Files in yinscapital/retina-analysis-reference
Tools for plotting and analyzing vertebrate retinas.
.DS_Store
.Rbuildignore
.Rhistory
.gitignore
.travis.yml
DESCRIPTION
Infusion-Pitch-Final.pdf
NAMESPACE
R/composite.R
R/development.md
R/matrix_retobj.R
R/plotting_functions.R
R/polar_plot_from_mat.R
R/poly_smoothing.R
R/retina-package.r
R/retina_object.R
R/retistruct_processing_functions.R
R/spin_optimization.R
README.md
appveyor.yml
data/reef_fish.rdata
demo/.Rapp.history
demo/00Index
demo/batch_retina_object_gen_for_tests.R
demo/composite_retina.R
demo/fit_diagnostics.R
demo/process_retinas.R
demo/retinal_perimeter_estimation.R
demo/retinaplot_demo.R
demo/smoothing_params.R
demo/spin_optimization.R
demo/tricomposite.R
inst/.DS_Store
inst/extdata/.DS_Store
inst/extdata/Ntae_381/P.csv
inst/extdata/Ntae_381/T.csv
inst/extdata/Ntae_381/datapoints.csv
inst/extdata/Ntae_381/falc.txt
inst/extdata/Ntae_381/falciform.txt
inst/extdata/Ntae_381/markup.csv
inst/extdata/Ntae_381/ntae_381_preoutline.png
inst/extdata/Ntae_381/outline.roi
inst/extdata/Ntae_381/xyz.csv
inst/extdata/Pmol_752/P.csv
inst/extdata/Pmol_752/Pmol_752_outline.png
inst/extdata/Pmol_752/Pmol_752_ssite_locations.csv
inst/extdata/Pmol_752/Pmol_site_counts.csv
inst/extdata/Pmol_752/T.csv
inst/extdata/Pmol_752/datapoints.csv
inst/extdata/Pmol_752/falc.txt
inst/extdata/Pmol_752/markup.csv
inst/extdata/Pmol_752/outline.roi
inst/extdata/Pmol_752/xyz.csv
inst/extdata/Pmol_753/P.csv
inst/extdata/Pmol_753/Pmol_753.PNG
inst/extdata/Pmol_753/T.csv
inst/extdata/Pmol_753/datapoints.csv
inst/extdata/Pmol_753/falc.txt
inst/extdata/Pmol_753/falciform.roi
inst/extdata/Pmol_753/falciform.txt
inst/extdata/Pmol_753/markup.csv
inst/extdata/Pmol_753/outline.roi
inst/extdata/Pmol_753/r.Rdata
inst/extdata/Pmol_753/r.mat
inst/extdata/Pmol_753/xyz.csv
inst/extdata/northern_elephant_seals/NES_count_summary.pdf
inst/extdata/northern_elephant_seals/NES_count_summary_MA_11_36.pdf
inst/extdata/test_retinas/3hgbqg/diagram_retina/P.csv
inst/extdata/test_retinas/3hgbqg/diagram_retina/T.csv
inst/extdata/test_retinas/3hgbqg/diagram_retina/datapoints.csv
inst/extdata/test_retinas/3hgbqg/diagram_retina/falc.txt
inst/extdata/test_retinas/3hgbqg/diagram_retina/markup.csv
inst/extdata/test_retinas/3hgbqg/diagram_retina/outline.png
inst/extdata/test_retinas/3hgbqg/diagram_retina/outline.roi
inst/extdata/test_retinas/3hgbqg/diagram_retina/xyz.csv
inst/extdata/test_retinas/3hgbqg/main.r
inst/extdata/test_retinas/40oik5/40oik5.PNG
inst/extdata/test_retinas/40oik5/diagram_retina/P.csv
inst/extdata/test_retinas/40oik5/diagram_retina/T.csv
inst/extdata/test_retinas/40oik5/diagram_retina/datapoints.csv
inst/extdata/test_retinas/40oik5/diagram_retina/falc.txt
inst/extdata/test_retinas/40oik5/diagram_retina/markup.csv
inst/extdata/test_retinas/40oik5/diagram_retina/outline.roi
inst/extdata/test_retinas/40oik5/diagram_retina/xyz.csv
inst/extdata/test_retinas/40oik5/main.r
inst/extdata/test_retinas/8pm223/8pm223.PNG
inst/extdata/test_retinas/8pm223/README.txt
inst/extdata/test_retinas/8pm223/diagram_retina/P.csv
inst/extdata/test_retinas/8pm223/diagram_retina/T.csv
inst/extdata/test_retinas/8pm223/diagram_retina/datapoints.csv
inst/extdata/test_retinas/8pm223/diagram_retina/falc.txt
inst/extdata/test_retinas/8pm223/diagram_retina/markup.csv
inst/extdata/test_retinas/8pm223/diagram_retina/outline.roi
inst/extdata/test_retinas/8pm223/diagram_retina/xyz.csv
inst/extdata/test_retinas/8pm223/main.r
inst/extdata/test_retinas/bjii4t/bjii4t.png
inst/extdata/test_retinas/bjii4t/bjii4t.xlsx
inst/extdata/test_retinas/bjii4t/diagram_retina/P.csv
inst/extdata/test_retinas/bjii4t/diagram_retina/T.csv
inst/extdata/test_retinas/bjii4t/diagram_retina/datapoints.csv
inst/extdata/test_retinas/bjii4t/diagram_retina/falc.txt
inst/extdata/test_retinas/bjii4t/diagram_retina/markup.csv
inst/extdata/test_retinas/bjii4t/diagram_retina/outline.roi
inst/extdata/test_retinas/bjii4t/diagram_retina/xyz.csv
inst/extdata/test_retinas/bjii4t/main.r
inst/extdata/test_retinas/gv3igs/README.txt
