These codes produce the results of figure S1. The files used are located in the folder named “Datations” and contain the AMS dating for the three sediment cores.
#install.packages("Bchron") #if not already installed
library("Bchron")
## Warning: package 'Bchron' was built under R version 4.0.5
dirs<-c('Datations/')
Files<-list.files(dirs)
Rosalia<-read.table(file='Datations/Rosalia_AMS.txt',h=T)
Rosalia_output = Bchronology(ages=Rosalia$ages,ageSds=Rosalia$ageSds,
calCurves=Rosalia$calCurves,positions=Rosalia$position,
positionThicknesses=Rosalia$thickness,ids=Rosalia$id,
predictPositions=seq(0,143,by=0.5))
summary(Rosalia_output) # Default is for quantiles of ages at predictPosition values
## Quantiles of predicted ages by depth:
## Depth 2.5% 25% 50% 75% 97.5%
## 0.0 -68.000 -67.00 -66.0 -65.00 -64.000
## 0.5 -55.000 -33.00 -16.0 53.00 508.050
## 1.0 -45.000 0.00 33.0 158.25 735.125
## 1.5 -35.000 35.00 83.0 245.00 939.225
## 2.0 -25.000 68.00 132.5 321.25 1139.175
## 2.5 -12.000 101.75 182.0 397.00 1248.000
## 3.0 -1.000 136.75 232.0 464.00 1323.175
## 3.5 9.975 171.00 280.0 544.25 1450.250
## 4.0 21.975 205.00 330.0 608.50 1475.375
## 4.5 35.925 241.75 378.0 660.25 1522.175
## 5.0 47.975 276.00 425.0 717.50 1561.350
## 5.5 59.975 309.75 472.5 771.25 1618.375
## 6.0 71.000 346.25 520.5 823.50 1708.400
## 6.5 82.975 382.75 569.0 880.25 1743.750
## 7.0 94.000 417.75 616.5 938.25 1792.100
## 7.5 106.950 448.00 664.0 984.50 1817.450
## 8.0 117.000 485.00 711.5 1028.25 1870.125
## 8.5 127.975 521.00 759.5 1069.25 1894.300
## 9.0 143.950 556.00 803.0 1120.00 1927.025
## 9.5 160.900 591.75 851.0 1161.50 1945.275
## 10.0 176.925 620.00 900.5 1225.50 1962.300
## 10.5 189.900 657.00 947.0 1266.25 1980.325
## 11.0 203.000 693.75 992.5 1317.75 2011.275
## 11.5 215.975 730.25 1040.5 1362.50 2060.225
## 12.0 238.000 770.50 1092.0 1400.25 2086.425
## 12.5 249.900 817.00 1138.0 1443.25 2135.450
## 13.0 265.925 852.75 1180.0 1492.00 2171.275
## 13.5 278.925 883.00 1230.5 1536.00 2180.425
## 14.0 290.925 923.75 1274.5 1578.00 2212.175
## 14.5 303.925 978.00 1320.5 1626.50 2241.075
## 15.0 344.975 1044.75 1368.0 1661.00 2265.050
## 15.5 368.825 1076.75 1412.0 1697.75 2284.075
## 16.0 394.700 1122.50 1459.0 1738.00 2301.000
## 16.5 428.825 1175.00 1499.0 1779.00 2319.250
## 17.0 443.825 1226.25 1541.0 1826.50 2345.025
## 17.5 474.725 1275.50 1588.5 1862.25 2361.025
## 18.0 494.975 1318.50 1641.0 1899.25 2373.150
## 18.5 534.625 1371.75 1685.5 1939.00 2387.200
## 19.0 578.000 1410.75 1736.5 1971.00 2404.175
## 19.5 606.900 1463.50 1784.5 2012.50 2425.050
## 20.0 634.750 1508.25 1831.5 2052.25 2439.025
## 20.5 694.375 1558.50 1881.0 2092.25 2451.075
## 21.0 754.450 1616.75 1926.0 2128.25 2470.025
## 21.5 789.800 1666.00 1969.5 2165.25 2481.050
## 22.0 841.725 1720.00 2014.0 2201.25 2494.000
## 22.5 913.975 1774.50 2060.5 2230.00 2508.150
## 23.0 997.400 1835.50 2110.5 2271.25 2525.025
## 23.5 1112.950 1898.00 2160.0 2309.25 2537.100
## 24.0 1174.550 1964.75 2211.5 2347.25 2553.025
## 24.5 1254.950 2030.00 2259.0 2387.00 2569.025
## 25.0 1374.950 2103.00 2305.5 2425.25 2585.025
## 25.5 1460.575 2182.00 2359.0 2466.25 2600.050
## 26.0 1549.850 2263.75 2408.0 2506.00 2617.075
## 26.5 1751.725 2342.75 2459.0 2547.00 2637.000
## 27.0 1990.825 2434.75 2516.0 2593.00 2668.025
## 27.5 2269.825 2507.00 2591.0 2655.00 2770.000
## 28.0 2456.000 2557.00 2637.5 2695.00 2903.175
## 28.5 2481.925 2596.00 2673.0 2730.00 3031.125
## 29.0 2496.950 2624.00 2701.0 2767.00 3081.325
## 29.5 2515.950 2646.00 2724.0 2801.25 3147.100
## 30.0 2530.000 2670.75 2748.5 2842.00 3179.125
## 30.5 2543.000 2695.00 2775.0 2881.25 3205.000
## 31.0 2556.875 2716.00 2799.0 2911.25 3255.375
## 31.5 2571.825 2737.00 2823.5 2937.25 3292.250
## 32.0 2591.900 2759.75 2852.0 2960.25 3318.125
## 32.5 2601.925 2783.75 2879.5 2991.25 3340.075
## 33.0 2611.925 2804.75 2904.5 3019.25 3369.025
## 33.5 2627.775 2825.00 2932.0 3047.50 3381.025
## 34.0 2637.975 2848.00 2958.5 3073.75 3390.000
## 34.5 2653.900 2871.00 2984.5 3100.25 3399.000
## 35.0 2662.000 2896.50 3009.0 3132.00 3409.025
## 35.5 2679.950 2918.00 3034.0 3160.00 3423.125
## 36.0 2694.950 2941.75 3061.0 3182.00 3438.025
## 36.5 2713.950 2965.75 3086.0 3208.00 3445.025
## 37.0 2726.975 2989.75 3113.5 3230.25 3456.000
## 37.5 2742.975 3016.00 3142.0 3253.00 3469.025
## 38.0 2758.825 3039.75 3168.0 3278.00 3479.025
## 38.5 2780.950 3060.75 3196.5 3297.25 3483.100
## 39.0 2800.825 3087.50 3224.5 3319.00 3494.075
## 39.5 2812.975 3121.00 3251.0 3340.00 3505.075
## 40.0 2835.950 3156.00 3278.0 3363.00 3515.025
## 40.5 2859.775 3190.75 3303.5 3385.25 3522.075
## 41.0 2887.950 3219.50 3331.0 3408.00 3533.000
## 41.5 2915.775 3254.00 3359.0 3431.00 3542.025
## 42.0 2934.825 3288.25 3385.0 3451.00 3551.025
## 42.5 2959.900 3318.00 3411.0 3471.00 3559.025
## 43.0 2984.825 3355.50 3438.0 3492.00 3567.000
## 43.5 3045.850 3394.00 3466.5 3513.00 3576.025
## 44.0 3105.975 3433.00 3495.0 3533.00 3586.025
## 44.5 3165.575 3469.75 3524.0 3553.00 3597.025
## 45.0 3223.950 3512.75 3553.0 3574.00 3615.000
## 45.5 3375.975 3556.00 3582.0 3608.25 3710.025
## 46.0 3505.925 3587.00 3618.0 3656.00 3890.000
## 46.5 3583.000 3625.00 3662.0 3711.00 4004.025
## 47.0 3609.000 3664.75 3711.5 3770.00 4070.025
## 47.5 3623.000 3705.00 3756.0 3830.25 4114.275
## 48.0 3640.000 3746.00 3799.0 3881.00 4151.125
## 48.5 3652.925 3788.00 3843.5 3929.25 4201.050
## 49.0 3666.950 3829.00 3886.5 3978.25 4224.125
## 49.5 3679.925 3871.75 3932.0 4024.00 4251.000
## 50.0 3703.925 3914.00 3976.5 4068.25 4269.075
## 50.5 3722.950 3960.75 4023.0 4101.50 4283.075
## 51.0 3740.000 4003.00 