# shelltrace v3.5.1

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## Bivalve Growth and Trace Element Accumulation Model

Contains all the formulae of the growth and trace element uptake model described in the equally-named
Geoscientific Model Development paper (de Winter, 2017, <doi:10.5194/gmd-2017-137>). The model takes as input a file with X- and Y-coordinates of digitized
growth increments recognized on a longitudinal cross section through the bivalve shell, as well as a BMP file of an elemental map of the
cross section surface with chemically distinct phases separated by phase analysis. It proceeds by a step-by-step process described in
the paper, by which digitized growth increments are used to calculate changes in shell height, shell thickness, shell volume, shell mass
and shell growth rate through the bivalve's life time. Then, results of this growth modelling are combined with the trace element mapping
results to trace the incorporation of trace elements into the bivalve shell. Results of various modelling parameters can be exported in
the form of XLSX files.

## Functions in shelltrace

Name | Description | |

M_el_mat | Matrix of modelled mass accumulation rates per trace element | |

M_el_mat_c | Matrix of modelled cumulative mass accumulation rates per trace element | |

Oyster_Mass_gain | Formula that calculates mass increase of bivalve shell with time | |

Oyster_Shell_height | Formula that calculates shell height through time | |

Oyster_Convert_cross_section | Function that converts XY-data of digitized cross section | |

Oyster_Export | Function that exports data of the growth model | |

BMP | BMP image of phase map of cross section of modern oyster. | |

IncG | Interpolated subincrements in cross section of modern oyster rescaled to the same X-axis. | |

O1_input | Digitized growth increments in cross section of modern oyster. | |

O1_phase | Characteristics of phase in XRF map of oyster | |

Oyster_Shell_thickness | Formula that calculates average shell thickness through time | |

Oyster_Volumes | Formula that calculates volume of the shell through time | |

Oyster_combined_run | Runs the growth and trace element model | |

Oyster_el_time | Calculate concentrations of trace elements per sub-increment | |

Oyster_phase_matrix_BMP | Function that calculates phase matrix | |

Oyster_Z_matrices | Function that calculates matrices of Z-values for all sub-increments and all X-values | |

Oyster_accumulation | Calculate trace element accumulation rates | |

Oyster_length | Measured length of the shell | |

Oyster_phase_export | Export results of trace element model | |

Oyster_run_sec5 | Runs complete Step 5 of the trace element model | |

Oyster_ellipse_parameters | Function that calculates the parameters of the base ellipse used for bivalve growth modelling | |

Oyster_growth_run | Runs the entire growth model | |

Oyster_incr_area | Area between shell increments | |

Oyster_incr_cross_section | Formula that interpolates shell increments | |

Oyster_plot_incr_fill | Plot the result of interpolation of sub-increments with a coloured area plot | |

Oyster_run_sec6 | Runs complete Step 6 of the trace element model | |

image_length | Length (in mm) of the digitized phase map image. | |

incr_matrix0 | Matrix containing data calculated for each growth band. | |

phase_mat | Matrix listing the amount of pixels of each phase in every subincrement | |

Oyster_height | Measured height of the shell | |

Oyster_import_BMP | Function that imports a BMP of an XRF map | |

Oyster_phase_run | Runs the entire trace element model | |

Oyster_phase_stats | Function that exports phase statistics | |

Oyster_subincr_area | Formula that calculates area between sub-increments | |

Oyster_subincr_av_thickness | Formula that calculates average shell thickness through time | |

TIF | TIF image of phase map of cross section of modern oyster. | |

Z_mat | Z-values describing the base ellipse of the oyster | |

Oyster_run_sec2 | Runs complete Step 2 of the growth model | |

cross_section | Digitized growth increments in cross section of modern oyster rescaled to the same X-axis. | |

el_time | Matrix listing the concentrations of elements in every subincrement | |

incr_matrix1 | Matrix containing data calculated for each growth band. | |

incr_matrix2 | Matrix containing data calculated for each growth band. | |

subincr_matrix1 | Matrix containing data calculated for each growth band. | |

subincr_matrix2 | Matrix containing data calculated for each growth band. | |

pma | Function to do an n-point moving average | |

subincr_matrix0 | Matrix containing data calculated for each growth band. | |

subincr_matrix3 | Matrix containing data calculated for each growth band. | |

subincr_matrix4 | Matrix containing data calculated for each growth band. | |

phase_stat | Statistics of elemental concentrations in XRF map of oyster | |

Oyster_import_TIF | Function that imports a TIF file | |

Oyster_import_phases | Function that imports phase data | |

Oyster_plot_cross_section | Plot the converted shell cross section | |

Oyster_subincr_shell_height | A fomula to calculate shell height per sub-increment | |

Oyster_phase_matrix_TIF | Function that calculates phase matrix | |

Oyster_run_sec3 | Runs complete Step 3 of the growth model | |

Oyster_run_sec4 | Runs complete Step 4 of the growth model | |

Oyster_subincr_av_thickness_X | Formula that calculates average shell thickness through time | |

Oyster_subincr_phases | Calculates proportion of phases in each sub-increment | |

Oyster_plot_incr_CS | Plot the result of interpolation of sub-increments | |

phasemat | Matrix of phases names for each pixel in the phase map | |

pixelsize | Size of pixels in phase map in mm | |

ShellTrace | ShellTrace: Growth and trace element uptake modelling in bivalve shells | |

incr_matrix3 | Matrix containing data calculated for each growth band. | |

lengthfactor | Multiplier used to convert shell cross section from pixels to mm | |

subincr_matrix5 | Matrix containing data calculated for each growth band. | |

subincr_matrix6 | Matrix containing data calculated for each growth band. | |

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## Last month downloads

## Details

Type | Package |

Date | 2017-09-27 |

License | GPL-3 |

LazyData | true |

URL | https://github.com/nielsjdewinter/ShellTrace, https://doi.org/10.5194/gmd-2017-137-supplement, http://nidewint.wixsite.com/nielsdewinter |

BugReports | https://github.com/nielsjdewinter/ShellTrace/issues |

RoxygenNote | 6.0.1 |

NeedsCompilation | no |

Packaged | 2017-10-06 11:17:04 UTC; Niels |

Repository | CRAN |

Date/Publication | 2017-10-06 11:35:20 UTC |

imports | bmp , grDevices , stats , tiff , xlsx |

depends | R (>= 3.1.0) |

Contributors | Niels de Winter |

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