MCAgeDepth 0.1: Probabilistic age-depth models for continuous sediment records
User’s Guide, updated December, 2008 Philip Higuera Montana State University, University of Illinois
[email protected] www.montana.edu/phiguera This program has been placed in the public domain with the understanding that it will not be used for profit and that the user has read and agrees to the disclaimer. The program has been tested, though not rigorously, and is correct to the best of my knowledge. If you find any errors or have suggestions for improvement, please contact me at the e-mail above.
Contents 1 2 3 3.1
Background . . . . . . . Program Requirements Input Data . . . . . . . . Input data in the .xls file 3.1.1 InputParams . . 3.1.2 InputData . . . . 3.1.3 Pb210Data . . . 3.2 .B00 files from Calib . . 4 Running the Program . 5 Output Data . . . . . . . 5.1 calibDates . . . . . . . . 5.2 chronology . . . . . . . 6 Disclaimer . . . . . . . . 7 References . . . . . . .
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1 Background
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2
Background
MCAgeDepth is a program for developing age-depth models from 14 C and 210 Pb dates in continuous sediment records. Age-depth models predict the age of different stratigraphic levels in a sediment core based on a limited number of estimated ages from radiometric dates. With both 14 C and 210 Pb dates, age estimates have associated uncertainty, and in the case of 14 C, uncertainty is often not normally distributed. MCAgeDepth uses a Monte Carlo approach to generate confidence intervals that incorporate the probabilistic nature of calibrated 14 C dates 210 Pb dates. For each of a user-defined number of simulations, a chronology is made based on ages randomly selected from the probability distribution of each date. Randomly-selected ages come from a normal distribution in the case of 210 Pb dates and from the calibrated probability distribution output from the program Calib (Reimer et al., 2004) in the case of 14 C dates. The importance of each age in the fitted spline is weighted based on its standard deviation, such that ages with larger associated errors have less influence in the model (c.f. Telford et al. 2004a). The MCAgeDepth program has been used in the following publications: Higuera et al. (in press), Whitlock et al. (in press), and Briles et al. (2008).
2
Program Requirements
Matlab *or* MCRInstaller MCAgeDepth can be run from within Matlab or as a standalone program on Windows machines (MCAgeDepth.exe). Download the .m files for use in Matlab or the .exe file for use in Windows (XP or Vista) from the website: http://www. montana.edu/phiguera/software Microsoft Excel MCAgeDepth uses (and requires) Excel to interface with the input data and return the output data. Download the .xls template file from the website: http: //www.montana.edu/phiguera/software/software.html .B00 files from Calib The program Calib (available online for free: http://calib. qub.ac.uk/calib/) is used to calibrate 14 C dates against different calibration curves. MCAgeDepth uses the .B00 output files from Calib as part of the input files. Calibrate your dates as you would normally in Calib, but be sure to select “write output file” and then place the .B00 files in the same directory as you input .xls file. NOTE, you also have to replace all “#” symbols in the .B00 files with “%”. The “%” symbol tells Matlab to ignore the text following the symbol. Alternatively, you could delete all non-numeric data from the .B00 files.
3 Input Data
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Input Data
Each section below corresponds to a tab in the .xls file provided, templateAgeDepthData.xls. Fill in this file with your parameters and data, and then save the file under a new name.
3.1
Input data in the .xls file
Use the templateAgeDepthData.xls file to input the data to be used to construct the agedepth model, in the three tabs listed below: 3.1.1
InputParams
Input the parameters used to generate the age-depth model, plot the age-depth model, and save the results. SiteName Text used to label figure x_min Minimum depth (cm) to plot x_max Maximum depth (cm) to plot y_min Minimum age(yr BP) to plot y_max Maximum age (yr BP) to plot spline stiffness - 210 Pb Spline stiffness for the 210 Pb chronology. This varies from 01, where 1 = natural cubic spline, and 0 = linear regression. If you input 0, then this parameter will be determined based on the number of samples in the 210 Pb chronology, as follows:p = 1/(1 + h3 /60), where pis spline stiffness and h is the average distance (cm) between all 210 Pb dates. spline stiffness - 14 C
Same as above, except using the formula:p = 1/(1 + h3 /12).
alpha Alpha level for confidence intervals around calibrated dates and chronology. mc_runs Number of Monte Carlo simulations used to generate confidence intervals for age-depth model.
3 Input Data
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save data 1 = save data and figures; 0 = do not save. The figure is saves as a .tiff file with 300 dpi resolution, and the data are saved in the output file. Be sure the input file is closed if you want the data to be saves. 3.1.2
InputData
DateFile Each row in this column corresponds to the .B00 file associated with each 14 C date. Input the exact name of the .B00 file. The program uses this text to open each .B00 file. TopCm Input the top depth (cm) of each 14 C date. BottomCm Input the bottom depth (cm) of each14 C date. C14Age Input the 14 C age of each sample. C14Error Input the standard deviation associated with each14 C age. GoodDate? Input “1” if you want the 14 C date to be used in the chronology or “0” if you want the date plotted but not used in the chronology. sampleCm Input all depth (cm) for which you want an age predicted. This column will have many more value than all the other columns, one for each point in your age-depth curve. e.g., if you have a charcoal sample every 0.5 cm depth, input depth at 0.5-cm intervals in this columns. 3.1.3
Pb210Data
topCm Input the top depth (cm) of each 210 Pb date. ageBP Input the age (yr BP) at the top of each 210 Pb date. ageStd Input the standard deviation of each 210 Pb date.
