Package: kindisperse 0.10.3

kindisperse: Simulate and Estimate Close-Kin Dispersal Kernels

Functions for simulating and estimating kinship-related dispersal. Based on the methods described in M. Jasper, T.L. Schmidt., N.W. Ahmad, S.P. Sinkins & A.A. Hoffmann (2019) <doi:10.1111/1755-0998.13043> "A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito". Assumes an additive variance model of dispersal in two dimensions, compatible with Wright's neighbourhood area. Simple and composite dispersal simulations are supplied, as well as the functions needed to estimate parent-offspring dispersal for simulated or empirical data, and to undertake sampling design for future field studies of dispersal. For ease of use an integrated Shiny app is also included.

Authors:Moshe-Elijah Jasper [aut, cre]

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

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

Peer review:

Bug tracker:https://github.com/moshejasper/kindisperse/issues

Datasets:
  • mentari - Position & kinship information of _Aedes aegypti_ from Mentari Court, Malaysia

On CRAN:

3.70 score 1 stars 5 scripts 168 downloads 93 exports 71 dependencies

Last updated 1 months agofrom:6a9cb4b59d. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winOKNov 20 2024
R-4.5-linuxOKNov 20 2024
R-4.4-winOKNov 20 2024
R-4.4-macOKNov 20 2024
R-4.3-winOKNov 20 2024
R-4.3-macOKNov 20 2024

Exports:axialsaxials_addaxials_combineaxials_decomposeaxials_standardaxials_subtractaxpermuteaxpermute_standardaxpermute_subtractbreeding_cyclebreeding_stagebreedsigmabreedsigma<-csv_to_kinpairdf_to_kinpairdispersal_modeldispersal_vectorDispersalModeldisplay_appdatadistanceselongatefiltertypefiltertype<-fsget_dispersal_modelgravsigmagravsigma<-hsinitializeinitsigmainitsigma<-is.DispersalModelis.KinPairDatais.KinPairSimulationkernelshapekerneltypekerneltype<-kin_pair_datakin_pair_simulationkinpair_to_csvkinpair_to_tibblekinpair_to_tsvKinPairDataKinPairSimulationKinPairSimulation_compositeKinPairSimulation_customKinPairSimulation_simplekinshipkinship<-lifestagelifestage<-lowerlower<-mount_appdataovisigmaovisigma<-posigmaposigma<-read_kindatarebase_dimsreset_appdatareset_tempdataretrieve_appdataretrieve_tempdataretrieveall_appdatarun_kindispersesample_kindistsampledimssampledims<-samplenumsamplenum<-sampling_stagesampling_stage<-showsimdimssimdims<-simgraph_datasimgraph_graphsimtypesimtype<-simulate_kindist_compositesimulate_kindist_customsimulate_kindist_simplespacingspacing<-stagestsv_to_kinpairunmount_appdataupperupper<-vector_to_kinpairvisible_stagewrite_kindata

Dependencies:base64encbitbit64bslibcachemclicliprcolorspacecommonmarkcpp11crayondigestdplyrfansifarverfastmapfontawesomefsgenericsggplot2ggrepelgluegtableherehmshtmltoolshttpuvisobandjquerylibjsonlitelabelingLaplacesDemonlaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigprettyunitsprogresspromisesR6rappdirsRColorBrewerRcppreadrrlangrprojrootsassscalesshinyshinythemessourcetoolsstringistringrtibbletidyselecttzdbutf8vctrsviridisLitevroomwithrxtable

using-kindisperse

Moshe-Elijah Jasper

Rendered fromusing-kindisperse.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2021-07-23
Started: 2020-12-08

