Package: shelltrace 3.5.1

Niels J. de Winter

shelltrace: 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.

Authors:Niels J. de Winter

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shelltrace.pdf |shelltrace.html✨
shelltrace/json (API)
NEWS

# Install 'shelltrace' in R:
install.packages('shelltrace', repos = c('https://nielsjdewinter.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/nielsjdewinter/shelltrace/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT
Datasets:
  • 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.
  • 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
  • O1_input - Digitized growth increments in cross section of modern oyster.
  • O1_phase - Characteristics of phase in XRF map of oyster
  • Oyster_height - Measured height of the shell
  • Oyster_length - Measured length of the shell
  • TIF - TIF image of phase map of cross section of modern oyster.
  • Z_mat - Z-values describing the base ellipse of the oyster
  • 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
  • image_length - Length (in mm) of the digitized phase map image.
  • incr_matrix0 - Matrix containing data calculated for each growth band.
  • incr_matrix1 - Matrix containing data calculated for each growth band.
  • incr_matrix2 - Matrix containing data calculated for each growth band.
  • incr_matrix3 - Matrix containing data calculated for each growth band.
  • lengthfactor - Multiplier used to convert shell cross section from pixels to mm
  • phase_mat - Matrix listing the amount of pixels of each phase in every subincrement
  • phase_stat - Statistics of elemental concentrations in XRF map of oyster
  • phasemat - Matrix of phases names for each pixel in the phase map
  • pixelsize - Size of pixels in phase map in mm
  • subincr_matrix0 - 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.
  • subincr_matrix3 - Matrix containing data calculated for each growth band.
  • subincr_matrix4 - Matrix containing data calculated for each growth band.
  • subincr_matrix5 - Matrix containing data calculated for each growth band.
  • subincr_matrix6 - Matrix containing data calculated for each growth band.

On CRAN:

bivalvechemistryelementsfisheriesgrowthmolluskpalaeobiologypalaeoecologypaleobiologypaleoclimateshell

2.49 score 31 scripts 91 downloads 36 exports 5 dependencies

Last updated 7 years agofrom:34dd076d72. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 03 2024
R-4.5-winOKNov 03 2024
R-4.5-linuxOKNov 03 2024
R-4.4-winOKNov 03 2024
R-4.4-macOKNov 03 2024
R-4.3-winOKNov 03 2024
R-4.3-macOKNov 03 2024

Exports:Oyster_accumulationOyster_combined_runOyster_Convert_cross_sectionOyster_el_timeOyster_ellipse_parametersOyster_ExportOyster_growth_runOyster_import_BMPOyster_import_phasesOyster_import_TIFOyster_incr_areaOyster_incr_cross_sectionOyster_Mass_gainOyster_phase_exportOyster_phase_matrix_BMPOyster_phase_matrix_TIFOyster_phase_runOyster_phase_statsOyster_plot_cross_sectionOyster_plot_incr_CSOyster_plot_incr_fillOyster_run_sec2Oyster_run_sec3Oyster_run_sec4Oyster_run_sec5Oyster_run_sec6Oyster_Shell_heightOyster_Shell_thicknessOyster_subincr_areaOyster_subincr_av_thicknessOyster_subincr_av_thickness_XOyster_subincr_phasesOyster_subincr_shell_heightOyster_VolumesOyster_Z_matricespma

Dependencies:bmprJavatiffxlsxxlsxjars

Readme and manuals

Help Manual

Help pageTopics
BMP image of phase map of cross section of modern oyster.BMP
Digitized growth increments in cross section of modern oyster rescaled to the same X-axis.cross_section
Matrix listing the concentrations of elements in every subincrementel_time
Length (in mm) of the digitized phase map image.image_length
Interpolated subincrements in cross section of modern oyster rescaled to the same X-axis.IncG
Matrix containing data calculated for each growth band.incr_matrix0
Matrix containing data calculated for each growth band.incr_matrix1
Matrix containing data calculated for each growth band.incr_matrix2
Matrix containing data calculated for each growth band.incr_matrix3
Multiplier used to convert shell cross section from pixels to mmlengthfactor
Matrix of modelled mass accumulation rates per trace elementM_el_mat
Matrix of modelled cumulative mass accumulation rates per trace elementM_el_mat_c
Digitized growth increments in cross section of modern oyster.O1_input
Characteristics of phase in XRF map of oysterO1_phase
Calculate trace element accumulation ratesOyster_accumulation
Runs the growth and trace element modelOyster_combined_run
Function that converts XY-data of digitized cross sectionOyster_Convert_cross_section
Calculate concentrations of trace elements per sub-incrementOyster_el_time
Function that calculates the parameters of the base ellipse used for bivalve growth modellingOyster_ellipse_parameters
Function that exports data of the growth modelOyster_Export
Runs the entire growth modelOyster_growth_run
Measured height of the shellOyster_height
Function that imports a BMP of an XRF mapOyster_import_BMP
Function that imports phase dataOyster_import_phases
Function that imports a TIF fileOyster_import_TIF
Area between shell incrementsOyster_incr_area
Formula that interpolates shell incrementsOyster_incr_cross_section
Measured length of the shellOyster_length
Formula that calculates mass increase of bivalve shell with timeOyster_Mass_gain
Export results of trace element modelOyster_phase_export
Function that calculates phase matrixOyster_phase_matrix_BMP
Function that calculates phase matrixOyster_phase_matrix_TIF
Runs the entire trace element modelOyster_phase_run
Function that exports phase statisticsOyster_phase_stats
Plot the converted shell cross sectionOyster_plot_cross_section
Plot the result of interpolation of sub-incrementsOyster_plot_incr_CS
Plot the result of interpolation of sub-increments with a coloured area plotOyster_plot_incr_fill
Runs complete Step 2 of the growth modelOyster_run_sec2
Runs complete Step 3 of the growth modelOyster_run_sec3
Runs complete Step 4 of the growth modelOyster_run_sec4
Runs complete Step 5 of the trace element modelOyster_run_sec5
Runs complete Step 6 of the trace element modelOyster_run_sec6
Formula that calculates shell height through timeOyster_Shell_height
Formula that calculates average shell thickness through timeOyster_Shell_thickness
Formula that calculates area between sub-incrementsOyster_subincr_area
Formula that calculates average shell thickness through timeOyster_subincr_av_thickness
Formula that calculates average shell thickness through timeOyster_subincr_av_thickness_X
Calculates proportion of phases in each sub-incrementOyster_subincr_phases
A fomula to calculate shell height per sub-incrementOyster_subincr_shell_height
Formula that calculates volume of the shell through timeOyster_Volumes
Function that calculates matrices of Z-values for all sub-increments and all X-valuesOyster_Z_matrices
Matrix listing the amount of pixels of each phase in every subincrementphase_mat
Statistics of elemental concentrations in XRF map of oysterphase_stat
Matrix of phases names for each pixel in the phase mapphasemat
Size of pixels in phase map in mmpixelsize
Function to do an n-point moving averagepma
ShellTrace: Growth and trace element uptake modelling in bivalve shellsShellTrace
Matrix containing data calculated for each growth band.subincr_matrix0
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.subincr_matrix3
Matrix containing data calculated for each growth band.subincr_matrix4
Matrix containing data calculated for each growth band.subincr_matrix5
Matrix containing data calculated for each growth band.subincr_matrix6
TIF image of phase map of cross section of modern oyster.TIF
Z-values describing the base ellipse of the oysterZ_mat