4066.0 4138.50 4307.000
## 51.5 3758.000 4047.75 4110.0 4179.00 4329.050
## 52.0 3792.950 4090.75 4153.0 4216.00 4349.050
## 52.5 3832.000 4137.00 4198.0 4253.00 4367.050
## 53.0 3886.975 4181.00 4240.5 4289.00 4383.000
## 53.5 3966.975 4226.75 4281.0 4327.00 4400.050
## 54.0 4073.975 4279.00 4326.0 4367.00 4423.025
## 54.5 4240.975 4332.00 4381.0 4421.00 4653.025
## 55.0 4318.000 4387.75 4434.0 4488.00 4993.050
## 55.5 4343.000 4430.00 4479.0 4567.50 5284.125
## 56.0 4366.950 4462.00 4523.0 4643.00 5338.100
## 56.5 4383.975 4493.75 4570.0 4725.00 5486.450
## 57.0 4398.000 4521.75 4615.0 4793.25 5586.025
## 57.5 4414.975 4553.75 4657.5 4856.25 5653.100
## 58.0 4429.975 4584.00 4702.0 4917.50 5712.325
## 58.5 4440.950 4615.50 4745.5 4978.25 5783.025
## 59.0 4455.975 4646.00 4787.5 5036.50 5875.100
## 59.5 4475.000 4680.00 4830.0 5098.50 5907.175
## 60.0 4490.975 4711.75 4872.5 5145.50 5941.400
## 60.5 4510.925 4741.75 4915.5 5201.00 5964.550
## 61.0 4527.975 4772.75 4958.5 5245.50 6005.050
## 61.5 4541.850 4803.75 5000.0 5296.25 6048.100
## 62.0 4560.950 4836.75 5046.5 5336.25 6101.000
## 62.5 4584.775 4868.00 5091.0 5373.00 6143.150
## 63.0 4597.875 4906.00 5134.5 5420.25 6174.075
## 63.5 4610.000 4943.00 5178.5 5454.75 6193.175
## 64.0 4632.850 4979.75 5220.5 5504.75 6206.150
## 64.5 4651.975 5006.75 5263.5 5547.00 6224.025
## 65.0 4664.000 5047.25 5305.0 5593.25 6237.025
## 65.5 4679.000 5090.75 5348.0 5626.25 6251.100
## 66.0 4695.900 5127.00 5390.5 5686.75 6292.075
## 66.5 4722.750 5168.00 5429.0 5727.00 6307.425
## 67.0 4738.775 5214.50 5472.0 5770.25 6320.400
## 67.5 4748.000 5247.25 5514.5 5804.25 6332.400
## 68.0 4769.900 5293.50 5558.0 5834.00 6366.100
## 68.5 4791.975 5334.75 5600.0 5876.00 6389.025
## 69.0 4808.825 5369.50 5644.0 5916.00 6412.000
## 69.5 4828.925 5411.50 5687.0 5946.50 6423.325
## 70.0 4845.925 5457.00 5730.0 5987.50 6435.275
## 70.5 4894.450 5500.75 5772.0 6019.50 6447.250
## 71.0 4915.900 5538.75 5817.5 6058.00 6458.250
## 71.5 4936.975 5580.00 5859.0 6092.25 6470.175
## 72.0 4972.900 5622.75 5900.0 6125.50 6486.025
## 72.5 5021.675 5662.75 5942.0 6162.25 6498.025
## 73.0 5050.800 5711.75 5986.0 6194.25 6512.000
## 73.5 5075.850 5756.25 6031.5 6226.25 6526.050
## 74.0 5096.875 5799.50 6074.0 6260.25 6551.075
## 74.5 5149.775 5844.00 6117.5 6294.00 6561.050
## 75.0 5171.900 5898.75 6158.5 6329.25 6571.000
## 75.5 5202.725 5952.00 6201.5 6361.25 6581.025
## 76.0 5255.350 6012.25 6241.0 6393.00 6591.050
## 76.5 5311.000 6063.50 6284.5 6419.25 6601.025
## 77.0 5371.575 6123.50 6325.0 6449.00 6610.075
## 77.5 5436.725 6176.00 6370.0 6479.00 6621.000
## 78.0 5553.650 6231.50 6413.0 6507.00 6628.025
## 78.5 5661.625 6290.75 6456.0 6536.00 6638.050
## 79.0 5794.500 6357.00 6499.0 6567.00 6649.025
## 79.5 5861.775 6432.75 6544.0 6599.00 6659.025
## 80.0 5998.700 6518.00 6592.0 6633.00 6686.025
## 80.5 6206.950 6596.75 6643.0 6669.00 6746.000
## 81.0 6515.900 6648.00 6672.0 6700.00 6847.100
## 81.5 6642.000 6673.00 6696.0 6737.00 6924.025
## 82.0 6650.000 6690.75 6719.5 6767.00 7022.050
## 82.5 6660.950 6705.00 6739.5 6801.25 7077.050
## 83.0 6668.975 6719.00 6760.0 6831.00 7112.000
## 83.5 6674.000 6733.00 6779.0 6861.00 7133.300
## 84.0 6677.975 6748.00 6798.0 6887.25 7202.050
## 84.5 6685.950 6763.75 6816.0 6909.00 7251.100
## 85.0 6688.975 6777.00 6835.5 6938.00 7281.000
## 85.5 6694.950 6792.00 6855.0 6968.25 7310.025
## 86.0 6704.000 6805.00 6873.5 6997.00 7332.075
## 86.5 6710.975 6818.00 6892.5 7015.25 7352.000
## 87.0 6715.000 6834.00 6911.0 7034.25 7360.025
## 87.5 6719.975 6847.75 6929.5 7056.25 7374.050
## 88.0 6724.950 6864.00 6949.0 7076.00 7386.125
## 88.5 6732.925 6878.00 6968.0 7099.00 7400.025
## 89.0 6740.900 6892.00 6986.0 7117.25 7408.250
## 89.5 6753.975 6908.00 7003.0 7138.25 7431.050
## 90.0 6759.000 6926.00 7021.0 7158.00 7448.100
## 90.5 6768.925 6937.75 7039.0 7181.50 7467.100
## 91.0 6773.925 6954.00 7059.0 7202.00 7484.000
## 91.5 6780.000 6971.00 7079.0 7218.25 7501.050
## 92.0 6784.975 6983.50 7094.0 7235.00 7514.025
## 92.5 6791.975 7000.00 7112.0 7255.25 7522.000
## 93.0 6797.000 7016.00 7132.5 7273.00 7534.050
## 93.5 6803.975 7038.00 7151.5 7289.25 7542.075
## 94.0 6814.975 7050.25 7170.0 7305.25 7551.050
## 94.5 6827.975 7068.00 7187.5 7321.00 7564.050
## 95.0 6837.000 7082.25 7206.0 7337.00 7571.000
## 95.5 6848.975 7098.00 7226.0 7355.75 7577.025
## 96.0 6857.950 7114.75 7244.0 7371.25 7587.000
## 96.5 6872.975 7131.75 7262.5 7390.00 7595.025
## 97.0 6879.975 7151.00 7282.0 7402.25 7604.200
## 97.5 6900.950 7168.75 7301.0 7412.25 7617.025
## 98.0 6909.975 7187.75 7318.0 7428.25 7627.000
## 98.5 6923.975 7202.50 7338.0 7444.25 7632.125
## 99.0 6930.975 7222.75 7357.0 7460.25 7643.025
## 99.5 6937.975 7241.50 7376.5 7476.25 7648.025
## 100.0 6955.900 7264.75 7395.5 7493.00 7654.025
## 100.5 6969.000 7284.75 7413.0 7507.25 7660.000
## 101.0 6984.825 7299.50 7432.0 7526.25 7665.000
## 101.5 6996.000 7321.00 7449.0 7539.00 7671.000
## 102.0 7007.900 7339.00 7466.0 7554.00 7680.100
## 102.5 7018.950 7360.50 7484.0 7568.25 7685.100
## 103.0 7031.975 7382.75 7502.0 7580.00 7692.000
## 103.5 7039.975 7408.50 7519.5 7593.00 7698.050
## 104.0 7057.900 7426.00 7537.0 7604.25 7706.025
## 104.5 7078.675 7452.75 7554.0 7618.25 7716.000
## 105.0 7109.450 7473.00 7573.5 7633.00 7720.000
## 105.5 7156.825 7495.75 7592.0 7646.00 7725.000
## 106.0 7172.950 7512.00 7609.5 7660.00 7730.000
## 106.5 7201.825 7539.75 7625.5 7674.00 7738.000
## 107.0 7223.900 7563.75 7645.0 7687.25 7745.025
## 107.5 7305.250 7595.00 7663.0 7700.25 7753.025
## 108.0 7354.600 7632.00 7682.0 7715.00 7762.025
## 108.5 