, 0.909606938810288, 0.726203964235328, 0.63174380758208, 0.827670510708034, 0.796140009519362, 0.908331184943455, 1.24437229369026, 1.01038032593664, 1.20106590210506, 1.47001915216196, 1.4216087908593, 1.19649249116061, 1.28729733432818, 1.050493946874, 0.490028901207541, 0.472897051757391, 0.474117219731324, 0.85500755809614, 1.16164758242536, 1.3257510136531, 1.28575789166575, 1.63477173725642, 2.45069111586777, 2.50502453325512, 1.70995863697504, 2.4729188484128, 2.65244156137921, 2.52288384634894, 2.91133218222026, 2.80631798084833, 2.85068631154525, 2.50623525545215, 2.39950652546403, 2.49930350794263, 2.47640980454363, 2.5743114316923, 2.27093700546959, 1.9784591153946, 1.794185941834, 1.59685624413893, 1.21577767933037, 1.1993875662254, 0.905547156548879, 0.791419465032495, 1.5777113878502, 1.46727507228871, 1.03812304747397, 1.04471285876448, 0.89791346550258, 1.00531560652384, 1.03963310517253, 1.55611837868102, 1.32499035130457, 1.32064172678175, 1.61378461617361, 1.77550053496517, 1.7444038412628, 1.88853641144745, 1.44554726136069, 1.52169806808946, 1.38482876983135, 1.50693746767208, 1.56467290333013, 1.55664813927757, 1.65044541980974, 1.50357779174674, 0.764054807030921, 0.495778285132959, 0.596411488294826, 0.693937433662632, 0.932011439769366, 1.10514738904478, 0.904927677550852, 0.969827490109055, 1.05101670841548, 1.12392075468322, 1.33509689588176, 1.20342821574007, 0.993967001310557, 1.20898145783709, 1.05447146612782, 0.744232955898758, 0.844458068128595, 0.780144262373508, 0.547168299748365, 2.83490197058459, 1.23839568773548, 1.10988758878693, 0.867733363063826, 0.73962833236251, 0.85416901457008, 0.784618799106827, 0.725934558423183, 0.834658973996715, 0.875948198454898, 0.881964176473614, 0.933974735332668, 0.870382237844421, 0.772181200080244, 0.829814527221943, 0.929018949289857, 0.892966747157662, 0.891484338497291, 0.942086202624782, 0.671953671900624, 0.788435092592626, 0.620007838797593, 0.87841213508972, 1.09789753017474, 0.917411139887858, 1.12120717286975)),
row.names = c(2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L, 80L, 81L, 82L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L, 93L, 94L, 95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L, 105L, 106L, 107L, 108L, 109L, 110L, 111L, 112L, 113L, 114L, 115L, 116L, 117L, 118L, 119L, 120L, 121L, 122L, 123L, 124L, 125L, 126L, 127L, 128L, 129L, 130L, 131L, 132L, 133L, 134L, 135L, 136L, 137L, 138L, 139L, 140L, 141L, 142L, 143L, 144L, 145L, 146L, 147L, 148L, 149L, 150L, 151L, 152L, 153L, 154L, 155L, 156L, 158L, 159L, 160L, 161L, 162L, 163L, 164L, 165L, 166L, 167L, 168L, 169L, 170L, 171L, 172L, 173L, 174L, 175L, 176L, 177L, 178L, 179L, 180L, 181L, 182L, 183L, 184L, 185L, 186L, 187L, 188L, 189L, 190L, 191L, 192L, 193L, 194L, 195L, 196L, 197L, 198L, 199L, 200L, 201L, 202L),
class = "data.frame")
Related
I'm trying to make a heatmap of locations using latitude and longitude. My map works but the points in an area are being grouped together too much. What I want is something like what I have but with the heat traced much more granularly so that you can see smaller differences between places.
This is the relevant code:
bbox <- c(left = -79.1, bottom = 38, right = -71.8, top = 41.5)
coords.map <- get_stamenmap(bbox, zoom = 9, maptype = "toner-lite")
coords.map <- ggmap(coords.map, extent="device", legend="none")
coords.map <- coords.map + stat_density2d(data=recruits2,
aes(x=MailingLong, y=MailingLat, fill=..level.., alpha=..level..),
bins = 20, geom = "polygon")
coords.map <- coords.map + scale_fill_gradientn(colours=rev(brewer.pal(20, "Spectral")))
coords.map <- coords.map + theme_bw()
coords.map
This is what I'm getting
Edit: Here is the first 200 rows of recruits from dput
structure(list(MailingLong = c(-77.024196799, -77.003914977,
-76.800101376, -77.116797729, -77.018188811, -77.120614114, -76.975844627,
-77.147034967, -77.089368856, -76.97864858, -76.844030329, -76.9639802739999,
-77.257533391, -76.822314419, -80.0753704429999, -76.551298185,
-76.767346001, -78.7422733669999, -77.2918568269999, -74.252185664,
-77.035277127, -76.957338864, -77.403195991, -77.6319986669999,
-73.944649177, -76.5599475129999, -73.571443862, -76.989599958,
-76.8866457089999, -76.8900467889999, -77.027862935, -76.763716223,
-74.035259712, -77.075101833, -76.9065139969999, -77.009444624,
-76.991265512, -76.998362508, -77.0138546809999, -76.92147388,
-76.937957008, -73.897316132, -77.2021361069999, -76.9865863379999,
-77.057626187, -77.2698420199999, -73.962312531, -77.061793597,
-74.118483634, -73.8812691919999, -84.1753095879999, -76.849177244,
-76.9494415629999, -77.011200646, -77.12310071, -76.8884595649999,
-77.0061180499999, -77.017453829, -76.946342907, -76.980566735,
-76.923624123, -77.010469798, -77.02638151, -76.918852741, -76.9224746959999,
-87.802292575, -76.813914677, -73.9355411179999, -77.0086792399999,
-76.9349190729999, -77.020158344, -76.9487103719999, -73.846362546,
-77.015177632, -80.255301241, -77.428318142, -77.0007635819999,
-76.929540264, -76.947718204, -76.93487089, -77.019630846, -77.018265258,
-73.893035738, -76.887356744, -74.746807223, -76.825205743, -76.8953029259999,
-76.962229153, -77.0435782929999, -73.844867129, -76.926558429,
-76.8879371259999, -73.8547164669999, -76.920915296, -81.556675863,
-77.088045767, -76.8971086939999, -73.2218500929999, -77.283520263,
-77.0097035049999, -73.995325534, -82.7629230599999, -76.952207819,
-77.012592416, -77.0260711729999, -76.942692268, -76.981824075,
-73.261707374, -77.0867976709999, -76.904238182, -77.172019128,
-76.9965300979999, -77.0255964739999, -76.984859179, -76.9812736649999,
-77.081601215, -76.759961416, -74.6169999639999, -77.043506263,
-77.202603773, -76.949909772, -76.9530278129999, -76.7527797119999,
-75.053749344, -76.746774219, -71.778088926, -77.02110899, -76.854547506,
-77.084631879, -76.997437527, -76.901572162, -73.870879122, -76.878514023,
-74.1344631809999, -74.318660444, -82.7075784359999, -74.7182968279999,
-76.797062055, -77.5707813399999, -77.6124343819999, -75.5027960319999,
-76.987749881, -76.9821815619999, -75.828326588, -79.783059322,
-76.9499001519999, -80.259390617, -77.117644909, -77.2343587779999,
-73.8982356609999, -77.472350213, -76.9425510419999, -76.977082436,
-76.9939519549999, -77.1868244199999, -74.7314534239999, -76.965619788,
-77.007779215, -76.967062614, -76.951343771, -77.396949305, -76.999679182,
-76.9883032339999, -77.0871543499999, -76.901727819, -77.106636225,
