Package: ipmr 0.0.7
ipmr: Integral Projection Models
Flexibly implements Integral Projection Models using a mathematical(ish) syntax. This package will not help with the vital rate modeling process, but will help convert those regression models into an IPM. 'ipmr' handles density dependence and environmental stochasticity, with a couple of options for implementing the latter. In addition, provides functions to avoid unintentional eviction of individuals from models. Additionally, provides model diagnostic tools, plotting functionality, stochastic/deterministic simulations, and analysis tools. Integral projection models are described in depth by Easterling et al. (2000) <doi:10.1890/0012-9658(2000)081[0694:SSSAAN]2.0.CO;2>, Merow et al. (2013) <doi:10.1111/2041-210X.12146>, Rees et al. (2014) <doi:10.1111/1365-2656.12178>, and Metcalf et al. (2015) <doi:10.1111/2041-210X.12405>. Williams et al. (2012) <doi:10.1890/11-2147.1> discuss the problem of unintentional eviction.
Authors:
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ipmr.pdf |ipmr.html✨
ipmr/json (API)
NEWS
# Install 'ipmr' in R: |
install.packages('ipmr', repos = c('https://padrinodb.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/padrinodb/ipmr/issues
- gen_di_det_ex - A general deterministic IPM example
- iceplant_ex - Raw demographic data to construct an example IPM
- monocarp_proto - A 'proto_ipm' for a monocarpic perennial
- sim_di_det_ex - Simple deterministic IPM example
demographyintegral-projection-models
Last updated 22 days agofrom:71915cd3cd. Checks:OK: 1 NOTE: 8. Indexed: yes.
Target | Result | Date |
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Doc / Vignettes | OK | Nov 01 2024 |
R-4.5-win-x86_64 | NOTE | Nov 01 2024 |
R-4.5-linux-x86_64 | NOTE | Nov 01 2024 |
R-4.4-win-x86_64 | NOTE | Nov 01 2024 |
R-4.4-mac-x86_64 | NOTE | Nov 01 2024 |
R-4.4-mac-aarch64 | NOTE | Nov 01 2024 |
R-4.3-win-x86_64 | NOTE | Nov 01 2024 |
R-4.3-mac-x86_64 | NOTE | Nov 01 2024 |
R-4.3-mac-aarch64 | NOTE | Nov 01 2024 |
Exports:.data%^%%>%collapse_pop_stateconv_plotdefine_domainsdefine_env_statedefine_impldefine_kerneldefine_pop_statediscrete_extremadiscretize_pop_vectordomainsenexprenexprsenquoenquosensymensymsexprformat_mega_kernelinit_ipmint_meshipm_to_dfis_conv_to_asymptotickernel_formulaekernel_formulae<-lambdaleft_evleft_multmake_impl_args_listmake_ipmmake_ipm_reportmake_ipm_report_bodymake_iter_kernelmat_powermean_kernelnew_fun_formparametersparameters<-pop_statequoquo_namequosright_evright_multsymsymstruncated_distributionsuse_vr_modelvital_rate_exprsvital_rate_exprs<-vital_rate_funs
Age-Size IPMs
Rendered fromage_x_size.Rmd
usingknitr::rmarkdown
on Nov 01 2024.Last update: 2022-11-29
Started: 2020-06-26
Density Dependent IPMs
Rendered fromdensity-dependence.Rmd
usingknitr::rmarkdown
on Nov 01 2024.Last update: 2021-05-18
Started: 2020-10-16
General IPMs
Rendered fromgeneral-ipms.Rmd
usingknitr::rmarkdown
on Nov 01 2024.Last update: 2022-11-29
Started: 2020-01-13
Index Notation in ipmr
Rendered fromindex-notation.Rmd
usingknitr::rmarkdown
on Nov 01 2024.Last update: 2022-02-09
Started: 2021-05-18
Introduction to ipmr
Rendered fromipmr-introduction.Rmd
usingknitr::rmarkdown
on Nov 01 2024.Last update: 2022-11-29
Started: 2019-02-05
proto_ipm Data Structure
Rendered fromproto-ipms.Rmd
usingknitr::rmarkdown
on Nov 01 2024.Last update: 2021-05-18
Started: 2019-07-12
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Raise a matrix to a power | %^% mat_power |
Convert to bare matrices | as.matrix.ipmr_ipm as.matrix.ipmr_matrix |