7435.675 7670.75 7702.0 7730.25 7773.000
## 109.0 7567.000 7703.75 7726.0 7751.00 7785.025
## 109.5 7710.975 7750.00 7781.0 7820.00 8193.150
## 110.0 7735.975 7790.00 7837.0 7930.25 8608.150
## 110.5 7752.975 7823.00 7890.0 8027.50 8839.375
## 111.0 7769.975 7857.00 7942.5 8122.25 9032.650
## 111.5 7784.000 7892.00 7996.5 8205.00 9150.625
## 112.0 7798.000 7925.75 8048.0 8284.75 9247.300
## 112.5 7810.975 7959.00 8098.5 8358.25 9356.300
## 113.0 7823.000 7996.00 8151.5 8424.00 9409.050
## 113.5 7837.925 8032.00 8203.0 8488.25 9511.175
## 114.0 7848.975 8065.75 8251.0 8566.50 9540.025
## 114.5 7860.950 8100.75 8299.0 8635.25 9629.025
## 115.0 7873.950 8137.75 8351.0 8702.50 9744.250
## 115.5 7887.950 8177.00 8399.0 8758.00 9792.250
## 116.0 7899.000 8212.75 8450.0 8808.50 9869.200
## 116.5 7910.925 8250.00 8504.0 8872.25 9885.325
## 117.0 7922.875 8287.50 8550.0 8912.75 9922.125
## 117.5 7936.950 8326.00 8604.5 8965.50 9961.025
## 118.0 7952.925 8376.75 8656.5 9025.00 9988.150
## 118.5 7964.950 8418.00 8706.5 9072.25 10005.475
## 119.0 7992.850 8463.00 8762.5 9131.75 10050.000
## 119.5 8012.950 8500.75 8807.5 9192.50 10070.150
## 120.0 8027.875 8555.00 8855.5 9237.25 10086.075
## 120.5 8042.950 8597.25 8908.0 9287.25 10112.650
## 121.0 8057.900 8635.00 8959.0 9329.75 10155.450
## 121.5 8070.900 8667.75 9008.5 9384.25 10171.600
## 122.0 8087.900 8708.75 9060.5 9448.00 10188.700
## 122.5 8102.875 8759.00 9110.0 9487.50 10204.800
## 123.0 8120.925 8796.25 9159.0 9536.25 10233.500
## 123.5 8146.650 8844.50 9207.5 9593.25 10278.025
## 124.0 8159.700 8890.50 9258.5 9649.25 10325.225
## 124.5 8192.900 8942.00 9310.0 9700.25 10387.150
## 125.0 8234.525 8987.75 9360.5 9751.00 10407.250
## 125.5 8271.750 9042.00 9408.0 9789.25 10426.075
## 126.0 8295.925 9101.00 9459.0 9822.25 10446.125
## 126.5 8307.975 9139.00 9507.0 9856.25 10465.000
## 127.0 8324.950 9185.75 9561.0 9894.25 10499.400
## 127.5 8376.650 9222.75 9611.0 9945.75 10538.150
## 128.0 8395.725 9283.25 9654.0 9982.25 10563.225
## 128.5 8412.975 9333.50 9711.0 10023.25 10586.200
## 129.0 8432.900 9370.50 9762.0 10061.00 10613.100
## 129.5 8462.700 9431.00 9809.5 10101.25 10627.050
## 130.0 8528.350 9477.50 9864.0 10135.25 10641.075
## 130.5 8576.600 9533.50 9909.0 10172.50 10664.125
## 131.0 8642.275 9581.25 9953.0 10217.50 10676.100
## 131.5 8691.700 9638.50 10001.0 10259.50 10687.100
## 132.0 8753.675 9687.75 10051.5 10305.50 10702.050
## 132.5 8780.875 9743.50 10100.5 10340.25 10714.200
## 133.0 8825.000 9805.25 10146.5 10384.75 10733.125
## 133.5 8869.625 9852.75 10202.0 10432.00 10766.100
## 134.0 8913.750 9903.75 10250.5 10471.25 10788.225
## 134.5 8982.400 9966.00 10298.5 10511.00 10820.200
## 135.0 9045.450 10030.25 10351.0 10549.00 10833.225
## 135.5 9124.600 10099.50 10401.5 10586.75 10855.000
## 136.0 9194.975 10155.50 10453.0 10622.00 10875.050
## 136.5 9275.475 10213.75 10506.0 10658.25 10885.125
## 137.0 9294.850 10284.00 10552.5 10697.00 10904.100
## 137.5 9338.875 10359.50 10599.0 10734.50 10923.100
## 138.0 9528.375 10440.00 10645.0 10767.25 10948.125
## 138.5 9683.775 10526.75 10696.5 10807.25 10979.075
## 139.0 9853.850 10608.75 10750.0 10853.00 11005.000
## 139.5 10041.925 10698.75 10804.0 10906.25 11034.050
## 140.0 10331.875 10776.50 10866.0 10972.00 11138.525
## 140.5 10665.575 10839.75 10945.5 11045.25 11439.150
## 141.0 10796.975 10896.00 11012.5 11116.00 11667.775
## 141.5 10816.000 10935.00 11056.5 11190.25 11955.400
## 142.0 10830.925 10966.00 11094.0 11255.25 12068.425
## 142.5 10843.975 10995.00 11130.5 11322.25 12203.000
## 143.0 10855.975 11019.75 11168.5 11379.25 12342.225
summary(Rosalia_output, type='convergence') # Check model convergence
## Convergence check (watch for too many small p-values):
## p-value
## RateMean 0.00903
## Outlier 3 0.02243
## Outlier 5 0.03239
## RateVar 0.07826
## Outlier 2 0.07844
## Outlier 4 0.08759
## ULA-7272 0.09171
## ULA-9710 0.11318
## Outlier 1 0.15866
## ULA-9709 0.16391
## ULA-7269 0.23983
## ULA-7271 0.24596
## Outlier 6 0.35450
## Top-1 0.40730
## ULA-7270 0.46414
## Outlier 7 0.49709
summary(Rosalia_output, type='outliers') # Look at outlier probabilities
## Posterior outlier probability by date:
## Date OutlierProb
## Top-1 0.003
## ULA-7269 0.005
## ULA-7270 0.006
## ULA-9709 0.013
## ULA-7271 0.010
## ULA-9710 0.011
## ULA-7272 0.008
plot(Rosalia_output,xlab='Age (cal years BP)',ylab='Depth (cm)',las=1)
dirs<-c('Datations/')
Files<-list.files(dirs)
Pikku<-read.table(file='Datations/Pikku_AMS.txt',h=T)
Pikku_output = Bchronology(ages=Pikku$ages,ageSds=Pikku$ageSds,
calCurves=Pikku$calCurves,positions=Pikku$position,
positionThicknesses=Pikku$thickness,ids=Pikku$id,
predictPositions=seq(0,131,by=0.5))
summary(Pikku_output) # Default is for quantiles of ages at predictPosition values
