`install.packages('shelltrace')`

89

3.5.1

GPL-3

October 6th, 2017

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.