Package: Morphoscape 1.0.2

Blake Dickson

Morphoscape: Computation and Visualization of Adaptive Landscapes

Implements adaptive landscape methods first described by Polly et al. (2016) <doi:10.1080/02724634.2016.1111225> for the integration, analysis and visualization of biological trait data on a phenotypic morphospace - typically defined by shape metrics.

Authors:Blake Dickson [aut, cre], Stephanie Pierce [aut], Noah Greifer [aut], Robert Brocklehurst [aut]

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|Morphoscape.html✨
Morphoscape/json (API)
NEWS

# Install 'Morphoscape' in R:

install.packages('Morphoscape', repos = c('https://blakedickson.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/blakedickson/morphoscape/issues

Datasets:

turtles - Turtle Humeri
turtles_tree - Trutle Phylogeny
warps - Simulated Shape Warps

On CRAN:

5.65 score 3 stars 8 scripts 122 downloads 25 exports 80 dependencies

Last updated 5 months agofrom:7998f8de54. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Oct 09 2024
R-4.5-win	WARNING	Oct 09 2024
R-4.5-linux	WARNING	Oct 09 2024
R-4.4-win	WARNING	Oct 09 2024
R-4.4-mac	WARNING	Oct 09 2024
R-4.3-win	WARNING	Oct 09 2024
R-4.3-mac	WARNING	Oct 09 2024

Exports:as_fnc_df calc_all_lscps calc_lscp calc_lscp_Pareto calc_Ri calcGrpWprime calcPoly calcWprimeBy div_lscps generate_weights get_grid krige_new_data krige_surf lands.grp.test mult_lscps multi.lands.grp.test multiPoly plot_ggPareto plot_ggsurf plot_ggtrade plot_lscp_Pareto resample_grid sp_vals_from_grid sub_lscps sum_lscps

Dependencies:abind alphahull automap class classInt cli colorspace concaveman cpp11 curl DBI deldir dplyr e1071 fansi farver FNN generics ggplot2 glue gstat gtable igraph interp intervals isoband jsonlite KernSmooth labeling lattice lazyeval lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig plyr polyclip proxy R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppEigen RcppParallel reshape rlang rPref s2 scales sf sftime sgeostat sp spacetime spatial spatstat.data spatstat.geom spatstat.random spatstat.univar spatstat.utils splancs stars tibble tidyselect units utf8 V8 vctrs viridisLite withr wk xts zoo

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Morphoscape

Rendered fromMorphoscape.Rmdusingknitr::rmarkdownon Oct 09 2024.

Last update: 2022-06-30
Started: 2022-05-23

Pareto

Rendered fromPareto.rmdusingknitr::rmarkdownon Oct 09 2024.

Last update: 2024-03-27
Started: 2024-01-11

Plotting

Rendered fromNewPlots.Rmdusingknitr::rmarkdownon Oct 09 2024.

Last update: 2024-03-27
Started: 2024-03-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert a data frame to a 'fnc_df'	as_fnc_df fnc_df
Calculate adaptive landscapes for a matrix of weights	calc_all_lscps
Calculate a single weighted adaptive landscape	calc_lscp calc_lscp.all_lscps calc_lscp.kriged_surfaces wtd_lscp
calc_lscp_Pareto	calc_lscp_Pareto
Function for calculating Pareto optimality, using the formula of Deakin et al	calc_Ri
Compute optimally weighted adaptive landscapes	calcGrpWprime print.grp_Wprime
Calculate polynomial fits over a surface	calcPoly multiPoly
Compute optimally weighted adaptive landscapes by subgroup	calcWprimeBy print.by_Wprime print.summary.by_Wprime summary.by_Wprime
Generate a matrix containing weight combinations	generate_weights
get_grid	get_grid
Interpolate functional characteristics over a grid	kriged_surfaces krige_new_data krige_surf
Significance tests between sets of weights	lands.grp.test multi.lands.grp.test print.lands.grp.test print.multi.lands.grp.test
Simple Operations on Spatial Data	div_lscps mult_lscps sub_lscps sum_lscps
plot_ggPareto	plot_ggPareto
plot_ggsurf	plot_ggsurf
plot_ggtrade	plot_ggtrade
Utility functions for calculating Pareto optimality	plot_lscp_Pareto
Plots Kriged surfaces of functional characteristics	plot.kriged_surfaces
Plot Adaptive Landscapes	plot.by_Wprime plot.grp_Wprime plot.wtd_lscp
Create a full grid from a set of coordinates	resample_grid
sp_vals_from_grid	sp_vals_from_grid
Turtle Humeri	turtles
Trutle Phylogeny	turtles_tree
Simulated Shape Warps	warps