## Quantiles of predicted ages by depth:
## Depth 2.5% 25% 50% 75% 97.5%
## 0.0 -68.000 -67.00 -66.0 -65.00 -64.000
## 0.5 -59.000 -42.25 -34.0 -12.00 251.000
## 1.0 -51.025 -19.00 -3.0 36.50 381.125
## 1.5 -43.025 5.00 28.0 83.00 455.100
## 2.0 -36.025 28.75 59.0 121.50 498.000
## 2.5 -28.050 51.75 90.0 166.00 522.025
## 3.0 -21.050 77.00 120.0 207.25 548.175
## 3.5 -12.025 102.00 151.0 236.25 581.050
## 4.0 -2.000 129.00 182.0 272.25 596.225
## 4.5 9.950 155.00 214.5 306.25 625.000
## 5.0 20.950 179.00 246.0 336.50 639.000
## 5.5 30.950 205.00 278.5 371.00 654.150
## 6.0 39.975 229.00 307.5 411.25 669.150
## 6.5 49.975 257.00 338.0 443.25 686.075
## 7.0 65.975 289.75 367.5 473.25 702.075
## 7.5 81.975 325.00 398.0 500.25 715.000
## 8.0 92.950 351.75 427.5 527.25 728.025
## 8.5 120.950 388.00 460.0 554.00 746.025
## 9.0 138.950 419.75 492.0 577.25 761.075
## 9.5 152.950 447.00 523.0 609.25 770.025
## 10.0 183.825 476.75 554.0 636.25 782.000
## 10.5 199.000 510.00 585.0 663.00 796.125
## 11.0 234.800 536.00 614.0 687.00 814.025
## 11.5 250.950 575.50 644.0 712.00 826.025
## 12.0 267.925 609.75 676.5 737.00 836.025
## 12.5 304.675 641.75 706.0 761.00 851.000
## 13.0 338.900 674.00 735.0 787.00 866.025
## 13.5 393.850 708.00 764.0 811.00 878.025
## 14.0 470.850 745.00 791.0 835.25 892.025
## 14.5 561.950 786.75 822.0 868.00 911.000
## 15.0 718.975 827.00 865.0 912.00 1053.100
## 15.5 818.975 879.00 926.0 972.25 1295.225
## 16.0 865.975 930.00 976.0 1037.25 1406.025
## 16.5 888.000 975.00 1026.0 1093.25 1480.025
## 17.0 913.000 1019.00 1076.0 1153.00 1537.175
## 17.5 933.950 1069.00 1127.0 1212.75 1589.125
## 18.0 950.000 1115.75 1178.0 1264.75 1634.025
## 18.5 967.000 1165.00 1228.5 1321.25 1671.025
## 19.0 988.975 1214.00 1282.0 1372.00 1696.150
## 19.5 1005.950 1265.00 1333.5 1420.00 1734.075
## 20.0 1027.825 1315.00 1385.0 1469.25 1756.050
## 20.5 1055.925 1362.75 1433.0 1517.00 1789.125
## 21.0 1084.875 1415.00 1485.0 1556.25 1809.150
## 21.5 1109.950 1466.00 1536.0 1606.00 1837.050
## 22.0 1135.950 1515.75 1586.0 1656.00 1854.025
## 22.5 1160.000 1569.75 1638.5 1702.25 1870.000
## 23.0 1223.700 1627.00 1691.0 1747.00 1888.000
## 23.5 1267.800 1679.75 1740.0 1795.50 1904.025
## 24.0 1346.950 1733.00 1792.0 1841.00 1921.025
## 24.5 1428.950 1791.00 1844.0 1885.00 1940.025
## 25.0 1553.925 1857.00 1895.0 1928.00 1974.000
## 25.5 1804.000 1920.00 1946.0 1975.00 2068.100
## 26.0 1916.975 1959.75 1987.0 2020.00 2225.100
## 26.5 1935.000 1985.00 2016.0 2067.00 2409.025
## 27.0 1949.975 2004.00 2044.0 2111.00 2479.425
## 27.5 1961.975 2025.00 2072.0 2150.50 2547.000
## 28.0 1969.975 2044.00 2099.0 2189.25 2579.200
## 28.5 1979.000 2065.00 2126.5 2224.00 2614.050
## 29.0 1990.000 2085.00 2152.0 2265.00 2663.075
## 29.5 1998.975 2109.00 2176.0 2302.25 2712.075
## 30.0 2008.000 2128.75 2204.0 2333.00 2750.075
## 30.5 2014.000 2146.75 2232.0 2365.00 2792.025
## 31.0 2024.900 2168.00 2260.0 2391.25 2840.025
## 31.5 2031.975 2191.75 2286.0 2417.25 2852.075
## 32.0 2039.950 2213.50 2310.0 2444.25 2864.100
## 32.5 2045.000 2234.75 2335.5 2476.25 2882.250
## 33.0 2053.975 2254.75 2360.0 2505.00 2893.150
## 33.5 2063.975 2276.00 2386.5 2535.00 2918.025
## 34.0 2075.900 2300.00 2413.0 2563.50 2946.150
## 34.5 2086.975 2320.25 2438.0 2588.00 2980.175
## 35.0 2100.975 2345.00 2463.0 2617.25 2996.075
## 35.5 2114.925 2365.75 2490.0 2640.50 3019.075
## 36.0 2129.950 2387.75 2516.0 2661.25 3032.050
## 36.5 2140.000 2410.00 2542.0 2690.00 3045.000
## 37.0 2145.000 2430.75 2568.0 2709.50 3059.025
## 37.5 2153.000 2452.75 2594.0 2743.50 3068.025
## 38.0 2165.875 2480.75 2620.0 2767.00 3078.025
## 38.5 2199.900 2505.00 2644.5 2790.25 3089.125
## 39.0 2208.925 2530.75 2669.0 2815.25 3098.150
## 39.5 2217.950 2556.75 2696.0 2844.50 3119.225
## 40.0 2240.975 2582.75 2721.5 2864.00 3136.050
## 40.5 2263.850 2605.00 2749.0 2883.25 3143.050
## 41.0 2273.850 2628.00 2780.0 2909.25 3157.050
## 41.5 2279.950 2653.75 2803.0 2934.00 3164.050
## 42.0 2287.975 2683.75 2829.5 2960.25 3173.075
## 42.5 2312.000 2708.00 2857.0 2982.00 3181.075
## 43.0 2324.950 2737.00 2880.5 3003.25 3195.000
## 43.5 2336.925 2764.75 2907.5 3019.50 3203.025
## 44.0 2362.650 2787.00 2936.0 3037.75 3214.000
## 44.5 2395.000 2819.75 2960.0 3055.00 3225.025
## 45.0 2426.650 2847.00 2985.5 3075.00 3236.025
## 45.5 2446.975 2877.00 3009.5 3098.50 3247.000
## 46.0 2495.950 2909.00 3039.0 3119.00 3254.025
## 46.5 2538.700 2943.50 3064.0 3140.00 3262.025
## 47.0 2563.900 2979.50 3088.5 3160.00 3271.000
## 47.5 2594.750 3010.75 3114.5 3180.00 3280.025
## 48.0 2641.600 3043.00 3141.0 3201.25 3291.025
## 48.5 2673.775 3079.75 3166.0 3224.00 3301.000
## 49.0 2705.925 3121.00 3193.0 3243.00 3312.025
## 49.5 2810.800 3162.00 3220.0 3265.00 3325.025
## 50.0 2974.000 3205.00 3247.5 3290.00 3347.000
## 50.5 3093.800 3242.75 3284.5 3328.25 3456.400
## 51.0 3191.875 3277.00 3320.0 3359.00 3599.325
## 51.5 3260.000 3314.75 3357.0 3403.00 3771.075
## 52.0 3279.975 3344.75 3387.5 3451.00 3835.100
## 52.5 3295.975 3370.00 3419.0 3491.25 3909.050
## 53.0 3308.950 3395.00 3449.0 3532.25 3951.025
## 53.5 3320.000 3422.75 3481.0 3568.00 3990.475
## 54.0 3330.000 3449.75 3511.5 3608.25 4034.025
## 54.5 3340.975 3473.00 3543.0 3645.75 4060.125
## 55.0 3353.000 3494.75 3576.0 3683.25 4101.150
## 55.5 3364.975 3519.75 3610.0 3728.25 4132.100
## 56.0 3376.000 3543.00 3642.0 3767.00 4150.025
## 56.5 3387.975 3568.00 3671.0 3798.25 4168.000
## 57.0 3398.950 3592.00 3701.0 3825.25 4183.000
## 57.5 3410.975 3618.75 3734.0 3860.00 4199.050
## 58.0 3422.925 3645.75 3767.5 3889.25 4216.100
## 58.5 3435.000 3674.00 3801.0 3922.25 4234.100
## 59.0 3448.950 3698.75 3831.5 3954.00 4255.100
## 59.5 3459.000 3723.00 3864.0 3986.50 4282.050
## 60.0 3468.975 3754.25 3895.0 4027.25 4299.050
## 60.5 3479.925 3778.75 3926.0 4057.00 4314.025
## 61.0 3494.875 3810.75 3957.0 4082.25 4329.000
## 61.5 3512.950 3839.75 3991.0 4110.25 4344.000
## 62.0 3525.925 3869.75 4020.5 4140.00 4359.025
## 62.5 3548.900 3906.00 4051.0 4168.00 4377.000
## 63.0 3579.950 3945.25 4081.5 4191.00 4388.025
## 63.5 3613.000 3977.50 4110.5 4217.00 4405.000
## 64.0 3624.975 4009.00 4143.0 4242.50 4420.050
## 64.5 3646.825 4040.00 4173.0 4264.00 4432.050
## 65.0 3663.850 4072.00 4203.5 4292.25 4449.025
## 65.5 3682.000 4106.25 4234.0 4316.00 4465.000
## 66.0 3711.625 4145.75 4264.5 4343.25 4477.050
## 66.5 3739.750 4184.50 4295.0 4368.00 4488.075
## 67.0 3789.950 4224.00 4328.5 4394.25 4500.025