-75.01563442, -84.127288743, -84.4811913569999, -88.267507704,
-77.011828453, -74.081075439, -72.669365125, -73.007336905, -76.923843066,
-77.019205179, -76.9821401839999, -73.927507514, -77.0365238109999,
-76.695715095, -76.871854318, -76.831811042, -75.341965451, -74.0187008359999,
-76.851878874, -72.8766466989999, -76.9806527699999, -77.327771618,
-73.9872406649999, -73.9230185489999, -74.127273734, -74.050468364,
-77.044012991, -74.068816409, -73.950062444, -76.874810759, -76.976120023,
-77.0778578119999, -77.410060892, -104.726662525), MailingLat = c(38.9681180370001,
38.728353848, 38.795798179, 38.8259334890001, 38.7331564900001,
38.8947512510001, 38.5234046750001, 38.8229569550001, 38.85372949,
38.9289913380001, 39.2386466790001, 38.929587806, 38.7748015860001,
39.4697715190001, 40.4490489200001, 39.126109242, 38.808320123,
35.80390168, 38.605807435, 40.1699337740001, 38.6193497140001,
38.922676057, 38.6439925450001, 39.9533144690001, 40.7054857840001,
39.345963984, 41.1666994920001, 38.81984234, 38.9428468840001,
38.733140373, 38.982152528, 38.824874175, 40.1742035030001, 38.78925345,
39.0010581130001, 38.9664260480001, 38.8579487740001, 38.946905756,
38.8784059170001, 38.902325202, 38.911513062, 40.9063276460001,
38.8638673040001, 38.9097773670001, 38.9240989080001, 38.8797625300001,
40.5770966100001, 38.792493279, 40.6751541570001, 42.8175953150001,
33.5073237140001, 38.9272529080001, 38.8836017150001, 38.8243908630001,
38.8446904240001, 38.8658511960001, 38.917771981, 38.938885574,
38.8719206270001, 38.885876071, 38.8924471080001, 38.833980207,
38.9562671210001, 38.8918037330001, 38.876033218, 41.914514481,
39.3841564950001, 40.8475071350001, 38.8235965260001, 38.9344933350001,
39.0245538930001, 38.639340094, 42.666483283, 38.7850074940001,
36.093245149, 38.210712964, 38.8477400190001, 38.888638916, 38.867858267,
38.8906912090001, 38.929587746, 38.9521219760001, 40.8675224940001,
38.8787024690001, 41.140377415, 38.804541885, 38.852253413, 38.8221755930001,
38.9213773750001, 40.8910776750001, 38.88197389, 39.0817835830001,
40.8247535940001, 38.8854398610001, 30.1117637080001, 39.087920518,
38.940159973, 41.2659053740001, 38.801129729, 38.896368373, 40.8391054510001,
33.720799115, 38.8651627890001, 38.826764516, 38.9238514780001,
38.9046515320001, 38.925578864, 44.0306323230001, 39.035399668,
38.5953835010001, 39.119000919, 38.9563723100001, 38.976737762,
38.960012873, 38.934212899, 38.961016375, 38.6100870970001, 40.2422624710001,
38.9248050900001, 38.85129355, 38.90282683, 38.8914932600001,
38.576783327, 40.0710674210001, 38.62669212, 42.292809602, 38.956420038,
38.845185488, 38.859804126, 38.904392242, 38.9032118310001, 40.6809593840001,
38.887417929, 40.6499415820001, 40.9926879540001, 28.0700605050001,
40.2071700650001, 38.761238259, 38.7582776680001, 38.8111178980001,
39.956535079, 38.8784065950001, 38.903570121, 44.0488523160001,
40.4418602050001, 38.9028348410001, 26.1337374180001, 38.8889284410001,
39.185845467, 40.9479277930001, 38.769957467, 38.869303099, 38.901602515,
38.8247793570001, 38.770411516, 40.1243989540001, 38.935076042,
38.9514988700001, 38.87461904, 38.8908902330001, 38.457439761,
38.8236920620001, 38.883861181, 38.938825771, 38.854090721, 38.715420469,
40.8443550060001, 41.4013022350001, 34.0559358790001, 40.0861231000001,
38.8252308690001, 40.729698834, 42.1328508010001, 40.9432147800001,
38.8837031510001, 38.845665739, 38.84924341, 41.0833210810001,
38.911186511, 39.0930236410001, 39.0773085930001, 38.990928769,
40.633318704, 40.7794771000001, 38.946823571, 41.665512818, 38.929088312,
38.861215551, 40.588697102, 40.830763007, 40.664786738, 41.044012874,
39.077050066, 40.714393369, 40.5922452140001, 38.8516571170001,
38.85133934, 39.059085399, 38.431202824, 38.7833722510001)), row.names = c(1L,
2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L,
16L, 17L, 18L, 19L, 20L, 21L, 23L, 24L, 25L, 26L, 27L, 28L, 29L,
30L, 31L, 32L, 33L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L,
44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L,
57L, 60L, 61L, 62L, 64L, 65L, 66L, 67L, 68L, 69L, 71L, 72L, 73L,
74L, 75L, 77L, 78L, 79L, 80L, 81L, 82L, 83L, 84L, 85L, 86L, 87L,
88L, 89L, 90L, 92L, 93L, 94L, 95L, 96L, 97L, 99L, 100L, 101L,
102L, 103L, 104L, 105L, 106L, 107L, 108L, 109L, 110L, 111L, 112L,
113L, 114L, 115L, 116L, 117L, 118L, 120L, 121L, 122L, 123L, 124L,
125L, 126L, 127L, 128L, 129L, 130L, 131L, 132L, 133L, 134L, 135L,
138L, 140L, 141L, 142L, 143L, 144L, 145L, 146L, 147L, 149L, 150L,
151L, 152L, 153L, 154L, 155L, 156L, 157L, 158L, 159L, 160L, 161L,
162L, 163L, 164L, 165L, 166L, 167L, 168L, 169L, 170L, 171L, 172L,
173L, 174L, 175L, 176L, 177L, 178L, 179L, 180L, 181L, 182L, 183L,
184L, 185L, 186L, 187L, 189L, 190L, 191L, 192L, 193L, 195L, 197L,
198L, 200L, 201L, 202L, 203L, 204L, 205L, 207L, 208L, 209L, 212L,
213L, 214L, 215L, 216L, 217L, 218L, 219L, 220L, 221L), class = "data.frame")
I am currently trying to find a solution to a transportation problem. I have a table with the travel times from 30 customers to each other. The goal is to use dynamic program to go from this table with direct durations to a table with shortest duration possible (via possible subtours between pairs of customers)
I have no clue how to solve this. The question states "Let 𝐷𝑖,𝑗,𝑘 be the shortest (in duration) path between customer 𝑖 and 𝑗, using only nodes 0 to 𝑘 as intermediaries."
Is there someone who can help me with this?
Thank you in advance. :-)
to use only nodes 0 to k as intermediates.
structure(list(ID = 1:30, X1 = c(0L, 98L, 132L, 245L, 17L, 69L,
139L, 112L, 207L, 35L, 249L, 43L, 215L, 62L, 152L, 237L, 59L,
119L, 45L, 59L, 23L, 12L, 16L, 66L, 177L, 31L, 118L, 165L, 117L,
193L), X2 = c(37L, 0L, 74L, 176L, 91L, 111L, 143L, 208L, 202L,
40L, 172L, 101L, 163L, 51L, 220L, 180L, 48L, 98L, 45L, 62L, 91L,
9L, 50L, 145L, 198L, 48L, 3L, 163L, 159L, 176L), X3 = c(118L,
10L, 0L, 138L, 108L, 115L, 221L, 274L, 231L, 89L, 197L, 36L,
175L, 93L, 174L, 184L, 13L, 109L, 109L, 22L, 172L, 91L, 12L,
149L, 140L, 108L, 8L, 133L, 168L, 139L), X4 = c(252L, 137L, 112L,
0L, 248L, 276L, 373L, 350L, 353L, 137L, 31L, 186L, 49L, 170L,
325L, 81L, 117L, 184L, 175L, 185L, 279L, 182L, 120L, 205L, 130L,
132L, 133L, 226L, 158L, 67L), X5 = c(40L, 93L, 118L, 188L, 0L,
38L, 147L, 106L, 208L, 46L, 228L, 26L, 208L, 54L, 163L, 212L,
81L, 49L, 45L, 84L, 12L, 82L, 114L, 81L, 173L, 67L, 52L, 63L,
146L, 156L), X6 = c(54L, 117L, 143L, 296L, 74L, 0L, 78L, 97L,
