Package: mobr 3.0.2

Daniel McGlinn

mobr: Measurement of Biodiversity

Functions for calculating metrics for the measurement biodiversity and its changes across scales, treatments, and gradients. The methods implemented in this package are described in: Chase, J.M., et al. (2018) <doi:10.1111/ele.13151>, McGlinn, D.J., et al. (2019) <doi:10.1111/2041-210X.13102>, McGlinn, D.J., et al. (2020) <doi:10.1101/851717>, and McGlinn, D.J., et al. (2023) <doi:10.1101/2023.09.19.558467>.

Authors:Daniel McGlinn [aut, cre, cph], Xiao Xiao [aut], Brian McGill [aut], Felix May [aut], Thore Engel [aut], Caroline Oliver [aut], Shane Blowes [aut], Tiffany Knight [aut], Oliver Purschke [aut], Nicholas Gotelli [aut], Jon Chase [aut]

mobr_3.0.2.tar.gz
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mobr.pdf |mobr.html✨
mobr/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/mobiodiv/mobr/issues

Datasets:

On CRAN:

biodiversityconservationecologyrarefactionspeciesstatistics

8.64 score 23 stars 90 scripts 226 downloads 5 mentions 24 exports 54 dependencies

Last updated 16 days agofrom:d1c219314d. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxWARNINGOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:avg_nn_distcalc_beta_divcalc_C_targetcalc_chao1calc_comm_divcalc_comm_div_cicalc_divcalc_PIEcalc_S_Ccalc_SPIEChatcompare_samp_rarefactionget_delta_statsget_mob_statsget_null_commget_samplesinvChatkNCN_averagemake_mob_inplot_abuplot_comm_divplot_Nplot_rarefactionrarefaction

Dependencies:classclassIntclicolorspacecpp11DBIdplyre1071eggfansifarvergenericsgeosphereggplot2gluegridExtragtableisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepbapplypillarpkgconfigplotrixproxypurrrR6RColorBrewerRcpprlangs2scalesscamsfspstringistringrtibbletidyrtidyselectunitsutf8vctrsviridisLitewithrwk

Analysis of scale-dependent biodiversity changes with mobr

Rendered frommobr_intro.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-31
Started: 2016-12-15

Beta diversity demonstration

Rendered frombeta_div_demo.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-08-10
Started: 2024-08-08

Readme and manuals

Help Manual

Help pageTopics
Compute average nearest neighbor distanceavg_nn_dist
Calculate beta diversity from sites by species table.calc_beta_div
Calculate the recommended target coverage value for the computation of beta_Ccalc_C_target
Estimation of species richnesscalc_chao1
Calculate biodiversity statistics from sites by species table.calc_comm_div
Compute non-parametric confidence intervals across diversity indices.calc_comm_div_ci
Compute various diversity indices from a vector of species abundances (i.e., one row of a community matrix)calc_div
Calculate probability of interspecific encounter (PIE)calc_PIE
Calculate species richness for a given coverage level.calc_S_C
Calculate S_PIEcalc_SPIE
Calculate expected sample coverage C_hatChat
Compare all sample-based curves (random, spatially constrained-k-NN, spatially constrained-k-NCN)compare_samp_rarefaction
Fire data setfire_comm fire_plot_attr
Conduct the MoB tests on drivers of biodiversity across scales.get_delta_stats
Carry out biodiversity metric comparisons between groups.get_mob_stats
Generate a null community matrixget_null_comm
Generate distribution of sampled community matrices from an original matrix.get_samples
Invasive plants datasetinv_comm inv_plot_attr
Number of individuals corresponding to a desired coverage (inverse C_hat)invChat
Construct spatially constrained sample-based rarefaction (sSBR) curve using the k-Nearest-Centroid-neighbor (k-NCN) algorithmkNCN_average
Create the 'mob_in' object.make_mob_in
Measurement of Biodiversity in Rmobr-package mobr
Plot distributions of species abundanceplot_abu
Plot alpha-, beta-, and gamma-scale biodiversity statistics for a MoB analysisplot_comm_div
Plot the relationship between the number of plots and the number of individualsplot_N
Plot rarefaction curves for each treatment groupplot_rarefaction
Plot the multiscale MoB analysis output generated by 'get_delta_stats'.plot.mob_out
Plot statistics for a MoB analysisplot.mob_stats
Rarefied Species Richnessrarefaction
Subset the rows of the mob data input objectsubset.mob_in
Cattle tank data settank_comm tank_plot_attr