## 67.5 3827.850 4267.00 4362.5 4422.25 4514.000
## 68.0 3898.325 4312.75 4395.0 4447.00 4525.050
## 68.5 3976.900 4364.00 4424.0 4477.00 4540.000
## 69.0 4095.625 4413.00 4453.5 4507.00 4559.000
## 69.5 4327.950 4460.00 4511.0 4548.00 4761.025
## 70.0 4460.975 4510.00 4557.5 4601.00 4920.250
## 70.5 4480.000 4547.00 4595.0 4653.00 5088.125
## 71.0 4493.975 4573.00 4631.0 4705.00 5171.050
## 71.5 4509.000 4601.00 4667.0 4764.25 5256.275
## 72.0 4521.950 4631.00 4698.5 4807.25 5324.350
## 72.5 4539.950 4662.00 4733.0 4852.00 5384.125
## 73.0 4551.775 4689.75 4767.0 4891.00 5410.175
## 73.5 4563.000 4720.00 4802.0 4937.00 5451.225
## 74.0 4571.975 4748.00 4836.0 4981.00 5477.000
## 74.5 4579.975 4775.00 4868.5 5016.00 5497.025
## 75.0 4592.950 4803.25 4902.0 5060.00 5544.075
## 75.5 4609.900 4824.00 4935.0 5094.00 5573.225
## 76.0 4620.975 4856.50 4967.0 5128.25 5604.075
## 76.5 4632.975 4884.00 4999.0 5169.50 5616.175
## 77.0 4643.000 4913.00 5033.0 5201.00 5637.075
## 77.5 4650.975 4947.75 5067.5 5229.25 5659.050
## 78.0 4666.850 4980.75 5105.0 5260.25 5674.000
## 78.5 4680.950 5015.00 5139.0 5293.25 5707.050
## 79.0 4696.825 5042.75 5173.0 5327.00 5718.025
## 79.5 4712.925 5074.75 5204.0 5363.25 5729.000
## 80.0 4752.450 5104.75 5235.0 5390.00 5745.125
## 80.5 4778.600 5133.00 5271.0 5416.00 5755.075
## 81.0 4802.700 5161.50 5302.0 5443.00 5776.050
## 81.5 4822.000 5193.00 5336.5 5470.50 5790.025
## 82.0 4839.950 5229.75 5370.5 5503.00 5799.025
## 82.5 4853.000 5264.00 5405.5 5525.25 5808.025
## 83.0 4865.975 5305.00 5439.0 5562.00 5819.025
## 83.5 4888.975 5334.00 5473.0 5589.75 5829.025
## 84.0 4912.975 5362.00 5504.0 5622.25 5841.025
## 84.5 4936.675 5396.75 5538.0 5653.00 5853.000
## 85.0 4967.850 5429.50 5574.0 5680.25 5864.025
## 85.5 5008.000 5466.00 5606.0 5712.25 5877.000
## 86.0 5049.550 5509.00 5640.0 5735.00 5889.050
## 86.5 5074.925 5546.00 5673.0 5759.00 5901.025
## 87.0 5124.675 5583.00 5706.0 5784.25 5909.050
## 87.5 5160.775 5625.75 5738.0 5809.25 5915.100
## 88.0 5189.825 5671.75 5772.0 5837.00 5924.050
## 88.5 5259.000 5718.75 5805.0 5862.00 5936.000
## 89.0 5299.950 5763.75 5840.0 5885.00 5947.000
## 89.5 5399.950 5811.00 5873.0 5910.00 5960.000
## 90.0 5494.775 5861.75 5909.0 5937.00 5977.000
## 90.5 5707.825 5913.00 5941.0 5975.00 6093.200
## 91.0 5848.000 5949.00 5979.0 6017.25 6338.425
## 91.5 5940.000 5987.75 6018.0 6071.00 6456.025
## 92.0 5958.000 6015.00 6058.5 6126.25 6569.200
## 92.5 5971.975 6042.00 6097.0 6182.25 6656.000
## 93.0 5981.975 6068.00 6135.0 6235.25 6706.075
## 93.5 5996.975 6100.00 6172.0 6292.00 6767.075
## 94.0 6011.950 6128.50 6207.0 6337.00 6806.025
## 94.5 6022.000 6160.75 6243.0 6383.00 6832.225
## 95.0 6033.950 6185.50 6277.5 6417.00 6875.025
## 95.5 6042.000 6212.75 6313.5 6459.00 6896.300
## 96.0 6055.900 6243.00 6350.0 6493.25 6934.300
## 96.5 6066.950 6272.00 6387.0 6536.25 6973.150
## 97.0 6084.975 6302.75 6426.0 6574.25 6988.650
## 97.5 6094.000 6326.75 6464.0 6606.50 7032.125
## 98.0 6115.725 6355.75 6500.0 6643.00 7053.050
## 98.5 6129.000 6385.00 6535.0 6683.50 7073.000
## 99.0 6143.950 6418.50 6570.0 6709.25 7088.150
## 99.5 6161.850 6448.75 6608.0 6744.00 7112.050
## 100.0 6183.625 6489.00 6644.0 6778.00 7127.025
## 100.5 6197.975 6525.75 6682.0 6803.25 7154.075
## 101.0 6213.850 6565.25 6716.0 6837.75 7170.050
## 101.5 6227.950 6591.75 6753.0 6879.50 7182.025
## 102.0 6248.850 6629.00 6790.0 6909.75 7195.000
## 102.5 6262.975 6663.25 6824.0 6943.00 7209.075
## 103.0 6287.800 6704.75 6860.0 6973.00 7224.025
## 103.5 6303.000 6741.00 6896.5 7002.00 7239.075
## 104.0 6318.950 6782.00 6934.0 7032.00 7252.000
## 104.5 6338.975 6823.75 6972.5 7063.25 7263.025
## 105.0 6371.000 6864.75 7008.0 7095.25 7278.025
## 105.5 6395.975 6901.00 7046.0 7126.25 7292.000
## 106.0 6419.950 6943.75 7083.0 7153.00 7305.000
## 106.5 6456.925 6988.00 7120.0 7186.00 7319.000
## 107.0 6497.725 7035.50 7157.0 7219.00 7330.050
## 107.5 6555.700 7084.00 7193.0 7248.00 7344.000
## 108.0 6628.700 7141.50 7230.0 7279.00 7357.000
## 108.5 6720.950 7199.00 7268.0 7308.00 7372.000
## 109.0 6802.750 7260.00 7307.0 7336.00 7389.000
## 109.5 7080.900 7314.00 7342.5 7373.00 7413.025
## 110.0 7340.000 7375.00 7409.0 7444.00 7683.125
## 110.5 7366.975 7425.00 7463.0 7534.00 8055.225
## 111.0 7387.975 7468.00 7517.0 7619.50 8225.325
## 111.5 7405.000 7510.00 7570.5 7690.75 8385.200
## 112.0 7419.975 7552.00 7624.0 7768.00 8434.700
## 112.5 7434.975 7590.50 7678.0 7837.25 8488.275
## 113.0 7446.950 7634.75 7731.0 7904.50 8569.075
## 113.5 7460.925 7674.50 7783.0 7975.00 8659.050
## 114.0 7476.925 7718.75 7838.0 8037.25 8701.200
## 114.5 7493.950 7762.75 7893.0 8099.75 8741.075
## 115.0 7509.975 7799.50 7946.5 8163.00 8776.575
## 115.5 7530.875 7844.75 8001.0 8227.75 8817.125
## 116.0 7542.000 7891.00 8051.5 8283.25 8858.075
## 116.5 7568.925 7935.00 8104.0 8333.50 8896.025
## 117.0 7616.975 8000.75 8156.5 8386.50 8916.100
## 117.5 7635.950 8053.50 8211.0 8434.00 8938.325
## 118.0 7653.925 8091.25 8264.0 8485.25 8975.075
## 118.5 7677.875 8121.75 8316.0 8532.25 9004.050
## 119.0 7703.950 8171.00 8371.0 8573.50 9035.025
## 119.5 7739.975 8233.00 8422.0 8612.50 9058.025
## 120.0 7771.975 8287.50 8477.0 8657.75 9081.100
## 120.5 7800.875 8332.75 8528.5 8705.50 9100.025
## 121.0 7829.850 8384.00 8583.5 8749.50 9120.000
## 121.5 7865.925 8427.75 8635.0 8794.00 9139.050
## 122.0 7916.525 8471.50 8690.0 8840.25 9158.050
## 122.5 7954.850 8531.00 8743.0 8886.50 9180.075
## 123.0 8013.700 8591.75 8793.0 8928.25 9199.025
## 123.5 8040.575 8644.00 8845.0 8975.00 9220.025
## 124.0 8066.975 8706.75 8898.0 9021.50 9240.025
## 124.5 8152.450 8782.50 8954.0 9065.00 9261.050
## 125.0 8184.000 8832.00 9004.5 9108.00 9280.075
## 125.5 8215.800 8890.75 9059.0 9152.00 9300.100
## 126.0 8319.150 8954.00 9111.5 9194.00 9326.100
## 126.5 8410.875 9031.75 9165.0 9238.00 9347.000
## 127.0 8511.975 9107.75 9220.0 9278.00 9374.025
## 127.5 8676.175 9186.75 9275.0 9325.00 9412.000
## 128.0 8903.300 9265.00 9328.0 9380.00 9490.450
## 128.5 9161.975 9326.00 9374.5 9428.25 9705.075
## 129.0 9318.000 9369.00 9419.0 9488.00 9906.150
## 129.5 9331.000 9394.75 9451.0 9549.25 10107.125
## 130.0 9338.000 9413.00 9477.0 9599.25 10253.200
## 130.5 9346.950 9429.00 9506.0 9664.00 10346.300
## 131.0 9352.975 9444.00 9537.5 9705.25 10454.075
summary(Pikku_output, type='convergence') # Check model convergence