218L, 52L, 239L, 47L, 267L, 111L, 216L, 269L, 167L, 91L, 105L,
99L, 16L, 117L, 95L, 15L, 264L, 136L, 148L, 100L, 145L, 242L),
X7 = c(143L, 145L, 208L, 302L, 130L, 86L, 0L, 84L, 308L,
151L, 348L, 102L, 305L, 139L, 254L, 272L, 156L, 182L, 87L,
214L, 110L, 82L, 145L, 59L, 283L, 98L, 171L, 192L, 211L,
228L), X8 = c(142L, 195L, 238L, 336L, 161L, 80L, 2L, 0L,
289L, 135L, 342L, 134L, 307L, 169L, 197L, 347L, 261L, 143L,
128L, 243L, 52L, 128L, 169L, 97L, 318L, 214L, 229L, 225L,
287L, 288L), X9 = c(230L, 238L, 217L, 264L, 229L, 154L, 299L,
269L, 0L, 210L, 335L, 204L, 342L, 260L, 25L, 258L, 264L,
76L, 170L, 222L, 126L, 193L, 272L, 203L, 218L, 186L, 214L,
120L, 240L, 207L), X10 = c(2L, 30L, 34L, 186L, 75L, 96L,
161L, 179L, 244L, 0L, 199L, 17L, 181L, 59L, 240L, 178L, 101L,
117L, 1L, 48L, 79L, 72L, 24L, 60L, 236L, 5L, 32L, 151L, 203L,
133L), X11 = c(243L, 191L, 114L, 38L, 164L, 211L, 295L, 370L,
350L, 211L, 0L, 174L, 14L, 166L, 278L, 164L, 165L, 223L,
252L, 129L, 201L, 196L, 201L, 271L, 98L, 199L, 209L, 219L,
168L, 62L), X12 = c(22L, 14L, 64L, 164L, 68L, 113L, 117L,
115L, 208L, 8L, 239L, 0L, 204L, 36L, 230L, 217L, 37L, 62L,
41L, 30L, 64L, 25L, 22L, 60L, 150L, 30L, 90L, 109L, 92L,
178L), X13 = c(224L, 168L, 120L, 23L, 213L, 310L, 324L, 377L,
366L, 212L, 54L, 178L, 0L, 207L, 316L, 105L, 117L, 266L,
235L, 106L, 231L, 186L, 147L, 223L, 109L, 182L, 211L, 183L,
130L, 132L), X14 = c(66L, 22L, 77L, 204L, 23L, 143L, 93L,
171L, 259L, 37L, 182L, 68L, 218L, 0L, 216L, 186L, 56L, 139L,
65L, 44L, 118L, 64L, 19L, 112L, 183L, 14L, 40L, 142L, 96L,
131L), X15 = c(167L, 236L, 263L, 275L, 187L, 189L, 212L,
282L, 9L, 181L, 309L, 231L, 340L, 238L, 0L, 207L, 216L, 97L,
204L, 237L, 120L, 160L, 217L, 188L, 258L, 203L, 183L, 106L,
174L, 267L), X16 = c(173L, 196L, 161L, 152L, 168L, 268L,
322L, 280L, 265L, 230L, 133L, 160L, 102L, 209L, 193L, 0L,
162L, 168L, 228L, 208L, 283L, 159L, 195L, 270L, 14L, 233L,
176L, 172L, 48L, 38L), X17 = c(70L, 44L, 13L, 184L, 90L,
186L, 194L, 267L, 257L, 72L, 179L, 38L, 107L, 88L, 177L,
172L, 0L, 93L, 71L, 14L, 167L, 117L, 37L, 146L, 116L, 35L,
62L, 83L, 93L, 129L), X18 = c(115L, 128L, 153L, 196L, 78L,
109L, 147L, 185L, 103L, 138L, 218L, 123L, 200L, 85L, 91L,
178L, 86L, 0L, 35L, 125L, 67L, 68L, 142L, 42L, 202L, 84L,
81L, 91L, 87L, 210L), X19 = c(36L, 104L, 71L, 166L, 16L,
99L, 88L, 133L, 200L, 35L, 246L, 2L, 263L, 89L, 144L, 229L,
47L, 103L, 0L, 31L, 114L, 32L, 44L, 106L, 219L, 43L, 92L,
119L, 150L, 103L), X20 = c(74L, 66L, 22L, 101L, 76L, 101L,
194L, 211L, 170L, 21L, 179L, 105L, 197L, 36L, 180L, 204L,
48L, 71L, 59L, 0L, 178L, 32L, 58L, 125L, 180L, 46L, 16L,
77L, 130L, 75L), X21 = c(85L, 158L, 144L, 210L, 29L, 16L,
44L, 65L, 141L, 88L, 258L, 70L, 279L, 124L, 168L, 190L, 145L,
45L, 40L, 110L, 0L, 129L, 157L, 52L, 177L, 117L, 175L, 153L,
133L, 190L), X22 = c(25L, 44L, 124L, 236L, 62L, 39L, 108L,
149L, 175L, 18L, 177L, 16L, 259L, 44L, 163L, 179L, 74L, 110L,
28L, 104L, 110L, 0L, 97L, 123L, 216L, 5L, 112L, 170L, 153L,
196L), X23 = c(26L, 2L, 39L, 205L, 102L, 74L, 205L, 203L,
257L, 49L, 194L, 96L, 207L, 5L, 174L, 160L, 37L, 159L, 55L,
55L, 91L, 1L, 0L, 153L, 216L, 52L, 11L, 192L, 116L, 149L),
X24 = c(12L, 127L, 115L, 288L, 90L, 60L, 73L, 79L, 194L,
87L, 203L, 81L, 257L, 108L, 188L, 263L, 185L, 90L, 25L, 177L,
51L, 85L, 93L, 0L, 234L, 114L, 111L, 72L, 131L, 153L), X25 = c(194L,
120L, 191L, 143L, 212L, 253L, 281L, 318L, 291L, 160L, 108L,
174L, 94L, 188L, 203L, 43L, 127L, 153L, 204L, 162L, 170L,
237L, 194L, 251L, 0L, 237L, 122L, 149L, 75L, 104L), X26 = c(10L,
58L, 22L, 171L, 101L, 131L, 144L, 154L, 177L, 5L, 222L, 48L,
220L, 59L, 192L, 193L, 9L, 134L, 23L, 80L, 75L, 19L, 19L,
132L, 197L, 0L, 57L, 146L, 163L, 154L), X27 = c(104L, 58L,
15L, 175L, 46L, 178L, 206L, 185L, 199L, 44L, 191L, 115L,
211L, 33L, 200L, 148L, 25L, 104L, 47L, 8L, 154L, 35L, 41L,
106L, 159L, 14L, 0L, 171L, 88L, 87L), X28 = c(80L, 137L,
93L, 225L, 76L, 138L, 245L, 195L, 102L, 130L, 197L, 112L,
169L, 163L, 68L, 83L, 108L, 50L, 125L, 108L, 139L, 106L,
131L, 111L, 136L, 179L, 150L, 0L, 103L, 151L), X29 = c(170L,
113L, 89L, 120L, 138L, 172L, 224L, 263L, 233L, 155L, 170L,
132L, 194L, 133L, 160L, 99L, 106L, 86L, 154L, 90L, 132L,
158L, 142L, 209L, 55L, 127L, 118L, 93L, 0L, 67L), X30 = c(197L,
170L, 155L, 66L, 178L, 193L, 226L, 303L, 213L, 161L, 104L,
94L, 140L, 138L, 241L, 29L, 102L, 131L, 108L, 129L, 182L,
167L, 167L, 198L, 83L, 154L, 89L, 106L, 87L, 0L)), class = "data.frame", row.names = c(NA,
-30L))
Following up on my comment to use the igraph package, below is a way to accomplish what is described.
library(igraph)
m <- data.frame(X1 = c(0L, 98L, 132L, 245L, 17L, 69L, 139L, 112L, 207L, 35L, 249L, 43L, 215L, 62L, 152L, 237L, 59L, 119L, 45L, 59L, 23L, 12L, 16L, 66L, 177L, 31L, 118L, 165L, 117L, 193L),
X2 = c(37L, 0L, 74L, 176L, 91L, 111L, 143L, 208L, 202L, 40L, 172L, 101L, 163L, 51L, 220L, 180L, 48L, 98L, 45L, 62L, 91L, 9L, 50L, 145L, 198L, 48L, 3L, 163L, 159L, 176L),
X3 = c(118L, 10L, 0L, 138L, 108L, 115L, 221L, 274L, 231L, 89L, 197L, 36L, 175L, 93L, 174L, 184L, 13L, 109L, 109L, 22L, 172L, 91L, 12L, 149L, 140L, 108L, 8L, 133L, 168L, 139L),
X4 = c(252L, 137L, 112L, 0L, 248L, 276L, 373L, 350L, 353L, 137L, 31L, 186L, 49L, 170L, 325L, 81L, 117L, 184L, 175L, 185L, 279L, 182L, 120L, 205L, 130L, 132L, 133L, 226L, 158L, 67L),
X5 = c(40L, 93L, 118L, 188L, 0L, 38L, 147L, 106L, 208L, 46L, 228L, 26L, 208L, 54L, 163L, 212L, 81L, 49L, 45L, 84L, 12L, 82L, 114L, 81L, 173L, 67L, 52L, 63L, 146L, 156L),
X6 = c(54L, 117L, 143L, 296L, 74L, 0L, 78L, 97L, 218L, 52L, 239L, 47L, 267L, 111L, 216L, 269L, 167L, 91L, 105L, 99L, 16L, 117L, 95L, 15L, 264L, 136L, 148L, 100L, 145L, 242L),
X7 = c(143L, 145L, 208L, 302L, 130L, 86L, 0L, 84L, 308L, 151L, 348L, 102L, 305L, 139L, 254L, 272L, 156L, 182L, 87L, 214L, 110L, 82L, 145L, 59L, 283L, 98L, 171L, 192L, 211L, 228L),
X8 = c(142L, 195L, 238L, 336L, 161L, 80L, 2L, 0L, 289L, 135L, 342L, 134L, 307L, 169L, 197L, 347L, 261L, 143L, 128L, 243L, 52L, 128L, 169L, 97L, 318L, 214L, 229L, 225L, 287L, 288L),
X9 = c(230L, 238L, 217L, 264L, 229L, 154L, 299L, 269L, 0L, 210L, 335L, 204L, 342L, 260L, 25L, 258L, 264L, 76L, 170L, 222L, 126L, 193L, 272L, 203L, 218L, 186L, 214L, 120L, 240L, 207L),
X10 = c(2L, 30L, 34L, 186L, 75L, 96L, 161L, 179L, 244L, 0L, 199L, 17L, 181L, 59L, 240L, 178L, 101L, 117L, 1L, 48L, 79L, 72L, 24L, 60L, 236L, 5L, 32L, 151L, 203L, 133L),
X11 = c(243L, 191L, 114L, 38L, 164L, 211L, 295L, 370L, 350L, 211L, 0L, 174L, 14L, 166L, 278L, 164L, 165L, 223L, 252L, 129L, 201L, 196L, 201L, 271L, 98L, 199L, 209L, 219L, 168L, 62L),
