INSTRUCTIONS FOR USE OF HYBIM CODE (Ibarra and Chamberlain, 2015, American Journal of Science)



NOTES: 

- The following are instructions for use of HyBIM with A) the example dataset from Lake Miragoane, Haiti (Curtis and Hodell, 1993) and B) modification for use with any time series of d18O, Sr/Ca, and Mg/Ca derived from biogenic carbonate.

- The code and these instructions are provided “as is”

- Two figures will be created by the code 1) plot of the kernel smoothing of the raw inputted data; 2) results of the volume and temperature changes over the time series

- The "np" package is required for kernel smoothing and determining bandwidths. This package can be installed by typing "install.packages("np”)”. Similarly the "MASS" package is required for the "ginv" function (for matrix inversion and solving the system of equations)

- The input dataset (csv file) should be sorted from oldest to youngest. The required headers for the input dataset are "Age", "d18O", "Mg.Ca", "Sr.Ca”, where M.Ca values are given in mole ratio/1000 and d18O is in per mil





A) Lake Miragoane, Haiti Example

- The code requires one input csv file based on the dataset from Appendix 1 of Curtis and Hodell (1993), imported in line 13. https://urldefense.proofpoint.com/v2/url?u=http-3A__dx.doi.org_10.1029_GM078p0135&d=AwIGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=Mx7exv4Cdf8UlvCwAsMt_A&m=6mivVMVsamByZQ727T5bwLiHWfRtnu8bhaiHk-9IROc&s=Evek5KoW4DFHnKNiWB4zhKcxnCw-86X3rVDqgWbQcrU&e= . The data from both the long and short core should be combined and sorted from oldest to youngest.







B) Application any biogenic carbonate time series.

The following lines of HyBIM will need to be changed to apply this model to any biogenic carbonate time series:

- Line 72: Linear interpolation of data set to evenly spaced time series. “age.out” is the vector of ages that the time series will be interpolated to, set by the user.

- Lines 94 to 109: The limits of the x-axis (time) should be adjusted as appropriate for the time series.

- Line 113: The number of Monte Carlo iterations can be adjusted here.

- Lines 123 to 136: Input parameters should all be adjusted as appropriate to the lake system (stream/lake chemistry values) and species-specific calibrations. 

- Lines 164-166 (and 22 to 29): Other kernel smoothing functions can be substituted for the the “Epanechnikov” kernel.

- Lines 274 to 295: The limits of the x-axis (time) should be adjusted as appropriate for the time series.