## Convergence check (watch for too many small p-values):
## p-value
## ULA-7908 0.00166
## Outlier 4 0.01238
## Outlier 3 0.07844
## Outlier 5 0.11672
## Outlier 7 0.15866
## Outlier 2 0.16063
## ULA-7296 0.16851
## Top-1 0.17551
## Outlier 1 0.21691
## ULA-7295 0.21768
## Outlier 8 0.34768
## ULA-7297 0.35543
## Outlier 6 0.36157
## RateVar 0.39559
## ULA-9712 0.47179
## RateMean 0.48422
## ULA-7298 0.49252
## ULA-9711 0.49640
summary(Pikku_output, type='outliers') # Look at outlier probabilities
## Posterior outlier probability by date:
## Date OutlierProb
## Top-1 0.006
## ULA-7908 0.014
## ULA-7295 0.008
## ULA-7296 0.006
## ULA-9711 0.006
## ULA-7297 0.010
## ULA-9712 0.005
## ULA-7298 0.013
plot(Pikku_output,xlab='Age (cal years BP)',ylab='Depth (cm)',las=1)
dirs<-c('Datations/')
Files<-list.files(dirs)
Charly<-read.table(file='Datations/Charly_AMS.txt',h=T)
Charly_output = Bchronology(ages=Charly$ages,ageSds=Charly$ageSds,
calCurves=Charly$calCurves,positions=Charly$position,
positionThicknesses=Charly$thickness,ids=Charly$id,
predictPositions=seq(0,144,by=0.5))
summary(Charly_output) # Default is for quantiles of ages at predictPosition values
## Quantiles of predicted ages by depth:
## Depth 2.5% 25% 50% 75% 97.5%
## 0.0 -68.000 -66.00 -66.0 -65.00 -64.000
## 0.5 -56.000 -37.00 -32.0 -19.00 251.175
## 1.0 -45.000 -8.00 1.0 27.00 393.050
## 1.5 -35.000 20.00 35.0 73.00 459.125
## 2.0 -25.025 49.00 68.0 120.25 531.050
## 2.5 -15.025 77.00 102.0 166.25 570.075
## 3.0 -5.025 106.00 135.0 209.50 589.100
## 3.5 4.975 136.00 169.0 251.25 616.000
## 4.0 14.975 166.00 202.0 293.25 651.075
## 4.5 24.975 195.00 235.0 330.00 668.125
## 5.0 34.975 227.00 269.0 369.25 686.150
## 5.5 44.975 256.00 302.0 402.25 708.075
## 6.0 57.925 283.00 336.0 439.25 736.050
## 6.5 67.925 310.75 369.0 460.25 748.300
## 7.0 86.875 341.75 403.0 490.00 772.025
## 7.5 103.975 369.75 436.0 516.25 783.050
## 8.0 117.000 403.75 469.0 542.25 794.000
## 8.5 136.900 435.00 502.0 568.25 811.050
## 9.0 152.000 471.75 535.0 596.25 821.025
## 9.5 168.950 499.00 568.0 626.00 831.000
## 10.0 191.875 531.75 601.0 649.25 840.000
## 10.5 208.900 561.75 634.0 674.25 852.000
## 11.0 241.700 594.75 667.0 702.25 862.000
## 11.5 264.950 635.75 700.0 734.00 872.050
## 12.0 289.000 670.75 733.5 767.25 883.025
## 12.5 330.625 709.00 767.0 802.00 893.025
## 13.0 359.975 752.75 801.0 831.00 904.000
## 13.5 394.000 798.00 834.0 862.00 916.000
## 14.0 464.625 840.75 869.0 892.00 929.000
## 14.5 619.950 881.00 903.0 923.00 947.000
## 15.0 808.975 921.00 937.5 959.00 1053.075
## 15.5 933.000 958.00 978.0 1002.25 1254.100
## 16.0 958.975 994.00 1017.0 1048.00 1345.000
## 16.5 973.000 1031.00 1056.0 1088.00 1393.025
## 17.0 988.000 1069.00 1096.0 1130.00 1462.125
## 17.5 1001.000 1107.00 1135.5 1169.00 1497.050
## 18.0 1015.000 1145.00 1174.5 1209.25 1521.025
## 18.5 1028.975 1183.75 1214.0 1249.00 1549.050
## 19.0 1043.000 1221.00 1253.5 1289.00 1577.175
## 19.5 1058.000 1259.00 1292.0 1329.00 1613.050
## 20.0 1071.000 1296.00 1331.5 1369.00 1626.050
## 20.5 1086.975 1334.00 1370.5 1407.00 1639.025
## 21.0 1104.000 1371.00 1410.0 1447.25 1655.000
## 21.5 1119.975 1409.00 1450.0 1489.25 1671.025
## 22.0 1139.975 1448.75 1490.0 1529.25 1687.025
## 22.5 1160.950 1486.75 1530.0 1568.00 1703.000
## 23.0 1185.850 1525.00 1568.0 1605.00 1719.000
## 23.5 1201.975 1564.00 1606.0 1642.00 1736.025
## 24.0 1247.900 1603.00 1645.0 1679.25 1752.025
## 24.5 1327.800 1643.00 1684.0 1712.00 1776.025
## 25.0 1436.875 1690.75 1722.0 1749.00 1804.000
## 25.5 1642.775 1731.00 1753.0 1783.00 1836.025
## 26.0 1725.000 1748.75 1770.0 1799.00 1851.025
## 26.5 1730.000 1754.00 1777.0 1805.00 1860.000
## 27.0 1734.000 1759.00 1783.0 1810.00 1870.100
## 27.5 1738.975 1764.00 1788.0 1815.25 1876.000
## 28.0 1742.975 1769.00 1792.0 1821.00 1882.000
## 28.5 1745.000 1774.00 1797.0 1825.00 1885.025
## 29.0 1748.000 1778.00 1802.0 1830.00 1891.025
## 29.5 1751.975 1783.00 1806.0 1833.00 1899.025
## 30.0 1754.975 1787.00 1810.5 1837.25 1901.025
## 30.5 1758.000 1791.00 1815.0 1842.25 1906.025
## 31.0 1761.000 1796.00 1819.0 1847.00 1907.050
## 31.5 1763.000 1800.75 1824.0 1852.00 1912.000
## 32.0 1765.000 1805.00 1829.0 1856.25 1915.000
## 32.5 1767.000 1810.00 1834.0 1862.00 1917.000
## 33.0 1770.000 1815.00 1838.0 1865.00 1919.000
## 33.5 1772.975 1820.00 1842.0 1869.00 1922.000
## 34.0 1773.975 1824.00 1846.0 1873.00 1924.025
## 34.5 1776.000 1829.00 1851.0 1877.00 1929.000
## 35.0 1778.000 1833.00 1855.0 1880.25 1932.000
## 35.5 1780.000 1838.00 1859.0 1885.00 1935.025
## 36.0 1782.975 1842.00 1864.0 1889.00 1938.000
## 36.5 1785.000 1847.00 1868.0 1892.25 1940.000
## 37.0 1789.975 1851.00 1872.5 1896.25 1942.000
## 37.5 1793.000 1856.00 1877.0 1901.00 1944.000
## 38.0 1796.950 1860.00 1882.0 1905.00 1946.025
## 38.5 1800.000 1865.00 1886.0 1909.00 1950.000