X12 = c(22L, 14L, 64L, 164L, 68L, 113L, 117L, 115L, 208L, 8L, 239L, 0L, 204L, 36L, 230L, 217L, 37L, 62L, 41L, 30L, 64L, 25L, 22L, 60L, 150L, 30L, 90L, 109L, 92L, 178L),
X13 = c(224L, 168L, 120L, 23L, 213L, 310L, 324L, 377L, 366L, 212L, 54L, 178L, 0L, 207L, 316L, 105L, 117L, 266L, 235L, 106L, 231L, 186L, 147L, 223L, 109L, 182L, 211L, 183L, 130L, 132L),
X14 = c(66L, 22L, 77L, 204L, 23L, 143L, 93L, 171L, 259L, 37L, 182L, 68L, 218L, 0L, 216L, 186L, 56L, 139L, 65L, 44L, 118L, 64L, 19L, 112L, 183L, 14L, 40L, 142L, 96L, 131L),
X15 = c(167L, 236L, 263L, 275L, 187L, 189L, 212L, 282L, 9L, 181L, 309L, 231L, 340L, 238L, 0L, 207L, 216L, 97L, 204L, 237L, 120L, 160L, 217L, 188L, 258L, 203L, 183L, 106L, 174L, 267L),
X16 = c(173L, 196L, 161L, 152L, 168L, 268L, 322L, 280L, 265L, 230L, 133L, 160L, 102L, 209L, 193L, 0L, 162L, 168L, 228L, 208L, 283L, 159L, 195L, 270L, 14L, 233L, 176L, 172L, 48L, 38L),
X17 = c(70L, 44L, 13L, 184L, 90L, 186L, 194L, 267L, 257L, 72L, 179L, 38L, 107L, 88L, 177L, 172L, 0L, 93L, 71L, 14L, 167L, 117L, 37L, 146L, 116L, 35L, 62L, 83L, 93L, 129L),
X18 = c(115L, 128L, 153L, 196L, 78L, 109L, 147L, 185L, 103L, 138L, 218L, 123L, 200L, 85L, 91L, 178L, 86L, 0L, 35L, 125L, 67L, 68L, 142L, 42L, 202L, 84L, 81L, 91L, 87L, 210L),
X19 = c(36L, 104L, 71L, 166L, 16L, 99L, 88L, 133L, 200L, 35L, 246L, 2L, 263L, 89L, 144L, 229L, 47L, 103L, 0L, 31L, 114L, 32L, 44L, 106L, 219L, 43L, 92L, 119L, 150L, 103L),
X20 = c(74L, 66L, 22L, 101L, 76L, 101L, 194L, 211L, 170L, 21L, 179L, 105L, 197L, 36L, 180L, 204L, 48L, 71L, 59L, 0L, 178L, 32L, 58L, 125L, 180L, 46L, 16L, 77L, 130L, 75L),
X21 = c(85L, 158L, 144L, 210L, 29L, 16L, 44L, 65L, 141L, 88L, 258L, 70L, 279L, 124L, 168L, 190L, 145L, 45L, 40L, 110L, 0L, 129L, 157L, 52L, 177L, 117L, 175L, 153L, 133L, 190L),
X22 = c(25L, 44L, 124L, 236L, 62L, 39L, 108L, 149L, 175L, 18L, 177L, 16L, 259L, 44L, 163L, 179L, 74L, 110L, 28L, 104L, 110L, 0L, 97L, 123L, 216L, 5L, 112L, 170L, 153L, 196L),
X23 = c(26L, 2L, 39L, 205L, 102L, 74L, 205L, 203L, 257L, 49L, 194L, 96L, 207L, 5L, 174L, 160L, 37L, 159L, 55L, 55L, 91L, 1L, 0L, 153L, 216L, 52L, 11L, 192L, 116L, 149L),
X24 = c(12L, 127L, 115L, 288L, 90L, 60L, 73L, 79L, 194L, 87L, 203L, 81L, 257L, 108L, 188L, 263L, 185L, 90L, 25L, 177L, 51L, 85L, 93L, 0L, 234L, 114L, 111L, 72L, 131L, 153L),
X25 = c(194L, 120L, 191L, 143L, 212L, 253L, 281L, 318L, 291L, 160L, 108L, 174L, 94L, 188L, 203L, 43L, 127L, 153L, 204L, 162L, 170L, 237L, 194L, 251L, 0L, 237L, 122L, 149L, 75L, 104L),
X26 = c(10L, 58L, 22L, 171L, 101L, 131L, 144L, 154L, 177L, 5L, 222L, 48L, 220L, 59L, 192L, 193L, 9L, 134L, 23L, 80L, 75L, 19L, 19L, 132L, 197L, 0L, 57L, 146L, 163L, 154L),
X27 = c(104L, 58L, 15L, 175L, 46L, 178L, 206L, 185L, 199L, 44L, 191L, 115L, 211L, 33L, 200L, 148L, 25L, 104L, 47L, 8L, 154L, 35L, 41L, 106L, 159L, 14L, 0L, 171L, 88L, 87L),
X28 = c(80L, 137L, 93L, 225L, 76L, 138L, 245L, 195L, 102L, 130L, 197L, 112L, 169L, 163L, 68L, 83L, 108L, 50L, 125L, 108L, 139L, 106L, 131L, 111L, 136L, 179L, 150L, 0L, 103L, 151L),
X29 = c(170L, 113L, 89L, 120L, 138L, 172L, 224L, 263L, 233L, 155L, 170L, 132L, 194L, 133L, 160L, 99L, 106L, 86L, 154L, 90L, 132L, 158L, 142L, 209L, 55L, 127L, 118L, 93L, 0L, 67L),
X30 = c(197L, 170L, 155L, 66L, 178L, 193L, 226L, 303L, 213L, 161L, 104L, 94L, 140L, 138L, 241L, 29L, 102L, 131L, 108L, 129L, 182L, 167L, 167L, 198L, 83L, 154L, 89L, 106L, 87L, 0L))
system.time({
g <- graph_from_adjacency_matrix(as.matrix(m), "directed", TRUE, FALSE)
mOpt <- shortest.paths(g, V(g), V(g), mode = "out")
})
#> user system elapsed
#> 0 0 0
mOpt[1:10, 1:10]
#> X1 X2 X3 X4 X5 X6 X7 X8 X9 X10
#> X1 0 21 25 133 36 27 71 73 123 2
#> X2 18 0 10 122 40 45 89 91 127 17
#> X3 36 18 0 112 58 63 107 109 145 27
#> X4 130 112 117 0 152 157 201 203 239 129
#> X5 17 36 40 148 0 44 88 81 127 17
#> X6 39 48 52 160 28 0 86 68 142 41
#> X7 67 88 92 200 56 60 0 2 170 69
#> X8 88 109 113 221 77 81 84 0 191 90
#> X9 157 165 170 250 140 157 208 193 0 154
#> X10 22 19 23 131 34 49 92 94 121 0
mOptPaths <- lapply(V(g), function(from) all_shortest_paths(g, from = from, mode = "out"))
# optimal path from 1 to 2
(path_1_2 <- as.integer(mOptPaths[[1]]$res[[2]]))
#> [1] 1 10 26 22 2
# distances for path from 1 to 2
m[matrix(c(head(path_1_2, -1), path_1_2[-1]), ncol = 2)]
#> [1] 2 5 5 9
entrezid_downgene=structure(list(SYMBOL = c("ARHGEF16", "ILDR1", "TMPRSS4", "MAP7", "SERINC2", "C9orf152", "TSPAN1", "RHEX", "TMC4", "CRB3", "UGT8", "CD24", "MAPK13", "AGR2", "GJB1", "ERBB3", "CNDP2", "LOC105378644", "GCNT3", "CEACAM1", "GPR160", "PRSS8", "HOOK1", "ABHD17C", "MOCOS", "CWH43", "EHF", "ACSL5", "SLC44A4", "RAP1GAP", "MUC13", "PPM1H", "ATP2C2", "RAB25", "H2BC5", "H4C12", "TJP3", "RXFP1", "GSTO2", "OVOL2", "TMEM125", "LIMS1", "DLX5", "ST6GALNAC1", "HNF1B", "STX19", "F2RL1", "MT1G", "PLPP2", "TMEM238", "SLC30A2", "GABRP", "EPCAM", "CLDN10", "HOXB5", "PRAME", "MAL2", "PLA2G10", "TSPAN12", "FAM174B", "TMC5", "ASRGL1", "SCNN1A", "FOXL2", "ALDH3B2", "ELF3", "SLC7A1", "MT1F", "CLDN3", "SPINT2", "SFN", "VWC2", "C9orf116", "SLC39A6", "TCN1", "IL20RA", "ACSM3", "FOXL2NB", "HGD", "PAX8", "IDO1", "C4BPA", "RHPN2", "HMGCR", "UGT2B11", "PIGR", "MUC20", "SLC3A1", "PLLP", "PSAT1", "SCGB2A1", "WNT5A", "DEFB1", "FGL1", "SLC2A8", "HOXB8", "CYP2J2", "WWC1", "MUC1", "PRKX", "RASEF", "BAIAP2L2", "PAPSS1", "MME", "HOMER2", "STRA6", "ARG2", "MOGAT1", "CDS1", "SCGB2A2", "MPZL2", "PHYHIPL", "INAVA", "IDO2", "GALNT4", "TMEM101", "HSD17B2", "AOC1", "CDCA7", "CAPS", "TFCP2L1", "PAEP", "PLAC9P1", "GAL", "RORB", "CCNO", "XDH", "C15orf48", "SLC1A1", "GPT2", "VNN1", "NWD1", "HABP2", "UGT2B7", "CYP26A1", "MSX1", "ENPP3", "KIR2DL3", "ADAMTS9", "KIR2DL4", "BRINP1", "PROM1", "APCDD1", "AGR3", "EYA2", "SLC2A1", "GNLY", "COL7A1", "FOXJ1", "MS4A8", "C20orf85", "RSPH1", "SCGB1D2", "SPP1", "RASD1", "CST1", "SCGB1D4", "LEFTY1", "LAMC3", "TEKT1", "LCN2", "VTCN1", "IRX3", "ROPN1L", "FAM183A", "NDP", "TUBB3", "DIO2", "IL2RB", "ADAMTS8", "SERPINA5", "NKG7", "ABCC8", "STC1", "LRRC26"),
