{ "_id": "6a11c4b8acfb0bcc41cff9c7", "Package": "ream", "Title": "Density, Distribution, and Sampling Functions for Evidence\nAccumulation Models", "Version": "1.0-11", "Authors@R": "c(person(\"Raphael\", \"Hartmann\", email = \"raphael.hartmann@protonmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-4686-9329\")),\nperson(\"Matthew\", \"Murrow\", email = \"matthew.a.murrow@vanderbilt.edu\", role = c(\"aut\")))", "Description": "Calculate the probability density functions (PDFs) for two\nthreshold evidence accumulation models (EAMs). These are\ndefined using the following Stochastic Differential Equation\n(SDE), dx(t) = v(x(t),t)*dt+D(x(t),t)*dW, where x(t) is the\naccumulated evidence at time t, v(x(t),t) is the drift rate,\nD(x(t),t) is the noise scale, and W is the standard Wiener\nprocess. The boundary conditions of this process are the upper\nand lower decision thresholds, represented by b_u(t) and\nb_l(t), respectively. Upper threshold b_u(t) > 0, while lower\nthreshold b_l(t) < 0. The initial condition of this process\nx(0) = z where b_l(t) < z < b_u(t). We represent this as the\nrelative start point w = z/(b_u(0)-b_l(0)), defined as a ratio\nof the initial threshold location. This package generates the\nPDF using the same approach as the 'python' package it is based\nupon, 'PyBEAM' by Murrow and Holmes (2023)\n. First, it converts the SDE\nmodel into the forwards Fokker-Planck equation dp(x,t)/dt =\nd(v(x,t)*p(x,t))/dt-0.5*d^2(D(x,t)^2*p(x,t))/dx^2, then solves\nthis equation using the Crank-Nicolson method to determine\np(x,t). Finally, it calculates the flux at the decision\nthresholds, f_i(t) = 0.5*d(D(x,t)^2*p(x,t))/dx evaluated at x =\nb_i(t), where i is the relevant decision threshold, either\nupper (i = u) or lower (i = l). The flux at each thresholds\nf_i(t) is the PDF for each threshold, specifically its PDF. We\ndiscuss further details of this approach in this package and\n'PyBEAM' publications. Additionally, one can calculate the\ncumulative distribution functions of and sampling from the\nEAMs.", "NeedsCompilation": "yes", "SystemRequirements": "C++17", "VignetteBuilder": "knitr", "License": "GPL (>= 2)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "URL": "https://github.com/RaphaelHartmann/ream", "BugReports": "https://github.com/RaphaelHartmann/ream/issues", "Repository": "https://raphaelhartmann.r-universe.dev", "Date/Publication": "2026-01-15 14:57:22 UTC", "RemoteUrl": "https://github.com/raphaelhartmann/ream", "RemoteRef": "HEAD", "RemoteSha": "939e18895b215ec52294a441ba2bf201f20bc31b", "Packaged": { "Date": "2026-05-23 15:11:29 UTC", "User": "root" }, "Author": "Raphael Hartmann [aut, cre] (ORCID:\n),\nMatthew Murrow [aut]", "Maintainer": "Raphael Hartmann ", "MD5sum": "b3b168211ecbff1d7bc4585eb8645483", "_user": "raphaelhartmann", "_type": "src", "_file": "ream_1.0-11.tar.gz", "_fileid": "fe2b67ccffbe77ec64b72045298054764ce830640df28c2cc44c4fbb88b3acb4", "_filesize": 500855, "_sha256": "fe2b67ccffbe77ec64b72045298054764ce830640df28c2cc44c4fbb88b3acb4", "_created": "2026-05-23T15:11:29.000Z", "_published": "2026-05-23T15:16:08.760Z", "_distro": "noble", "_jobs": [ { "job": 77530253866, "time": 118, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7177764898" }, { "job": 77530253851, "time": 161, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7177768812" }, { "job": 77530253870, "time": 113, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7177764519" }, { "job": 77530253862, "time": 114, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7177764657" }, { "job": 77530253893, "time": 79, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7177761683" }, { "job": 77530253889, "time": 237, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7177775404" }, { "job": 77530253867, "time": 74, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7177761373" }, { "job": 77530253863, "time": 188, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7177770946" }, { "job": 77530083841, "time": 185, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7177754737" }, { "job": 