## 39.0 1803.925 1869.00 1890.0 1912.00 1953.025
## 39.5 1807.975 1873.00 1894.0 1916.00 1958.000
## 40.0 1811.000 1877.00 1898.5 1920.00 1961.000
## 40.5 1816.975 1883.00 1903.0 1924.00 1964.000
## 41.0 1822.000 1887.00 1908.0 1928.00 1969.000
## 41.5 1828.950 1892.00 1913.0 1932.00 1972.000
## 42.0 1838.000 1897.00 1917.0 1938.00 1975.000
## 42.5 1847.975 1901.75 1922.0 1942.00 1979.000
## 43.0 1860.000 1909.00 1930.0 1951.00 1988.000
## 43.5 1877.950 1919.00 1938.0 1962.00 2023.025
## 44.0 1894.000 1927.75 1948.0 1974.00 2071.050
## 44.5 1904.000 1940.00 1960.0 1988.00 2100.075
## 45.0 1914.000 1950.00 1974.0 2001.00 2135.025
## 45.5 1919.975 1961.00 1983.5 2013.00 2145.025
## 46.0 1925.000 1971.00 1995.0 2026.00 2153.125
## 46.5 1931.000 1982.00 2005.0 2037.00 2164.025
## 47.0 1937.000 1991.00 2016.0 2049.00 2179.000
## 47.5 1942.000 2000.00 2026.0 2063.00 2188.000
## 48.0 1948.875 2010.00 2038.0 2075.00 2198.000
## 48.5 1954.925 2019.00 2049.0 2086.00 2206.000
## 49.0 1959.000 2027.00 2061.0 2097.00 2214.025
## 49.5 1962.000 2036.00 2073.0 2107.00 2224.075
## 50.0 1966.975 2044.00 2084.0 2119.00 2232.000
## 50.5 1970.950 2053.00 2095.0 2129.00 2240.000
## 51.0 1975.925 2061.00 2107.0 2139.00 2245.025
## 51.5 1982.800 2069.00 2118.0 2150.00 2253.000
## 52.0 1986.800 2079.00 2129.0 2161.00 2258.025
## 52.5 1990.800 2088.00 2141.0 2171.00 2268.000
## 53.0 1995.975 2097.00 2152.0 2181.25 2271.050
## 53.5 2002.925 2107.00 2163.0 2193.00 2276.000
## 54.0 2008.950 2116.00 2174.0 2204.00 2281.050
## 54.5 2019.975 2126.00 2187.0 2215.00 2284.075
## 55.0 2035.000 2136.00 2199.0 2226.00 2288.050
## 55.5 2042.975 2145.00 2212.0 2237.00 2293.025
## 56.0 2050.000 2155.00 2224.0 2249.00 2296.025
## 56.5 2055.975 2164.75 2237.0 2261.00 2301.000
## 57.0 2069.000 2173.00 2250.0 2272.00 2307.000
## 57.5 2092.000 2183.75 2263.0 2284.00 2312.000
## 58.0 2101.925 2194.75 2275.0 2294.00 2315.050
## 58.5 2131.900 2205.00 2288.0 2305.00 2321.025
## 59.0 2164.950 2219.00 2303.0 2316.00 2331.000
## 59.5 2184.975 2267.00 2319.0 2338.00 2484.150
## 60.0 2218.975 2322.00 2351.0 2386.25 2740.725
## 60.5 2251.975 2351.00 2392.0 2439.00 2891.175
## 61.0 2277.950 2375.00 2432.0 2488.00 2983.250
## 61.5 2296.000 2405.00 2472.5 2544.50 3107.275
## 62.0 2320.950 2440.75 2514.0 2605.25 3178.350
## 62.5 2344.975 2472.00 2553.0 2654.00 3242.125
## 63.0 2366.950 2504.00 2594.0 2700.25 3296.025
## 63.5 2380.975 2542.00 2634.0 2747.25 3332.425
## 64.0 2394.975 2578.00 2673.5 2791.25 3387.225
## 64.5 2407.950 2613.75 2713.0 2838.00 3414.050
## 65.0 2420.950 2650.75 2754.0 2884.25 3461.150
## 65.5 2437.950 2682.75 2793.5 2930.25 3486.150
## 66.0 2452.900 2714.75 2833.0 2970.75 3507.325
## 66.5 2466.875 2747.00 2873.0 3010.00 3534.050
## 67.0 2479.800 2782.00 2913.0 3059.00 3549.025
## 67.5 2492.925 2811.00 2953.0 3097.25 3565.350
## 68.0 2513.750 2852.00 2994.0 3135.00 3592.200
## 68.5 2536.950 2887.00 3036.0 3171.25 3611.225
## 69.0 2567.350 2922.25 3077.5 3210.50 3622.300
## 69.5 2581.975 2961.00 3118.0 3246.50 3633.300
## 70.0 2598.950 2995.00 3158.0 3281.25 3656.050
## 70.5 2611.950 3034.75 3200.0 3318.50 3669.000
## 71.0 2634.950 3083.00 3241.0 3355.25 3682.100
## 71.5 2660.900 3117.50 3280.0 3387.25 3698.050
## 72.0 2683.950 3153.25 3319.5 3420.00 3710.025
## 72.5 2704.925 3183.50 3360.0 3455.00 3723.025
## 73.0 2725.875 3227.50 3399.0 3492.25 3736.025
## 73.5 2761.975 3276.00 3440.0 3526.25 3746.025
## 74.0 2784.975 3318.75 3481.5 3560.00 3757.025
## 74.5 2804.900 3364.25 3521.0 3598.00 3770.050
## 75.0 2874.650 3414.75 3563.5 3635.00 3781.000
## 75.5 2914.825 3471.75 3606.0 3673.00 3794.025
## 76.0 2981.650 3528.00 3645.5 3708.00 3810.075
## 76.5 3089.825 3586.00 3687.0 3743.25 3823.025
## 77.0 3162.975 3642.00 3728.0 3782.00 3842.000
## 77.5 3302.900 3709.00 3772.0 3819.00 3870.000
## 78.0 3469.900 3768.00 3822.0 3856.00 3938.000
## 78.5 3686.875 3817.00 3856.0 3885.25 4081.100
## 79.0 3758.950 3856.00 3885.0 3924.00 4206.700
## 79.5 3779.975 3876.75 3911.0 3963.25 4293.350
## 80.0 3800.975 3893.75 3937.0 4003.25 4385.075
## 80.5 3812.975 3910.75 3961.0 4044.00 4492.150
## 81.0 3825.975 3928.75 3986.0 4084.25 4551.750
## 81.5 3838.975 3945.00 4010.0 4119.00 4600.325
## 82.0 3850.875 3963.00 4032.5 4152.00 4633.175
## 82.5 3858.975 3982.00 4057.0 4185.50 4682.000
## 83.0 3868.000 4003.75 4081.0 4210.25 4710.275
## 83.5 3871.950 4023.00 4106.0 4239.25 4744.050
## 84.0 3881.950 4041.75 4129.0 4268.00 4757.100
## 84.5 3888.950 4059.75 4153.5 4298.00 4763.150
## 85.0 3899.975 4080.75 4177.0 4317.50 4793.125
## 85.5 3908.900 4103.75 4200.0 4346.50 4811.075
## 86.0 3914.925 4120.00 4224.0 4366.25 4821.075
## 86.5 3921.000 4141.00 4247.0 4391.00 4831.050
## 87.0 3926.000 4160.00 4271.0 4409.00 4842.225
## 87.5 3936.875 4181.75 4294.0 4436.00 4859.050
## 88.0 3948.950 4203.00 4318.0 4458.50 4866.000
## 88.5 3954.925 4219.00 4343.0 4481.25 4887.000
## 89.0 3961.975 4239.75 4366.0 4503.75 4896.125
## 89.5 3973.950 4256.25 4386.0 4530.00 4905.000
## 90.0 3981.925 4274.00 4410.0 4562.00 4917.000
## 90.5 3988.900 4294.75 4433.0 4582.25 4927.000
## 91.0 3994.900 4317.25 4455.0 4601.00 4933.075
## 91.5 4001.950 4336.50 4478.0 4625.25 4958.075
## 92.0 4007.925 4355.25 4502.0 4646.25 4967.075
## 92.5 4014.950 4370.75 4525.0 4664.25 4979.100
## 93.0 4021.950 4386.00 4548.0 4681.25 4988.100
## 93.5 4033.900 4401.00 4570.5 4699.00 5000.175
## 94.0 4050.000 4414.75 4595.0 4719.50 5017.025
## 94.5 4070.000 4440.00 4618.5 4741.75 5027.025
## 95.0 4081.975 4465.50 4642.0 4761.00 5038.025
## 95.5 4089.000 4484.25 4665.0 4776.50 5047.000
## 96.0 4113.925 4506.50 4687.0 4792.50 5056.025
## 