ENTREZID = c("27237", "286676", "56649", "9053", "347735", "401546", "10103", "440712", "147798", "92359", "7368", "100133941", "5603", "10551", "2705", "2065", "55748", "105378644", "9245", "634", "26996", "5652", "51361", "58489", "55034", "80157", "26298", "51703", "80736", "5909", "56667", "57460", "9914", "57111", "3017", "8362", "27134", "59350", "119391", "58495", "128218", "3987", "1749", "55808", "6928", "415117", "2150", "4495", "8612", "388564", "7780", "2568", "4072", "9071", "3215", "23532", "114569", "8399", "23554", "400451", "79838", "80150", "6337", "668", "222", "1999", "6541", "4494", "1365", "10653", "2810", "375567", "138162", "25800", "6947", "53832", "6296", "401089", "3081", "7849", "3620", "722", "85415", "3156", "10720", "5284", "200958", "6519", "51090", "29968", "4246", "7474", "1672", "2267", "29988", "3218", "1573", "23286", "4582", "5613", "158158", "80115", "9061", "4311", "9455", "64220", "384", "116255", "1040", "4250", "10205", "84457", "55765", "169355", "8693", "84336", "3294", "26", "83879", "828", "29842", "5047", "389033", "51083", "6096", "10309", "7498", "84419", "6505", "84706", "8876", "284434", "3026", "7364", "1592", "4487", "5169", "3804", "56999", "3805", "1620", "8842", "147495", "155465", "2139", "6513", "10578", "1294", "2302", "83661", "128602", "89765", "10647", "6696", "51655", "1469", "404552", "10637", "10319", "83659", "3934", "79679", "79191", "83853", "440585", "4693", "10381", "1734", "3560", "11095", "5104", "4818", "6833", "6781", "389816")),
row.names = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L, 80L, 81L, 82L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L, 93L, 94L, 95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L, 105L, 106L, 107L, 108L, 109L, 110L, 111L, 112L, 113L, 114L, 115L, 116L, 117L, 118L, 119L, 120L, 121L, 123L, 124L, 125L, 126L, 127L, 128L, 129L, 130L, 131L, 132L, 133L, 134L, 135L, 136L, 137L, 138L, 139L, 140L, 141L, 142L, 143L, 144L, 145L, 146L, 147L, 148L, 149L, 150L, 151L, 152L, 153L, 154L, 155L, 156L, 157L, 158L, 159L, 160L, 161L, 162L, 163L, 164L, 165L, 166L, 167L, 168L, 169L, 170L, 171L, 172L, 173L, 174L, 175L, 176L, 177L), class = "data.frame")
down_ekk <- enrichKEGG(gene= c(entrezid_downgene$ENTREZID),
organism = 'hsa',
pvalueCutoff = 0.05,
minGSSize = 50,
maxGSSize = 500,
)
dot <- dotplot(down_ekk,font.size=6,title='down_kegg')
dot
Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : Change the
parameter length to zero Warning message: In rep(yes, length.out =
len) : 'x' is NULL so the result will be NULL
please How to solve the error?
This is normal you can't plot the dotplot because you have no significant ontologies.
You can check with down_ekk :
downekk
#
# over-representation test
#
#...#organism hsa
#...#ontology KEGG
#...#keytype kegg
#...#gene chr [1:175] "27237" "286676" "56649" "9053" "347735" "401546" "10103" "440712" "147798" "92359" "7368" "100133941" "5603" "10551" "2705" "2065" "55748" "105378644" "9245" "634" "26996" "5652" ...
#...pvalues adjusted by 'BH' with cutoff <0.05
#...0 enriched terms found
#...Citation
Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He.
clusterProfiler: an R package for comparing biological themes among
gene clusters. OMICS: A Journal of Integrative Biology
2012, 16(5):284-287
"0 enriched terms found" so this is why you get the error as no dotplot can be plotted
I have irregular polygons defined by a set of points. I can find the the maximum chord location and length, but I'm not quite sure how to analyze the points to find the longest chord location and length that is perpendicular to the maximum chord.
Here's what I've got so far, some example data of points to define a polygon:
points_ex <- structure(list(V1 = c(68L, 67L, 66L, 66L, 65L, 65L, 64L, 63L,
62L, 61L, 61L, 60L, 59L, 58L, 57L, 56L, 56L, 55L, 55L, 55L, 55L,
54L, 54L, 54L, 54L, 54L, 54L, 54L, 53L, 53L, 53L, 52L, 52L, 52L,
51L, 51L, 50L, 50L, 49L, 49L, 49L, 48L, 48L, 47L, 47L, 46L, 46L,
45L, 45L, 45L, 44L, 44L, 44L, 44L, 44L, 44L, 44L, 43L, 43L, 42L,
42L, 41L, 41L, 41L, 41L, 40L, 40L, 40L, 40L, 40L, 40L, 39L, 39L,
38L, 38L, 38L, 38L, 37L, 37L, 36L, 36L, 36L, 35L, 35L, 35L, 35L,
35L, 34L, 34L, 34L, 33L, 33L, 33L, 32L, 32L, 32L, 32L, 32L, 32L,
32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L,
32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 33L, 33L,
33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L,
33L, 33L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 31L, 31L, 31L, 31L,
31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L,
30L, 30L, 30L, 30L, 30L, 30L, 30L, 30L, 30L, 30L, 30L, 30L, 30L,
30L, 30L, 30L, 30L, 30L, 30L, 30L, 30L, 30L, 30L, 30L, 31L, 31L,
31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L,
31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 31L, 32L, 32L, 33L, 33L,
34L, 34L, 35L, 36L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 43L,
44L, 44L, 45L, 46L, 46L, 47L, 47L, 48L, 48L, 49L, 49L, 50L, 51L,
51L, 51L, 52L, 52L, 52L, 52L, 53L, 53L, 53L, 53L, 54L, 54L, 54L,
54L, 54L, 54L, 54L, 53L, 53L, 53L, 53L, 53L, 53L, 52L, 52L, 52L,
51L, 51L, 51L, 51L, 51L, 51L, 51L, 51L, 52L, 52L, 52L, 52L, 52L,
53L, 53L, 54L, 54L, 55L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L,
63L, 64L, 65L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L,
76L, 77L, 78L, 79L, 80L, 81L, 82L, 83L, 84L, 84L, 85L, 85L, 86L,
86L, 86L, 87L, 87L, 88L, 88L, 88L, 89L, 89L, 90L, 90L, 91L, 91L,
92L, 93L, 94L, 95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L,
104L, 105L, 105L, 106L, 106L, 107L, 108L, 109L, 109L, 110L, 111L,
112L, 113L, 114L, 115L, 116L, 117L, 118L, 118L, 119L, 120L, 121L,
122L, 123L, 123L, 124L, 125L, 126L, 126L, 127L, 127L, 127L, 127L,
127L, 128L, 128L, 128L, 128L, 128L, 128L, 128L, 128L, 128L, 129L,
129L, 129L, 129L, 129L, 129L, 130L, 130L, 130L, 130L, 131L, 131L,
131L, 131L, 131L, 132L, 132L, 132L, 132L, 132L, 133L, 133L, 133L,
133L, 133L, 133L, 133L, 132L, 132L, 132L, 131L, 131L, 130L, 130L,
129L, 129L, 128L, 128L, 128L, 128L, 128L, 128L, 128L, 128L, 128L,
129L, 129L, 129L, 129L, 129L, 129L, 129L, 129L, 129L, 129L, 128L,
127L, 126L, 125L, 125L, 124L, 123L, 123L, 122L, 121L, 120L, 120L,
119L, 119L, 118L, 117L, 117L, 116L, 115L, 115L, 115L, 114L, 114L,
113L, 113L, 112L, 111L, 111L, 110L, 110L, 109L, 109L, 109L, 109L,
108L, 108L, 108L, 108L, 107L, 107L, 107L, 107L, 106L, 106L, 106L,
106L, 105L, 105L, 105L, 105L, 104L, 104L, 104L, 104L, 103L, 103L,
103L, 103L, 103L, 102L, 102L, 102L, 102L, 102L, 102L, 102L, 102L,
102L, 102L, 102L, 102L, 101L, 101L, 101L, 101L, 101L, 101L, 101L,
100L, 100L, 100L, 100L, 100L, 100L, 100L, 99L, 99L, 99L, 99L,
99L, 98L, 98L, 98L, 98L, 98L, 98L, 98L, 98L, 98L, 98L, 97L, 97L,
97L, 97L, 97L, 97L, 96L, 96L, 96L, 96L, 96L, 96L, 96L, 96L, 96L,
96L, 95L, 95L, 95L, 95L, 95L, 95L, 95L, 95L, 95L, 95L, 95L, 95L,
94L, 94L, 94L, 94L, 93L, 93L, 92L, 92L, 91L, 90L, 90L, 89L, 89L,
89L, 88L, 88L, 88L, 88L, 88L, 87L, 87L, 87L, 86L, 86L, 86L, 85L,
84L, 83L, 82L, 81L, 80L, 79L, 78L, 77L, 76L, 75L, 74L, 73L, 72L,
