Learn R Programming

shelltrace (version 3.5.1)

Bivalve Growth and Trace Element Accumulation Model

Description

Contains all the formulae of the growth and trace element uptake model described in the equally-named Geoscientific Model Development paper (de Winter, 2017, ). 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.

Copy Link

Version

Install

install.packages('shelltrace')

Monthly Downloads

128

Version

3.5.1

License

GPL-3

Issues

0

Pull Requests

0

Stars

0

Forks

0

Maintainer

Niels de Winter

Last Published

October 6th, 2017

Functions in shelltrace (3.5.1)

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.