Extract threshold based population size information | collapse_pop_state |
Helpers for IPM construction | define_domains define_env_state define_impl define_pop_state discretize_pop_vector make_impl_args_list |
Functions to initialize and define IPM kernels | define_kernel |
Accessor functions for (proto_)ipm objects | domains domains.default domains.proto_ipm int_mesh int_mesh.ipmr_ipm kernel_formulae kernel_formulae.default kernel_formulae.proto_ipm kernel_formulae<- kernel_formulae<-.proto_ipm new_fun_form parameters parameters.default parameters.proto_ipm parameters<- parameters<-.proto_ipm pop_state pop_state.default pop_state.proto_ipm vital_rate_exprs vital_rate_exprs.default vital_rate_exprs.proto_ipm vital_rate_exprs<- vital_rate_exprs<-.proto_ipm vital_rate_funs vital_rate_funs.ipmr_ipm |
Create iteration kernels from an IPM object | format_mega_kernel format_mega_kernel.age_x_size_ipm format_mega_kernel.default make_iter_kernel |
A general deterministic IPM example | gen_di_det_ex |
Raw demographic data to construct an example IPM | iceplant_ex |
Initialize an IPM | init_ipm |
Convert ipmr matrix to long data frame | ipm_to_df ipm_to_df.array ipm_to_df.default |
Check for model convergence to asymptotic dynamics | conv_plot conv_plot.ipmr_ipm is_conv_to_asymptotic is_conv_to_asymptotic.ipmr_ipm |
Compute the per-capita growth rate for an IPM object | lambda lambda.general_dd_det_ipm lambda.general_dd_stoch_kern_ipm lambda.general_dd_stoch_param_ipm lambda.general_di_det_ipm lambda.general_di_stoch_kern_ipm lambda.general_di_stoch_param_ipm lambda.simple_dd_det_ipm lambda.simple_dd_stoch_kern_ipm lambda.simple_dd_stoch_param_ipm lambda.simple_di_det_ipm lambda.simple_di_stoch_kern_ipm lambda.simple_di_stoch_param_ipm |
Methods to implement an IPM | make_ipm make_ipm.general_dd_det make_ipm.general_dd_stoch_kern make_ipm.general_dd_stoch_param make_ipm.general_di_det make_ipm.general_di_stoch_kern make_ipm.general_di_stoch_param make_ipm.simple_dd_det make_ipm.simple_dd_stoch_kern make_ipm.simple_dd_stoch_param make_ipm.simple_di_det make_ipm.simple_di_stoch_kern make_ipm.simple_di_stoch_param |
Generate an RMarkdown file with IPM metadata | make_ipm_report make_ipm_report.default make_ipm_report.ipmr_ipm make_ipm_report_body |
Mean kernels for stochastic models | mean_kernel |
A 'proto_ipm' for a monocarpic perennial | monocarp_proto |
Plot a matrix or an *_ipm object | plot.general_di_det_ipm plot.ipmr_matrix plot.simple_di_det_ipm plot.simple_di_stoch_kern_ipm plot.simple_di_stoch_param_ipm |
Print proto_ipms or *_ipm objects | print.general_dd_det_ipm print.general_dd_stoch_kern_ipm print.general_dd_stoch_param_ipm print.general_di_det_ipm print.general_di_stoch_kern_ipm print.general_di_stoch_param_ipm print.proto_ipm print.simple_dd_det_ipm print.simple_dd_stoch_kern_ipm print.simple_dd_stoch_param_ipm print.simple_di_det_ipm print.simple_di_stoch_kern_ipm print.simple_di_stoch_param_ipm |
Compute the standardized left and right eigenvectors via iteration | left_ev left_ev.general_di_det_ipm left_ev.general_di_stoch_kern_ipm left_ev.general_di_stoch_param_ipm left_ev.simple_di_det_ipm left_ev.simple_di_stoch_kern_ipm left_ev.simple_di_stoch_param_ipm right_ev right_ev.general_di_det_ipm right_ev.general_di_stoch_kern_ipm right_ev.general_di_stoch_param_ipm right_ev.simple_di_det_ipm right_ev.simple_di_stoch_kern_ipm right_ev.simple_di_stoch_param_ipm |
Right/left multiplication | left_mult right_mult |
Simple deterministic IPM example | sim_di_det_ex |
Eviction correction | discrete_extrema truncated_distributions |
Predict methods in ipmr | use_vr_model |