71L, 70L, 69L), V2 = c(20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L,
28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L,
41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L,
54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L,
67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L,
80L, 81L, 82L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L,
93L, 94L, 95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L,
105L, 106L, 107L, 108L, 109L, 110L, 111L, 112L, 113L, 114L, 115L,
116L, 117L, 118L, 119L, 120L, 121L, 122L, 123L, 124L, 125L, 126L,
127L, 128L, 129L, 130L, 131L, 132L, 133L, 134L, 135L, 136L, 137L,
138L, 139L, 140L, 141L, 142L, 143L, 144L, 145L, 146L, 147L, 148L,
149L, 150L, 151L, 152L, 153L, 154L, 155L, 156L, 157L, 158L, 159L,
160L, 161L, 162L, 163L, 164L, 165L, 166L, 167L, 168L, 169L, 170L,
171L, 172L, 173L, 174L, 175L, 176L, 177L, 178L, 179L, 180L, 181L,
182L, 183L, 184L, 185L, 186L, 187L, 188L, 189L, 190L, 191L, 192L,
193L, 194L, 195L, 196L, 197L, 198L, 199L, 200L, 201L, 202L, 203L,
204L, 205L, 206L, 207L, 208L, 209L, 210L, 211L, 212L, 213L, 214L,
215L, 216L, 217L, 218L, 219L, 220L, 221L, 222L, 223L, 224L, 225L,
226L, 227L, 228L, 229L, 230L, 231L, 232L, 233L, 234L, 235L, 236L,
237L, 238L, 239L, 240L, 241L, 242L, 243L, 244L, 245L, 246L, 247L,
248L, 249L, 250L, 251L, 252L, 253L, 254L, 255L, 256L, 257L, 258L,
259L, 260L, 261L, 262L, 263L, 264L, 265L, 266L, 267L, 268L, 269L,
270L, 271L, 272L, 273L, 274L, 275L, 276L, 277L, 278L, 279L, 280L,
281L, 282L, 283L, 284L, 285L, 286L, 287L, 288L, 289L, 290L, 291L,
292L, 293L, 294L, 295L, 296L, 297L, 298L, 299L, 300L, 301L, 302L,
303L, 304L, 305L, 306L, 307L, 308L, 308L, 308L, 309L, 309L, 309L,
310L, 310L, 310L, 311L, 311L, 312L, 312L, 312L, 312L, 312L, 312L,
312L, 311L, 311L, 310L, 310L, 310L, 310L, 309L, 308L, 307L, 306L,
305L, 304L, 303L, 302L, 301L, 300L, 299L, 298L, 297L, 296L, 295L,
294L, 293L, 292L, 291L, 290L, 289L, 288L, 287L, 286L, 285L, 284L,
283L, 282L, 281L, 280L, 279L, 279L, 278L, 277L, 276L, 275L, 274L,
273L, 272L, 271L, 270L, 269L, 268L, 267L, 266L, 265L, 264L, 263L,
262L, 261L, 260L, 259L, 258L, 257L, 256L, 255L, 254L, 253L, 252L,
252L, 251L, 250L, 249L, 248L, 247L, 246L, 245L, 244L, 243L, 242L,
241L, 240L, 239L, 238L, 237L, 236L, 235L, 234L, 233L, 232L, 231L,
230L, 229L, 228L, 227L, 226L, 225L, 224L, 223L, 222L, 221L, 220L,
219L, 218L, 217L, 216L, 215L, 214L, 213L, 212L, 211L, 210L, 209L,
208L, 207L, 206L, 205L, 204L, 203L, 202L, 201L, 200L, 199L, 198L,
197L, 196L, 195L, 194L, 193L, 192L, 191L, 190L, 189L, 188L, 187L,
186L, 185L, 184L, 183L, 182L, 181L, 180L, 179L, 178L, 177L, 176L,
175L, 174L, 173L, 172L, 171L, 170L, 169L, 168L, 167L, 166L, 165L,
164L, 163L, 162L, 161L, 160L, 159L, 158L, 157L, 156L, 155L, 154L,
153L, 152L, 151L, 150L, 149L, 148L, 147L, 146L, 145L, 144L, 143L,
142L, 141L, 140L, 139L, 138L, 137L, 136L, 135L, 134L, 133L, 132L,
131L, 130L, 129L, 128L, 127L, 126L, 125L, 124L, 123L, 122L, 121L,
120L, 119L, 118L, 117L, 116L, 115L, 114L, 113L, 112L, 111L, 110L,
109L, 108L, 107L, 106L, 105L, 104L, 103L, 102L, 101L, 100L, 99L,
98L, 97L, 96L, 95L, 94L, 93L, 92L, 91L, 90L, 89L, 88L, 87L, 86L,
85L, 84L, 83L, 82L, 81L, 80L, 79L, 78L, 77L, 76L, 75L, 74L, 73L,
72L, 71L, 70L, 69L, 68L, 67L, 66L, 65L, 64L, 63L, 62L, 61L, 60L,
59L, 58L, 57L, 56L, 55L, 54L, 53L, 52L, 51L, 50L, 49L, 48L, 47L,
46L, 45L, 44L, 43L, 42L, 41L, 40L, 39L, 38L, 37L, 36L, 35L, 34L,
33L, 32L, 31L, 30L, 29L, 28L, 27L, 26L, 26L, 26L, 25L, 25L, 24L,
24L, 23L, 23L, 22L, 22L, 21L, 21L, 20L, 20L, 20L)), class = "data.frame", row.names = c(NA,
-613L))
Looks like this:
I can find the maximum chord and draw that:
# draw max dimension points and line
suppressPackageStartupMessages(library(tidyverse))
df_dist = data.frame(as.matrix(dist(cbind(points_ex$V1,points_ex$V2))))
df_dist_x = df_dist %>%
mutate(row.1 = 1:nrow(df_dist)) %>%
mutate(Y = paste0("Y", row_number())) %>%
gather(X, distance, X1:nrow(.)) %>%
select(X, Y, distance) %>%
mutate_at(vars(X, Y), parse_number)
df_dist_x_max <-
df_dist_x %>%
dplyr::filter(distance == max(distance))
points(points_ex[df_dist_x_max$X[1],], col = "red", cex = 2)
points(points_ex[df_dist_x_max$X[2],], col = "red", cex = 2.5)
segments(points_ex[df_dist_x_max$X[1], 'V1'],
points_ex[df_dist_x_max$X[1], 'V2'],
points_ex[df_dist_x_max$X[2], 'V1'],
points_ex[df_dist_x_max$X[2], 'V2'],
col = "green")
And this is what I've been trying to get the longest chord perpendicular to the maximum length chord:
# transform the points and lines into spatial objects
library(sf)
library(sp)
library(rgeos)
points_sf <- st_as_sf(points_ex, coords = c("V1", "V2"))
newline = matrix(c(points_ex[df_dist_x_max$X[1], 'V1'],
points_ex[df_dist_x_max$X[1], 'V2'],
points_ex[df_dist_x_max$X[2], 'V1'],
points_ex[df_dist_x_max$X[2], 'V2']), byrow = T, nrow = 2)
spline <- as(st_as_sfc(st_as_text(st_linestring(newline))), "Spatial") # there is probably a more straighforward solution...
position <- gProject(spline, as(points_sf, "Spatial"))
position <- coordinates(gInterpolate(spline, position))
colnames(position) <- c("X2", "Y2")
segments <-
data.frame(st_coordinates(points_sf), position)
segments$dist <- NULL
for(i in 1:nrow(segments)){
segments$dist[i] <-
proxy::dist(data.frame(segments$X[i], segments$Y[i]),
data.frame(segments$X2[i], segments$Y2[i]))
}
# max width perpendicular to length axis
max_segment <- segments[which.max(segments$dist), ]
max_segment <- segments[segments$Y == max_segment$Y, ]
segments(max_segment$X[1], max_segment$Y[1],
max_segment$X2[1], max_segment$Y2[1],
col = "purple")
segments(max_segment$X[2], max_segment$Y[2],
max_segment$X2[2], max_segment$Y2[2],
col = "purple")
Looks roughly ok, but my problem is that this method for finding the longest chord perpendicular to maximum chord only looks at one side of the maximum chord for the longest distance to the edge of the polygon.
I don't know how to measure every distance from edge to edge of the polygon that is perpendicular to the maximum chord.
This means my method doesn't generalise well at all, here it is applied to another polygon (data here: https://pastebin.com/XpiB6UnX because the dput output made this post too long)
Obviously this is bad because the two purple segments should not be on the same side of the green segment, and it doesn't look like the right location at all for the longest chord perpendicular to the maximum chord.
How can I robustly find the longest chord that is perpendicular to the maximum chord?