inst/extdata/test_retinas/gv3igs/diagram_retina/P.csv
inst/extdata/test_retinas/gv3igs/diagram_retina/T.csv
inst/extdata/test_retinas/gv3igs/diagram_retina/datapoints.csv
inst/extdata/test_retinas/gv3igs/diagram_retina/falc.txt
inst/extdata/test_retinas/gv3igs/diagram_retina/markup.csv
inst/extdata/test_retinas/gv3igs/diagram_retina/outline.roi
inst/extdata/test_retinas/gv3igs/diagram_retina/xyz.csv
inst/extdata/test_retinas/gv3igs/gv3igs.png
inst/extdata/test_retinas/gv3igs/main.r
inst/extdata/test_retinas/jhvbwt/diagram_retina/P.csv
inst/extdata/test_retinas/jhvbwt/diagram_retina/T.csv
inst/extdata/test_retinas/jhvbwt/diagram_retina/datapoints.csv
inst/extdata/test_retinas/jhvbwt/diagram_retina/falc.txt
inst/extdata/test_retinas/jhvbwt/diagram_retina/markup.csv
inst/extdata/test_retinas/jhvbwt/diagram_retina/outline.roi
inst/extdata/test_retinas/jhvbwt/diagram_retina/xyz.csv
inst/extdata/test_retinas/jhvbwt/gv3igs.png
inst/extdata/test_retinas/jhvbwt/main.r
inst/extdata/test_retinas/key.md
inst/extdata/test_retinas/raxp91/diagram_retina/P.csv
inst/extdata/test_retinas/raxp91/diagram_retina/T.csv
inst/extdata/test_retinas/raxp91/diagram_retina/datapoints.csv
inst/extdata/test_retinas/raxp91/diagram_retina/falc.txt
inst/extdata/test_retinas/raxp91/diagram_retina/markup.csv
inst/extdata/test_retinas/raxp91/diagram_retina/outline.roi
inst/extdata/test_retinas/raxp91/diagram_retina/xyz.csv
inst/extdata/test_retinas/raxp91/main.r
inst/extdata/test_retinas/raxp91/raxp91.png
inst/extdata/tutorial_data/diagram_retina_screenshot.png
inst/extdata/tutorial_data/site_counts_from_stereology.csv
install.md
man/Ntae_381-backslash-t.Rd
man/Pmol_752.Rd
man/Pmol_753.Rd
man/RMat.Rd
man/add_contours.Rd
man/add_degrees.Rd
man/add_legend.Rd
man/assemble_markup_file.Rd
man/assemble_point_coordinates_file.Rd
man/assemble_tear_file.Rd
man/cartesian_rotation.Rd
man/composite_map.Rd
man/compute_longitude_label_location.Rd
man/compute_rotation_matrix.Rd
man/compute_thin_plate_spline_error.Rd
man/coordinate_IJ.Rd
man/count_to_rho.Rd
man/define_color_breaks_based_on_source.Rd
man/define_contour_breaks.Rd
man/degrees.Rd
man/draw_latitude_markings.Rd
man/draw_line_segments.Rd
man/dss_retistruct_processing.Rd
man/fit_error_histogram.Rd
man/fit_plot_azimuthal.Rd
man/fit_plots.Rd
man/getDssRemoved.Rd
man/import_xyz.Rd
man/init_square_mat_plot.Rd
man/map_composites.Rd
man/map_vec_sum.Rd
man/mat_from_ret_obj.Rd
man/nullify_vals_outside_the_circle.Rd
man/optimal_rotation.Rd
man/plot_circle_radial_lines.Rd
man/plot_degree_label_for_latitudes.Rd
man/plot_falciform_process.Rd
man/plot_from_MAT.Rd
man/plot_longitudinal_labels.Rd
man/plot_longitudinal_lines.Rd
man/plot_original_xy_locations.Rd
man/plot_radial_spokes_and_labels.Rd
man/plot_rotation_optimize.Rd
man/polynomial_vs_lambda.Rd
man/pretty_list_not_including_max.Rd
man/range_len.Rd
man/reef_fish.Rd
man/reflect_across_vertical_line.Rd
man/reorder_columns.Rd
man/retina.Rd
man/retina_object.Rd
man/retinal_arclen.Rd
man/retinal_phi0.Rd
man/retinaplot.Rd
man/rotation_optimize.Rd
man/run_all_demos.Rd
man/semi_ellipse_perimeter.Rd
man/sphere_visualize.Rd
man/spherical_coords.Rd
man/spline.poly.Rd
man/ssite_merge.Rd
man/tear_markup_plot.Rd
man/vector_retina_composite.Rd
man/write_labels_at_endpoint_locations.Rd
retina.Rproj
tests/testthat.R
tests/testthat/test_add_degrees.R
tests/testthat/test_density_functions.R
tests/testthat/test_matrix_reflection.R
tutorial.md
tutorial_pix/diagram_retina_screenshot.png
tutorial_pix/falc_traced.png
tutorial_pix/finished_tracing.png
tutorial_pix/make_xyz_mapping.png
tutorial_pix/markup_retistruct.png
tutorial_pix/menu_xy_coords.png
tutorial_pix/minx.png
tutorial_pix/newRfile.png
tutorial_pix/polygon_tracing.png
tutorial_pix/retina_plot_output_pmol753.jpg
tutorial_pix/retistruct_gui_open.png
tutorial_pix/roi_select.png
tutorial_pix/save_roi.png
tutorial_pix/select_polygon.png
tutorial_pix/setwd.png
tutorial_pix/site_counts_pic.png
tutorial_pix/source_or_run_line.png
tutorial_pix/xyz_template.png