4 Running the Program
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calibDates After the program has run, this sheet serves as a table for reporting raw and calibrated 14 C dates. Columns A through E are repeated information from the columns A through E in the “inputData” tab, thus you can copy the data from the “inputData” tab here. Columns F through H will be filled in after the program runs (if “saveData” = 1; describe below in “OutputData” section).
3.2
.B00 files from Calib
Place your .B00 files in the same directory as your .xls input data file. NOTE, you also have to replace all “#” symbols in the .B00 files with “%”. The “%” symbol tells Matlab to ignore the text following the symbol. Alternatively, you could delete all non-numeric data from the .B00 files.
4
Running the Program
From within Matlab, input “MCAgeDepth” in the command window and the program will start (so long as the file MCAgeDepth.m is in the working directory or a directory in Matlab’s path). At this point the command window will behave as the window opened when the self-executable file MCAgeDepth.exe is opened. The program prompts the user for the name of the input file. Input the full file name (including the suffix) in single quotation marks. e.g., ’exampleFile.xls’. The program will run, returning information to the command line, produce a figure, and save the figure and results (if you selected to do so).
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Output Data
Output data are placed within the “calibDates” and “chronology” tabs in the input file, as described below.
5.1
calibDates
After the program has run, this sheet serves as a table for reporting raw and calibrated 14 C dates. Columns A through E are repeated information from the columns A through E in the “inputData” tab, thus you can copy the data from the “inputData” tab here. Columns F through H will be filled in after the program has run with the median of the calibrated 14 C date (e.g., Telford et al., 2004b) and the selected confidence intervals (if “saveData” = 1).
6 Disclaimer
5.2
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chronology
Output data go into the “chronology” tab, described below. sampleCm Depth (cm) for each predicted age. calAge Calender age (yr BP) predicted for each depth in sampleCm. calAgeUci Upper confidence interval for calAge. calAgeLci Lower confidence interval for calAge. sedAcc Sediment accumulation rate (cm yr−1 ) for each sample. sedAccUci Upper confidence interval for sedAcc. sedAccLci Lower confidence interval for sedAcc. sampleRes Sample resolution (yr sample−1 ) for each sample. sampleResUci Upper confidence interval for sampleRes. sampleResLci Lower confidence interval for sampleRes.
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Disclaimer
THIS SOFTWARE PROGRAM AND DOCUMENTATION ARE PROVIDED “AS IS” AND WITHOUT WARRANTIES AS TO PERFORMANCE. THE PROGRAM MCAgeDepth IS PROVIDED WITHOUT ANY EXPRESSED OR IMPLIED WARRANTIES WHATSOEVER. BECAUSE OF THE DIVERSITY OF CONDITIONS AND HARDWARE UNDER WHICH THE PROGRAM MAY BE USED, NO WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE IS OFFERED. THE USER IS ADVISED TO TEST THE PROGRAM THOROUGHLY BEFORE RELYING ON IT. THE USER MUST ASSUME THE ENTIRE RISK AND RESPONSIBILITY OF USING THIS PROGRAM.
THE USE OF THE SOFTWARE DOWNLOADED FROM THE MONTANA STATE UNIVERSITY WEBSITE IS DONE AT YOUR OWN RISK AND WITH AGREEMENT THAT YOU ARE SOLELY RESPONSIBLE FOR ANY DAMAGE TO YOUR COMPUTER SYSTEM OR LOSS OF DATA THAT RESULTS FROM SUCH ACTIVITIES.
7 References
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References
References Briles, C. E., C. Whitlock, P. J. Bartlein, and P. E. Higuera. 2008. Regional and local controls on postglacial vegetation and fire in the Siskiyou Mountains, northern California, USA. Palaeogeography Palaeoclimatology Palaeoecology 265:159–169. Higuera, P. E., L. B. Brubaker, P. M. Anderson, F. S. Hu, and T. A. Brown. in press. Vegetation mediated the impacts of postglacial climate change on fire regimes in the southcentral Brooks Range, Alaska. Ecological Monographs . Reimer, P. J., M. G. L. Baillie, E. Bard, A. Bayliss, J. W. Beck, C. J. H. Bertrand, P. G. Blackwell, C. E. Buck, G. S. Burr, K. B. Cutler, P. E. Damon, R. L. Edwards, R. G. Fairbanks, M. Friedrich, T. P. Guilderson, A. G. Hogg, K. A. Hughen, B. Kromer, G. McCormac, S. Manning, C. B. Ramsey, R. W. Reimer, S. Remmele, J. R. Southon, M. Stuiver, S. Talamo, F. W. Taylor, J. van der Plicht, and C. E. Weyhenmeyer. 2004. IntCal04 terrestrial radiocarbon age calibration, 0-26 cal kyr BP. Radiocarbon 46:1029–1058. Telford, R. J., E. Heegaard, and H. J. B. Birks. 2004a. All age-depth models are wrong: but how badly? Quaternary Science Reviews 23:1–5. Telford, R. J., E. Heegaard, and H. J. B. Birks. 2004b. The intercept is a poor estimate of a calibrated radiocarbon age. The Holocene 14:296–298.