Here's a full solution. First some functions:
## this returns the i,j of the largest elements in matrix `m`
findmax <- function(m){
v = which.max(m) - 1
c(v %% nrow(m)+1, v %/% nrow(m)+1)
}
## Return an sf line through a point at an angle of a given length
pline <- function(pt, angle, length){
st_linestring(
cbind(
pt[1] + c(length,-length) * sin(angle),
pt[2] + c(length,-length) * cos(angle)
)
)
}
## return the line that is the chord at angle perp.angle of length through any of the polygon vertices
max_perp_chord <- function(polygon, perp.angle, length){
## get polygon vertices
pts = st_coordinates(polygon)[,c(1,2)]
## return the perpendicular lines
perplines = lapply(1:nrow(pts), function(i){
## through the i-th vertex
xy = pts[i,,drop=FALSE]
perpline = pline(xy, perp.angle, length)
## intersect it with the polygon
inters = st_intersection(polygon, perpline)
inters
}
)
## get the vector of intersection lengths, find the largest
perplengths = unlist(lapply(perplines, st_length))
longest = which.max(perplengths)
## return the longest line
perplines[[longest]]
}
### find the max length chord across all pairs of vertex points
max_chord <- function(polygon){
## get polygon coordinates
xy = st_coordinates(polygon)[,1:2]
## compute the distance matrix and find largest element
df_dist = as.matrix(dist(xy))
maxij = findmax(df_dist)
## those elements define the largest chord
chord = rbind(
xy[maxij[1],],
xy[maxij[2],]
)
chord
}
find_max_chord <- function(spolygon, chord=max_chord(spolygon)){
## Now compute the length and angle of the longest chord
chord.length = sqrt(diff(chord[,1])^2 + diff(chord[,2])^2)
chord.theta = atan2(diff(chord[,1]), diff(chord[,2]))
## The perpendicular is at this angle plus pi/2 radians
perp = chord.theta + pi/2
max_perp_chord(spolygon, perp, chord.length)
}
Here's how this goes together. The only dependency is sf - nothing else but base R is used:
library(sf)
Next massage your data into an sf polygon object:
## construct an sf polygon from points:
polygon = st_polygon(list(as.matrix(rbind(points_ex, points_ex[1,]))))
Get the max length chord between vertices:
chord = max_chord(polygon)
Plot the polygon and the chord and the chord points:
plot(polygon)
points(chord, col="red",cex=2)
lines(chord,col="green",lwd=2)
Now the meat. Get the chord perpendicular to the max chord through one of the polygon vertices:
## get the max perpendicular chord
pchord = find_max_chord(polygon, chord)
Plot it.
plot(pchord,add=TRUE)
I've tested this on another example, but not the second one you posted... Should work but...
It does...
If your polygon is monotone, you can apply the next approach:
I assume that polygon is rotated to make the maximum length chord vertical (as your two images show).
Start from the top point. Traverse left part in CCW direction, right part in clockwise direction.
Key moment: the longest chord must touch some polygon vertex (because max cannot be reached on the line segment between two inner points at edges).
So get vertex with the highest Y-coordinate (either at the left part or at the right part). Calculate point at the edge on opposite side. Get length.
Get vertex with the next Y-coordinate. Calculate point at the edge on opposite side. Get length. Continue.
When I want to change a column from factor to numeric with "as.numeric()", the final numbers are totally different from what I imported.
It is a problem due to the comma? Really strange...
Thanks!
dput(datatest)
structure(list(HOURS.at.sea = structure(c(261L, 84L, 83L, 260L,
307L, 292L, 252L, 72L, 59L, 343L, 244L, 78L, 56L, 256L, 9L, 269L,
291L, 254L, 69L, 65L, 267L, 283L, 1L, 80L, 169L, 1L, 115L, 67L,
75L, 3L, 309L, 59L, 33L, 52L, 75L, 37L, 51L, 75L, 22L, 2L, 49L,
83L, 21L, 2L, 53L, 70L, 19L, 3L, 57L, 70L, 22L, 3L, 58L, 78L,
36L, 49L, 2L, 66L, 115L, 52L, 72L, 114L, 57L, 78L, 116L, 56L,
68L, 116L, 55L, 70L, 327L, 6L, 257L, 2L, 107L, 176L, 182L, 4L,
114L, 35L, 46L, 3L, 67L, 34L, 46L, 3L, 79L, 40L, 50L, 69L, 38L,
52L, 2L, 69L, 38L, 85L, 49L, 70L, 64L, 70L, 3L, 1L, 206L, 231L,
58L, 55L, 109L, 212L, 220L, 53L, 56L, 125L, 3L, 5L, 214L, 231L,
57L, 55L, 107L, 217L, 228L, 52L, 57L, 105L, 210L, 231L, 56L,
55L, 105L, 215L, 232L, 55L, 54L, 90L, 210L, 230L, 58L, 54L, 108L,
218L, 228L, 57L, 56L, 96L, 213L, 228L, 55L, 57L, 106L, 217L,
232L, 58L, 73L, 110L, 217L, 233L, 57L, 59L, 117L, 7L, 222L, 233L,
59L, 56L, 107L, 219L, 231L, 57L, 56L, 109L, 221L, 233L, 56L,
57L, 106L, 1L, 1L, 247L, 317L, 159L, 316L, 229L, 306L, 129L,
120L, 29L, 74L, 287L, 12L, 151L, 109L, 68L, 125L, 270L, 1L, 56L,
224L, 180L, 76L, 281L, 86L, 79L, 258L, 83L, 1L, 229L, 23L, 132L,
56L, 59L, 76L, 115L, 110L, 28L, 235L, 226L, 16L, 134L, 55L, 57L,
66L, 124L, 117L, 28L, 240L, 1L, 52L, 335L, 32L, 59L, 186L, 71L,
4L, 7L, 5L, 39L, 59L, 2L, 3L, 4L, 293L, 4L, 66L, 99L, 110L, 54L,
2L, 4L, 148L, 221L, 322L, 31L, 170L, 1L, 286L, 162L, 336L, 129L,
138L, 70L, 71L, 125L, 241L, 277L, 6L, 8L, 76L, 84L, 320L, 339L,
117L, 137L, 69L, 80L, 1L, 243L, 92L, 139L, 149L, 54L, 67L, 262L,
1L, 240L, 78L, 73L, 1L, 187L, 48L, 65L, 97L, 263L, 332L, 187L,
103L, 29L, 79L, 266L, 334L, 188L, 303L, 96L, 264L, 313L, 184L,
45L, 66L, 105L, 263L, 330L, 184L, 53L, 24L, 96L, 97L, 272L, 331L,
185L, 47L, 68L, 102L, 265L, 342L, 187L, 97L, 49L, 58L, 264L,
333L, 195L, 96L, 31L, 181L, 265L, 1L, 236L, 79L, 270L, 89L, 246L,
45L, 207L, 166L, 79L, 41L, 177L, 55L, 128L, 1L, 152L, 205L, 57L,
168L, 195L, 284L, 94L, 118L, 340L, 82L, 123L, 57L, 73L, 118L,
58L, 227L, 18L, 51L, 323L, 178L, 49L, 120L, 26L, 59L, 52L, 67L,
67L, 114L, 234L, 1L, 15L, 201L, 163L, 42L, 72L, 47L, 10L, 66L,
106L, 224L, 17L, 189L, 44L, 200L, 164L, 45L, 69L, 47L, 67L, 102L,
275L, 14L, 190L, 30L, 199L, 161L, 47L, 71L, 52L, 276L, 32L, 199L,
161L, 48L, 73L, 46L, 70L, 103L, 273L, 23L, 271L, 47L, 74L, 46L,
57L, 308L, 23L, 1L, 66L, 338L, 242L, 155L, 72L, 249L, 57L, 80L,
94L, 225L, 341L, 104L, 1L, 116L, 44L, 5L, 90L, 293L, 50L, 238L,
84L, 46L, 216L, 46L, 278L, 325L, 57L, 314L, 48L, 108L, 44L, 50L,
59L, 1L, 289L, 49L, 42L, 295L, 53L, 304L, 3L, 49L, 59L, 1L, 74L,
15L, 84L, 26L, 244L, 129L, 80L, 82L, 158L, 126L, 45L, 79L, 65L,
344L, 258L, 106L, 81L, 75L, 95L, 4L, 144L, 140L, 25L, 83L, 76L,
1L, 209L, 99L, 42L, 79L, 312L, 1L, 27L, 238L, 76L, 70L, 119L,
115L, 69L, 305L, 1L, 318L, 139L, 187L, 84L, 67L, 150L, 44L, 131L,
73L, 172L, 123L, 57L, 73L, 251L, 1L, 122L, 254L, 28L, 5L, 4L,
4L, 4L, 6L, 156L, 247L, 88L, 248L, 81L, 78L, 42L, 258L, 87L,
165L, 50L, 173L, 80L, 98L, 41L, 72L, 108L, 102L, 48L, 74L, 102L,