96.5 4132.875 4533.00 4710.5 4809.50 5064.025
## 97.0 4149.975 4554.00 4734.0 4826.00 5072.000
## 97.5 4169.800 4571.50 4757.0 4844.00 5080.150
## 98.0 4190.925 4592.75 4780.0 4867.00 5091.125
## 98.5 4201.950 4616.50 4799.5 4887.00 5104.050
## 99.0 4224.975 4646.25 4822.0 4907.00 5115.000
## 99.5 4238.000 4674.75 4846.0 4929.25 5124.025
## 100.0 4257.925 4700.75 4868.5 4952.00 5135.025
## 100.5 4277.925 4728.00 4887.5 4975.25 5144.000
## 101.0 4309.825 4759.00 4912.0 4996.25 5148.025
## 101.5 4334.950 4785.75 4935.0 5018.00 5153.100
## 102.0 4358.600 4816.75 4959.5 5040.25 5163.000
## 102.5 4407.800 4847.00 4984.0 5060.25 5170.050
## 103.0 4453.925 4883.75 5007.5 5084.00 5178.100
## 103.5 4503.975 4915.75 5035.0 5106.25 5190.000
## 104.0 4551.975 4949.00 5059.5 5129.00 5200.025
## 104.5 4628.875 4976.00 5086.0 5151.25 5212.000
## 105.0 4670.875 5005.75 5110.0 5173.00 5224.000
## 105.5 4797.925 5038.00 5139.5 5194.25 5241.000
## 106.0 4964.875 5085.00 5178.0 5221.00 5263.025
## 106.5 5051.000 5151.75 5228.0 5269.25 5560.300
## 107.0 5074.000 5199.75 5268.0 5317.00 5880.000
## 107.5 5093.975 5228.00 5300.0 5364.00 6026.300
## 108.0 5112.000 5253.75 5330.0 5421.25 6121.500
## 108.5 5135.000 5278.75 5361.5 5479.50 6224.250
## 109.0 5153.000 5304.00 5395.0 5529.25 6325.250
## 109.5 5169.950 5331.00 5429.0 5579.00 6359.125
## 110.0 5183.950 5353.75 5464.5 5626.00 6409.150
## 110.5 5199.950 5377.00 5497.5 5673.00 6480.475
## 111.0 5212.950 5403.00 5530.0 5725.25 6523.450
## 111.5 5221.950 5430.00 5564.0 5767.25 6546.300
## 112.0 5232.000 5454.75 5595.5 5801.25 6575.225
## 112.5 5244.975 5476.75 5629.0 5855.25 6623.300
## 113.0 5257.875 5502.75 5659.0 5884.25 6669.900
## 113.5 5266.925 5524.50 5692.5 5930.00 6698.725
## 114.0 5276.925 5551.75 5725.5 5962.50 6748.125
## 114.5 5286.950 5579.75 5759.0 6002.50 6796.575
## 115.0 5299.925 5608.00 5790.0 6037.50 6821.675
## 115.5 5316.825 5628.00 5821.0 6073.00 6837.625
## 116.0 5323.925 5656.00 5853.5 6115.00 6875.100
## 116.5 5327.950 5681.50 5888.0 6149.75 6889.075
## 117.0 5338.925 5703.75 5927.0 6198.25 6912.200
## 117.5 5348.900 5730.75 5960.0 6225.00 6939.225
## 118.0 5373.600 5753.50 5994.5 6253.00 6960.025
## 118.5 5389.825 5780.50 6029.0 6294.00 6973.000
## 119.0 5400.825 5806.75 6059.5 6329.50 6988.500
## 119.5 5410.975 5840.75 6094.0 6359.25 7021.100
## 120.0 5428.975 5872.25 6127.0 6387.25 7043.300
## 120.5 5448.900 5894.75 6159.5 6419.25 7076.050
## 121.0 5458.850 5927.50 6193.0 6448.50 7090.075
## 121.5 5468.825 5957.25 6225.0 6476.00 7119.725
## 122.0 5483.900 5988.75 6259.0 6510.50 7158.075
## 122.5 5491.975 6021.25 6289.5 6540.25 7175.175
## 123.0 5501.000 6047.50 6322.5 6575.00 7192.000
## 123.5 5512.900 6074.25 6356.0 6607.25 7225.225
## 124.0 5533.875 6098.75 6388.0 6643.75 7243.100
## 124.5 5552.975 6132.50 6422.5 6673.00 7256.125
## 125.0 5571.750 6162.00 6456.0 6710.00 7265.000
## 125.5 5585.000 6205.25 6488.0 6743.00 7269.125
## 126.0 5597.875 6241.50 6523.0 6772.75 7280.075
## 126.5 5610.750 6270.50 6557.0 6799.25 7292.150
## 127.0 5623.950 6298.75 6589.0 6826.00 7306.150
## 127.5 5640.950 6338.75 6623.0 6851.00 7314.150
## 128.0 5681.650 6373.50 6655.0 6877.25 7329.050
## 128.5 5704.900 6401.00 6689.5 6904.25 7338.050
## 129.0 5714.925 6428.25 6721.5 6932.00 7347.050
## 129.5 5744.550 6455.25 6755.0 6964.25 7355.050
## 130.0 5756.625 6481.75 6786.0 6984.25 7364.025
## 130.5 5773.825 6525.00 6818.0 7015.25 7376.050
## 131.0 5813.000 6555.50 6849.0 7044.25 7386.175
## 131.5 5834.800 6579.50 6883.0 7072.00 7395.150
## 132.0 5866.675 6616.00 6917.0 7100.25 7409.000
## 132.5 5893.850 6652.50 6950.0 7127.25 7421.050
## 133.0 5919.750 6706.75 6984.5 7152.50 7426.150
## 133.5 5939.875 6744.00 7017.5 7180.00 7433.200
## 134.0 5995.200 6790.00 7049.5 7207.00 7449.025
## 134.5 6078.775 6834.75 7082.0 7230.25 7455.000
## 135.0 6131.750 6878.00 7118.0 7256.00 7460.025
## 135.5 6154.975 6914.75 7151.5 7282.25 7468.050
## 136.0 6198.675 6950.75 7185.0 7305.25 7477.025
## 136.5 6273.850 7001.75 7220.0 7328.25 7485.025
## 137.0 6303.825 7050.25 7254.0 7352.00 7495.025
## 137.5 6364.125 7094.75 7287.0 7377.00 7502.025
## 138.0 6409.775 7147.50 7320.0 7401.00 7513.025
## 138.5 6450.000 7196.75 7354.0 7428.00 7525.000
## 139.0 6521.725 7260.00 7388.0 7453.25 7535.000
## 139.5 6573.850 7318.75 7424.0 7477.00 7544.025
## 140.0 6689.950 7382.75 7459.0 7502.00 7556.025
## 140.5 6895.825 7443.00 7496.0 7529.25 7573.025
## 141.0 7175.800 7497.00 7531.0 7564.00 7651.300
## 141.5 7403.600 7531.00 7564.0 7595.00 7866.975
## 142.0 7521.000 7560.00 7591.0 7645.25 8104.375
## 142.5 7526.975 7575.00 7616.0 7706.00 8267.500
## 143.0 7530.000 7585.00 7638.5 7764.00 8374.075
## 143.5 7533.000 7596.00 7663.5 7815.00 8406.250
## 144.0 7536.000 7604.00 7686.0 7854.75 8521.200
summary(Charly_output, type='convergence') # Check model convergence
## Convergence check (watch for too many small p-values):
## p-value
## RateVar 0.00055
## RateMean 0.00206
## Outlier 4 0.00389
## Outlier 7 0.00389
## ULA-9715 0.01762
## Outlier 2 0.02243
## ULA-7907 0.02904
## Top-1 0.09001
## ULA-7299 0.12418
## ULA-7302 0.16159
## Outlier 1 0.27482
## Outlier 6 0.29694
## ULA-7301 0.32420
## ULA-7300 0.34252
## ULA-9714 0.37539
## Outlier 3 0.42540
## Outlier 5 0.42540
## Outlier 8 0.42872
summary(Charly_output, type='outliers') # Look at outlier probabilities
## Posterior outlier probability by date:
## Date OutlierProb
## Top-1 0.007
## ULA-7907 0.006
## ULA-7299 0.012
## ULA-7302 0.011
## ULA-9714 0.009
## ULA-7300 0.013
## ULA-9715 0.008
## ULA-7301 0.007
plot(Charly_output,xlab='Age (cal years BP)',ylab='Depth (cm)',las=1)