Readme and manuals

Help Manual

Help pageTopics
Access or assign dispersal sigmas of 'KinPairSimulation' objectsaccess_sigmas breedsigma breedsigma,KinPairSimulation-method breedsigma<- gravsigma gravsigma,KinPairSimulation-method gravsigma<- initsigma initsigma,KinPairSimulation-method initsigma<- ovisigma ovisigma,KinPairSimulation-method ovisigma<- posigma posigma,KinPairSimulation-method posigma<-
Estimate the axial dispersal distance of a kernelaxials
Add axial distributionsaxials_add
Combine axial distributions to produce a mixed distributionaxials_combine
Decompose an axial distribution into simple componentsaxials_decompose
Calculate the intergenerational (PO) dispersal kernel from the distributions of close kinaxials_standard
Subtract axial distributionsaxials_subtract
Estimate the axial dispersal distance of a kernel with confidence intervalsaxpermute
Calculate the intergenerational (PO) dispersal kernel from the distributions of close kin (bootstrapped)axpermute_standard
Subtract axial distributions with confidence intervalsaxpermute_subtract
Access breeding cycle at sampling of 'DispersalModel' object.breeding_cycle breeding_cycle,DispersalModel-method breeding_cycle,KinPairData-method
Access life stage at which breeding occurs of 'DispersalModel' objectbreeding_stage breeding_stage,DispersalModel-method
Check valid kinshipcheck_valid_kinship
Check valid lifestagecheck_valid_lifestage
Reads '.csv' and converts to 'KinPairData' objectcsv_to_kinpair
Convert dataframe or tibble to 'KinPairData' classdf_to_kinpair
Create Dispersal Model of an Organismdispersal_model
Access dispersal vector of 'DispersalModel' object.dispersal_vector dispersal_vector,DispersalModel-method
DispersalModel ClassDispersalModel DispersalModel-class initialize,DispersalModel-method show,DispersalModel-method
Show printout of named items stored in appdata.display_appdata
Access or assign 'distances' category of 'KinPairData' class objectsdistances distances,KinPairData-method
Change the shape (aspect ratio) of a rectangle while preserving areaelongate
Access or modify the 'filter' parameters of 'KinPairSimulation' objectsfilter_methods lower lower,KinPairSimulation-method lower<- lower<-,KinPairSimulation-method sampledims sampledims,KinPairSimulation-method sampledims<- sampledims<-,KinPairSimulation-method samplenum samplenum,KinPairSimulation-method samplenum<- samplenum<-,KinPairSimulation-method spacing spacing,KinPairSimulation-method spacing<- spacing<-,KinPairSimulation-method upper upper,KinPairSimulation-method upper<- upper<-,KinPairSimulation-method
Access filtertype of 'KinPairSimulation' objectfiltertype filtertype,KinPairSimulation-method filtertype<-
Access FS phase split point of 'DispersalModel' object.fs fs,DispersalModel-method
Access dispersal model of 'KinPairSimulation' objectget_dispersal_model get_dispersal_model,KinPairSimulation-method
Access HS phase split point of 'DispersalModel' object.hs hs,DispersalModel-method
Check if object is of class 'DispersalModel'is.DispersalModel
Check if object is of class KinPairDatais.KinPairData
Check if object is of class KinPairSimulationis.KinPairSimulation
Access kernel type of 'KinPairSimulation' objectkernelshape kernelshape,KinPairSimulation-method
Access or assign kerneltype of 'KinPairSimulation' objectkerneltype kerneltype,KinPairSimulation-method kerneltype<-
Make new KinPairData objectkin_pair_data
KinPairSimulationkin_pair_simulation
Write 'KinPairData' object to '.csv' formatkinpair_to_csv
Extract KinPairData class object to tibblekinpair_to_tibble
Write 'KinPairData' object to '.tsv' formatkinpair_to_tsv
Formal class KinPairDatainitialize,KinPairData-method KinPairData KinPairData-class show,KinPairData-method
Constructor for KinPairSimulation Class (composite)KinPairSimulation_composite
Constructor for KinPairSimulation Class (custom)KinPairSimulation_custom
Constructor for KinPairSimulation Class (simple)KinPairSimulation_simple
KinPairSimulation Classinitialize,KinPairSimulation-method KinPairSimulation KinPairSimulation-class show,KinPairSimulation-method
Access or assign 'kinship' category of 'KinPairData' class objectskinship kinship,KinPairData-method kinship<- kinship<-,KinPairData-method
Access or assign 'lifestage' category of 'KinPairData' class objectslifestage lifestage,KinPairData-method lifestage<- lifestage<-,KinPairData-method
Position & kinship information of _Aedes aegypti_ from Mentari Court, Malaysiamentari
Mount 'KinPairData' Objects for use in kindisperse appmount_appdata
Reads '.kindata' filetype back to 'KinPairData' or 'KinPairSimulation' object.read_kindata
Change the dimensions of a KinPairSimulation Object and shift kinpairs so at least one individual is within the arearebase_dims
Reset kindisperse appdatareset_appdata
Reset app tempdata (internal mem)reset_tempdata
Retrieve 'KinPairData' object from appdata (single)retrieve_appdata
Retrieve all tempdata (internal mem) from app (as list)retrieve_tempdata
Retrieve all 'KinPairData' objects from appdata (as list)retrieveall_appdata
Run kindisperse apprun_kindisperse
Subsample and filter a 'KinPairSimulation' or 'KinPairData' Objectsample_kindist
Access sampling stage of 'DispersalModel' or 'KinPairSimulation' object.sampling_stage sampling_stage,DispersalModel-method sampling_stage,KinPairData-method sampling_stage<- sampling_stage<-,DispersalModel-method
Access simulation dimensions of 'KinPairSimulation' objectsimdims simdims,KinPairSimulation-method simdims<-
Simple kin dispersal simulation for graphical display. (returns the data side as a tibble).simgraph_data
Simple kin dispersal simulation for graphical display. (graphs the pre-existing simulation).simgraph_graph
Access or assign simulation type of 'KinPairSimulation' objectsimtype simtype,KinPairSimulation-method simtype<-
Simulate kin dispersal distance pairs with composite sigmassimulate_kindist_composite
Simulate kin dispersal distance pairs with custom species dispersal models.simulate_kindist_custom
Simulate kin dispersal distance pairs with simple sigmasimulate_kindist_simple
Access breeding cycle stages of 'DispersalModel' object.stages stages,DispersalModel-method
Reads '.tsv' and converts to 'KinPairData' objecttsv_to_kinpair
Unmount a 'KinPairData' Object (clear slot from appdata environment)unmount_appdata
Convert vector of kin separation distances to 'KinPairData' classvector_to_kinpair
Access life stage at which individual is first visible to sampling (i.e. from which breeding cycles are calculated)visible_stage visible_stage,DispersalModel-method
Write 'KinPairData' or 'KinPairSimulation' object in '.kindata' formatwrite_kindata