223L, 103L, 48L, 5L, 5L, 67L, 98L, 226L, 104L, 57L, 4L, 3L, 3L,
2L, 72L, 98L, 228L, 105L, 48L, 3L, 4L, 4L, 4L, 78L, 94L, 234L,
103L, 2L, 26L, 3L, 3L, 4L, 4L, 3L, 3L, 60L, 98L, 84L, 218L, 11L,
45L, 1L, 158L, 175L, 95L, 4L, 65L, 112L, 311L, 216L, 146L, 1L,
131L, 217L, 55L, 302L, 60L, 202L, 66L, 56L, 167L, 79L, 179L,
142L, 2L, 54L, 145L, 1L, 196L, 60L, 70L, 118L, 23L, 91L, 42L,
197L, 50L, 67L, 77L, 83L, 44L, 66L, 140L, 44L, 83L, 337L, 1L,
52L, 319L, 1L, 47L, 62L, 50L, 234L, 81L, 57L, 254L, 56L, 61L,
45L, 232L, 80L, 57L, 253L, 121L, 234L, 77L, 51L, 241L, 49L, 63L,
44L, 234L, 81L, 54L, 250L, 2L, 1L, 153L, 338L, 107L, 141L, 68L,
55L, 128L, 225L, 100L, 171L, 193L, 194L, 160L, 338L, 112L, 139L,
3L, 68L, 2L, 65L, 130L, 49L, 139L, 1L, 50L, 310L, 76L, 279L,
141L, 1L, 1L, 74L, 251L, 204L, 1L, 217L, 84L, 198L, 43L, 54L,
298L, 268L, 26L, 208L, 49L, 51L, 297L, 226L, 92L, 199L, 42L,
54L, 299L, 267L, 26L, 199L, 31L, 58L, 298L, 218L, 96L, 203L,
43L, 58L, 299L, 267L, 288L, 25L, 183L, 42L, 315L, 92L, 199L,
32L, 56L, 300L, 1L, 105L, 103L, 96L, 90L, 76L, 248L, 290L, 294L,
274L, 94L, 56L, 133L, 136L, 72L, 67L, 67L, 115L, 244L, 174L,
112L, 84L, 68L, 143L, 240L, 1L, 220L, 147L, 209L, 117L, 157L,
321L, 113L, 138L, 13L, 154L, 118L, 139L, 111L, 55L, 1L, 102L,
51L, 80L, 208L, 241L, 70L, 96L, 80L, 259L, 103L, 70L, 223L, 326L,
57L, 285L, 53L, 324L, 67L, 255L, 105L, 221L, 105L, 76L, 53L,
54L, 83L, 84L, 247L, 91L, 68L, 106L, 30L, 324L, 59L, 65L, 296L,
79L, 20L, 79L, 301L, 52L, 70L, 1L, 135L, 245L, 53L, 217L, 247L,
83L, 75L, 2L, 78L, 242L, 192L, 249L, 56L, 77L, 99L, 82L, 75L,
65L, 241L, 6L, 63L, 112L, 82L, 80L, 49L, 239L, 191L, 101L, 1L,
14L, 222L, 71L, 74L, 98L, 215L, 325L, 282L, 117L, 325L, 226L,
97L, 91L, 92L, 57L, 72L, 246L, 1L, 211L, 53L, 70L, 131L, 239L,
237L, 217L, 53L, 70L, 93L, 242L, 329L, 43L, 92L, 104L, 127L,
50L, 306L, 328L, 256L, 76L, 49L, 280L, 1L, 201L, 103L, 73L, 4L,
4L, 4L, 242L, 125L), .Label = c("#VALUE!", "0,1", "0,2", "0,3",
"0,4", "0,5", "0,6", "0,8", "1,0", "1,3", "10,1", "10,2", "10,3",
"10,4", "10,5", "10,8", "10,9", "1023,7", "107,5", "108,5", "108,9",
"109,2", "11,0", "11,1", "11,2", "11,3", "11,4", "11,5", "11,6",
"11,7", "11,8", "11,9", "110,1", "110,2", "110,4", "110,7", "110,8",
"110,9", "111,1", "115,8", "12,0", "12,1", "12,2", "12,3", "12,4",
"12,5", "12,6", "12,7", "12,8", "12,9", "13,0", "13,1", "13,2",
"13,3", "13,4", "13,5", "13,6", "13,7", "13,8", "13,9", "132,9",
"133,8", "133,9", "138,1", "14,0", "14,1", "14,2", "14,3", "14,4",
"14,5", "14,6", "14,7", "14,8", "14,9", "15,0", "15,1", "15,2",
"15,3", "15,4", "15,5", "15,6", "15,7", "15,8", "15,9", "156,1",
"1569,2", "157,3", "157,6", "158,5", "16,0", "16,1", "16,2",
"16,3", "16,4", "16,5", "16,6", "16,7", "16,8", "16,9", "162,4",
"165,6", "17,0", "17,1", "17,2", "17,3", "17,4", "17,5", "17,6",
"17,7", "17,8", "17,9", "18,0", "18,2", "18,3", "18,4", "18,5",
"18,6", "18,7", "18,8", "18,9", "180,9", "181,4", "19,0", "19,1",
"19,3", "19,4", "19,5", "19,6", "19,7", "19,8", "19,9", "2,1",
"2,3", "2,5", "2,7", "2,8", "20,0", "20,1", "20,3", "20,5", "20,7",
"208,1", "21,0", "21,1", "21,3", "21,5", "21,6", "21,8", "2101,8",
"22,0", "22,1", "22,4", "22,5", "22,6", "225,8", "23,1", "23,2",
"23,3", "23,6", "23,9", "24,3", "24,9", "25,3", "25,4", "253,7",
"254,9", "255,3", "26,9", "27,7", "277,6", "278,9", "279,3",
"28,0", "288,3", "29,6", "297,3", "299,6", "3,2", "3,3", "3,8",
"30,3", "303,8", "32,1", "32,4", "32,5", "32,6", "32,7", "32,9",
"322,0", "322,2", "326,4", "326,7", "328,9", "329,4", "33,1",
"33,2", "33,3", "33,4", "33,5", "33,6", "33,7", "33,8", "33,9",
"331,4", "34,0", "34,4", "34,5", "34,7", "34,9", "35,0", "35,3",
"35,5", "35,6", "35,7", "35,8", "35,9", "36,0", "36,1", "36,2",
"36,3", "36,4", "36,5", "36,6", "36,7", "36,8", "36,9", "37,0",
"37,1", "37,2", "37,3", "37,4", "37,5", "37,6", "37,8", "37,9",
"370,8", "375,6", "38,0", "38,1", "38,2", "38,3", "38,4", "38,5",
"38,6", "38,7", "38,8", "38,9", "39,0", "39,1", "39,2", "39,3",
"39,4", "39,6", "39,7", "39,8", "39,9", "396,2", "40,1", "40,2",
"40,3", "40,7", "40,9", "41,3", "41,4", "41,6", "41,7", "41,8",
"41,9", "42,7", "42,8", "421,0", "43,5", "43,7", "433,0", "44,2",
"446,1", "448,9", "449,3", "45,4", "45,8", "47,7", "472,8", "49,2",
"492,3", "494,9", "497,9", "507,6", "520,8", "54,4", "541,6",
"575,4", "577,4", "6,6", "6,8", "60,0", "61,2", "61,4", "61,5",
"61,6", "61,7", "61,9", "619,1", "62,3", "62,9", "63,0", "63,5",
"64,0", "64,1", "64,6", "642,8", "646,2", "65,8", "663,5", "666,2",
"671,6", "7,2", "7,8", "708,7", "711,6", "8,1", "8,2", "8,3",
"8,5", "8,7", "8,8", "8,9", "804,0", "829,0", "856,0", "87,0",
"87,4", "87,5", "88,1", "88,3", "9,0", "9,1", "9,3", "9,5", "9,7",
"9,8", "9,9", "90,9", "928,2", "975,8"), class = "factor")), .Names = "HOURS.at.sea", class = "data.frame", row.names = c(NA,
-913L))
If the commas are thousands separators, a common problem when users save a formatted Excel spreadsheet as *.csv and then try to import it into R, then you have two problems. Commas are not allowed in numbers in R (or they are interpreted as decimal point - depends on your locale setting) so, e.g. as.numeric("1,000") will return NA, not 1000. You have to get rid of the commas and also convert from factor to numeric.
a <- factor(c("10","20","30","40","50"))
as.numeric(a) # returns the factor codes!!
# [1] 1 2 3 4 5
as.numeric(as.character(a)) # returns the factor levels, as numeric
# [1] 10 20 30 40 50
b <- factor(c(10,20,30,40,50))
as.numeric(b) # returns the factor codes!!
# [1] 1 2 3 4 5
c <- factor(c("1,000","2,000","3,000","4,000","5,000"))
as.numeric(c) # returns the factor codes
# [1] 1 2 3 4 5
as.numeric(as.character(c)) # returns NA - commas are NOT allowed in numbers in R
# [1] NA NA NA NA NA
# Warning message:
# NAs introduced by coercion
as.numeric(gsub(",","",c,fixed=TRUE))
# [1] 1000 2000 3000 4000 5000
In the last line, gsub(",","",c,fixed=TRUE) just removes the commas.
EDIT
As #CarlWitthoft points out in the comment, if the commas are decimal separators, you can import the data using:
df <- read.csv("mydata.csv", dec=",")
This will avoid a lot of problems later. Given the (already imported) dataset you present in the question, this will fix it:
datatest$HOURS.at.sea <- as.numeric(gsub(",",".",datatest$HOURS.at.sea,fixed=TRUE))
This replaces the "," with ".". Since gsub(...) returns a character vector, not a factor, you can use as.numeric(...) directly on that. Notice that you still get some NAs, because some of the rows have "#VALUE!" - looks like an Excel dump.