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for the boost::odeint solver for the CS model", "topics": [ "daisie_odeint_cs" ] }, { "page": "daisie_odeint_iw", "title": "Driver for the boost::odeint solver for the IW model", "topics": [ "daisie_odeint_iw" ] }, { "page": "DAISIE_plot_age_diversity", "title": "Plot clade age against clade diversity.", "topics": [ "DAISIE_plot_age_diversity" ] }, { "page": "DAISIE_plot_input", "title": "DAISIE tree plot", "topics": [ "DAISIE_plot_input" ] }, { "page": "DAISIE_plot_island", "title": "Plot colonisation and branching time of species found on an island dataset.", "topics": [ "DAISIE_plot_island" ] }, { "page": "DAISIE_plot_sims", "title": "Plot island species-through-time (STT) plots", "topics": [ "DAISIE_plot_sims" ] }, { "page": "DAISIE_probdist", "title": "The joint distribution of endemics and non-endemics under the DAISIE model", "topics": [ "DAISIE_probdist" ] }, { "page": "DAISIE_sim", "title": "Simulate (non-)oceanic islands with given parameters under time-constant rates", "concept": [ "simulation models" ], "topics": [ "DAISIE_sim", "DAISIE_sim_cr" ] }, { "page": "DAISIE_sim_cr_cs", "title": "Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate process", "topics": [ "DAISIE_sim_cr_cs" ] }, { "page": "DAISIE_sim_cr_gw", "title": "Simulates island replicates with an guild-wide (GW) diversity-dependent process", "topics": [ "DAISIE_sim_cr_gw" ] }, { "page": "DAISIE_sim_cr_iw", "title": "Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate process", "topics": [ "DAISIE_sim_cr_iw" ] }, { "page": "DAISIE_sim_cr_shift", "title": "Simulate (non-)oceanic islands with given parameters under a rate-shift regime", "concept": [ "simulation models" ], "topics": [ "DAISIE_sim_cr_shift" ] }, { "page": "DAISIE_sim_MW", "title": "Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters", "topics": [ "DAISIE_sim_MW" ] }, { "page": "daisie_sim_rcpp", "title": "Driver for the daisie sim time loop", "topics": [ "daisie_sim_rcpp" ] }, { "page": "DAISIE_sim_relaxed_rate", "title": "Simulate (non-)oceanic islands with given parameters under a relaxed-rate model", "concept": [ "simulation models" ], "topics": [ "DAISIE_sim_relaxed_rate" ] }, { "page": "DAISIE_sim_time_dep", "title": "Simulate (non-)oceanic islands with given parameters under a time-dependent regime", "concept": [ "simulation models" ], "topics": [ "DAISIE_sim_time_dep" ] }, { "page": "DAISIE_sim_time_dep_cs", "title": "Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent process", "topics": [ "DAISIE_sim_time_dep_cs" ] }, { "page": "DAISIE_sim_time_dep_gw", "title": "Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent process", "topics": [ "DAISIE_sim_time_dep_gw" ] }, { "page": "DAISIE_sim_time_dep_iw", "title": "Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process", "topics": [ "DAISIE_sim_time_dep_iw" ] }, { "page": "DAISIE_sim_trait_dep", "title": "Simulate islands with given trait-dependent parameters.", "topics": [ "DAISIE_sim_trait_dep" ] }, { "page": "DAISIE_sim_trait_dep_2K", "title": "Simulate islands with given trait-dependent parameters.", "topics": [ "DAISIE_sim_trait_dep_2K" ] }, { "page": "DAISIE_SR_loglik_CS", "title": "Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time", "topics": [ "DAISIE_SR_loglik_all", "DAISIE_SR_loglik_CS" ] }, { "page": "DAISIE_SR_ML", "title": "Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence", "topics": [ "DAISIE_SR_ML", "DAISIE_SR_ML_CS" ] }, { "page": "frogs_datalist", "title": "Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island.", "topics": [ "frogs_datalist" ] }, { "page": "frogs_datatable", "title": "Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola.", "topics": [ "frogs_datatable" ] }, { "page": "frogs_sim_datalist", "title": "Colonization and branching times of a data set simulated with the MLE parameters of frogs_datalist", "topics": [ "frogs_sim_datalist" ] }, { "page": "Galapagos_datalist", "title": "Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all", "topics": [ "Galapagos_datalist" ] }, { "page": "Galapagos_datalist_2types", "title": "Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all", "topics": [ "Galapagos_datalist_2types" ] }, { "page": "Galapagos_datatable", "title": "Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format.", "topics": [ "Galapagos_datatable" ] }, { "page": "islands_10reps_RAW", "title": 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parameters", "author": "Luis M. Valente, Albert B. Phillimore, Rampal S. Etienne", "engine": "knitr::rmarkdown", "headings": [ "DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction", "Loading data table", "Formatting table to run in DAISIE", "Optimizing parameters using maximum likelihood", "Example 1: Optimizing all parameters, with diversity-dependence in speciation and colonisation", "Example 2: Optimizing model without diversity-dependence", "Example 3: Optimizing model with no diversity-dependence and no anagenesis", "Example 4: Optimizing all parameters, but allowing Darwin’s finches to have a separate rate of cladogenesis.", "Example 5: Optimizing a model with no diversity-dependence, but allowing Darwin’s finches to have a separate rate of cladogenesis and extinction.", "Example 6: Optimizing a model with no diversity-dependence, using the DAISIE-DE approach." ], "created": "2019-03-19 19:18:07", "modified": "2026-03-27 14:21:52", "commits": 3 }, { "source": "demo_sim.Rmd", "filename": "demo_sim.html", "title": "Demo simulating islands", "author": "Luis M. Valente, Albert B. Phillimore, Rampal S. Etienne", "engine": "knitr::rmarkdown", "headings": [ "DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction", "Loading", "Simulating islands", "Example 5.1 – Simulating r n_replicates islands with no diversity-dependence, all species sharing the same parameters, and plotting the results", "Example 5.2 – Simulating r n_replicates islands with diversity-dependence (K’=10), all species sharing the same parameters, and plotting the results", "Example 5.3 – Simulating r n_replicates islands allowing Darwin’s finches to have a higher rate of cladogenesis:" ], "created": "2019-03-19 19:18:07", "modified": "2022-04-14 09:35:54", "commits": 6 }, { "source": "demo_CSvsIW.Rmd", "filename": "demo_CSvsIW.html", "title": "Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE", "engine": "knitr::rmarkdown", "headings": [ "1. Load, prepare and visualize data", "The table contains the following 4 columns (column headers need to be written exactly like this):", "1.1. Create DAISIE datalist from the input table", "1.2. View DAISIE datalist", "1.3. Visualise the data", "Plot age versus diversity", "2. Fit DAISIE models", "2.1 Fit DI model", "2.2 Fit CS model", "2.3 Fit CS_no_ana model", "2.4 Fit IW model", "2.5 Fit IW_no_ana model", "3. Simulate islands under given DAISIE models", "3.1 Simulate islands with the parameters estimated from the best model for the Hispaniolan Eleutherodacytlus data", "3.2 Plot the species-through-time plots resulting from the simulations." ], "created": "2020-08-11 15:30:48", "modified": "2022-04-14 09:35:54", "commits": 2 } ], "_score": 8.767155866082181, "_indexed": true, "_nocasepkg": "daisie", "_universes": [ "rsetienne" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "4.6.3", "date": "2026-06-04T11:30:33.000Z", "distro": "noble", "arch": "aarch64", "commit": "ef713fbdeba658e0cc7b670d798f1796a5272747", "fileid": "c72aed51b252e0fdb9f0def4eb6d381a257eedc9a5e50e7f798b1b1362a5874f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26948592422" }, { "r": "4.7.0", "os": "linux", "version": "4.6.3", "date": "2026-06-04T11:30:27.000Z", "distro": "noble", "arch": "x86_64", "commit": "ef713fbdeba658e0cc7b670d798f1796a5272747", "fileid": "8c6d61c0c9caa717c623ed8c999f2064a4ee07253890ab2be035ccab29eb5b72", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26948592422" }, { "r": "4.6.0", "os": "linux", "version": "4.6.3", "date": "2026-06-04T11:30:25.000Z", "distro": "noble", "arch": "aarch64", "commit": "ef713fbdeba658e0cc7b670d798f1796a5272747", "fileid": "4ff19cac3464004f48134382c10df479493b9bc9f76dc916c8e945310b8bd078", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26948592422" }, { "r": "4.6.0", "os": "linux", "version": "4.6.3", "date": "2026-06-04T11:30:26.000Z", "distro": "noble", "arch": "x86_64", "commit": "ef713fbdeba658e0cc7b670d798f1796a5272747", "fileid": "13c490502ed40f94b7852faad50314c6ddd854b83ec52d22005a65c68cf6b478", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26948592422" }, { "r": "4.5.3", "os": "mac", "version": "4.6.3", "date": "2026-06-04T11:43:55.000Z", "arch": "aarch64", "commit": "ef713fbdeba658e0cc7b670d798f1796a5272747", "fileid": "ad79d7636450195a94a35f1148495b4642f22a3172f849048f25bb358f3e98cd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26948592422" }, { "r": "4.5.3", "os": "mac", "version": "4.6.3", "date": "2026-06-04T11:44:30.000Z", "arch": "x86_64", "commit": "ef713fbdeba658e0cc7b670d798f1796a5272747", "fileid": "b2dd1d95f69d07e7aa5185ebb6503755f46a5d554e55486d0d380b57ab04454d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26948592422" }, { "r": "4.6.0", "os": "mac", "version": "4.6.3", "date": "2026-06-04T11:42:48.000Z", "arch": "aarch64", "commit": "ef713fbdeba658e0cc7b670d798f1796a5272747", "fileid": "d5c123e50bed3800807f4263818c377f81785744de3d4cb6d5212652f8fa7a51", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26948592422" }, { "r": "4.6.0", "os": "mac", "version": "4.6.3", "date": "2026-06-04T11:50:12.000Z", "arch": "x86_64", "commit": "ef713fbdeba658e0cc7b670d798f1796a5272747", "fileid": "2d0a8a6f5155d20507e9f04332b9929855f793e8d36b04659a0a663cc2635908", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26948592422" }, { "r": "4.6.0", "os": "wasm", "version": "4.6.3", "date": "2026-06-04T11:30:26.000Z", "arch": "emscripten", "commit": "ef713fbdeba658e0cc7b670d798f1796a5272747", "fileid": "3f0ef333f4bb6b77824e80b272961c32ae70d019e35b59aac88804f9345bb024", "status": "success", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26948592422" }, { "r": "4.7.0", "os": "win", "version": "4.6.3", "date": "2026-06-04T11:30:13.000Z", "arch": "x86_64", "commit": "ef713fbdeba658e0cc7b670d798f1796a5272747", "fileid": "ac446eea19c153dcbf474d8e5a25662f67b5f922b9737c82a649055ae97b4670", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26948592422" }, { "r": "4.5.3", "os": "win", "version": "4.6.3", "date": "2026-06-04T11:29:30.000Z", "arch": "x86_64", "commit": "ef713fbdeba658e0cc7b670d798f1796a5272747", "fileid": "d589f7e48e844baea1e235986908ab780e84aff2910570363bebd9866b34fbba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26948592422" }, { "r": "4.6.0", "os": "win", "version": "4.6.3", "date": "2026-06-04T11:29:42.000Z", "arch": "x86_64", "commit": "ef713fbdeba658e0cc7b670d798f1796a5272747", "fileid": "f0bffff2274cdb0074fcb4b25c22b808a502c9c5a8f7e5090dc5b5c447f985d7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26948592422" } ] }