77530253831, "time": 92, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7177762905" }, { "job": 77530253840, "time": 108, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7177764038" }, { "job": 77530253832, "time": 106, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7177763929" }, { "job": 77530253850, "time": 105, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7177763798" } ], "_buildurl": "https://github.com/r-universe/raphaelhartmann/actions/runs/26336145133", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/raphaelhartmann/ream", "_commit": { "id": "939e18895b215ec52294a441ba2bf201f20bc31b", "author": "Raphael Hartmann ", "committer": "Raphael Hartmann ", "message": "small adjustments\n", "time": 1768489042 }, "_maintainer": { "name": "Raphael Hartmann", "email": "raphael.hartmann@protonmail.com", "login": "raphaelhartmann", "description": "", "uuid": 36821713, "orcid": "0000-0003-4686-9329" }, "_registered": true, "_dependencies": [ { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "raphaelhartmann", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-50", "n": 11 }, { "week": "2025-51", "n": 6 }, { "week": "2026-03", "n": 1 } ], "_tags": [], "_stars": 5, "_contributors": [ { "user": "raphaelhartmann", "count": 66, "uuid": 36821713 } ], "_userbio": { "uuid": 36821713, "type": "user", "name": "Raphael" }, "_downloads": { "count": 166, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ream" }, "_devurl": "https://github.com/raphaelhartmann/ream", "_searchresults": 3, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/ream.html", "manual.pdf" ], "_homeurl": "https://github.com/raphaelhartmann/ream", "_realowner": "raphaelhartmann", "_cranurl": true, "_releases": [ { "version": "1.0-1", "date": "2024-09-10" }, { "version": "1.0-2", "date": "2024-09-16" }, { "version": "1.0-3", "date": "2024-09-17" }, { "version": "1.0-4", "date": "2024-09-20" }, { "version": "1.0-5", "date": "2024-09-26" }, { "version": "1.0-9", "date": "2025-12-18" }, { "version": "1.0-10", "date": "2025-12-19" } ], "_exports": [ "dCSTM_T", "dCSTM_TW", "dCSTM_TX", "dDDM", "dDDM_grid", "dDMC", "dDMC_grid", "dETM", "dETM_grid", "dLIM", "dLIM_grid", "dLIMF", "dLIMF_grid", "dLTM", "dLTM_grid", "dPAM", "dPAM_grid", "dRDMC", "dRDMC_grid", "dRTM", "dRTM_grid", "dSDDM", "dSDDM_grid", "dSDPM", "dSDPM_grid", "dSSP", "dSSP_grid", "dUGM", "dUGM_grid", "dUGMF", "dUGMF_grid", "dWDSTP", "dWDSTP_grid", "dWTM", "dWTM_grid", "pCSTM_T", "pCSTM_TW", "pCSTM_TX", "pDDM", "pDMC", "pETM", "pLIM", "pLIMF", "pLTM", "pPAM", "pRDMC", "pRTM", "pSDDM", "pSDPM", "pSSP", "pUGM", "pUGMF", "pWDSTP", "pWTM", "rCSTM_T", "rCSTM_TW", "rCSTM_TX", "rDDM", "rDMC", "rETM", "rLIM", "rLIMF", "rLTM", "rPAM", "rRDMC", "rRTM", "rSDDM", "rSDPM", "rSSP", "rUGM", "rUGMF", "rWDSTP", "rWTM" ], "_help": [ { "page": "CSTM_T", "title": "Custom Time-Dependent Drift Diffusion Model", "topics": [ "CSTM_T", "dCSTM_T", "pCSTM_T", "rCSTM_T" ] }, { "page": "CSTM_TW", "title": "Custom Time- and Weight-Dependent Drift Diffusion Model", "topics": [ "CSTM_TW", "dCSTM_TW", "pCSTM_TW", "rCSTM_TW" ] }, { "page": "CSTM_TX", "title": "Custom Time- and Evidence-Dependent Drift Diffusion Model", "topics": [ "CSTM_TX", "dCSTM_TX", "pCSTM_TX", "rCSTM_TX" ] }, { "page": "dDDM_grid", "title": "Generate Grid for PDF of the 7 Parameter Drift Diffusion Model", "topics": [ "dDDM_grid" ] }, { "page": "DDM", "title": "7 Parameter Drift Diffusion Model", "topics": [ "dDDM", "DDM", "pDDM", "rDDM" ] }, { "page": "dDMC_grid", "title": "Generate Grid for PDF of Diffusion Model of Conflict Tasks", "topics": [ "dDMC_grid" ] }, { "page": "dETM_grid", "title": "Generate Grid for PDF of the Exponential Threshold Model", "topics": [ "dETM_grid" ] }, { "page": "dLIM_grid", "title": "Generate Grid for PDF of the Leaky Integration Model", "topics": [ "dLIM_grid" ] }, { "page": "dLIMF_grid", "title": "Generate Grid for PDF of the Leaky Integration Model With Flip", "topics": [ "dLIMF_grid" ] }, { "page": "dLTM_grid", "title": "Generate Grid for PDF of the Linear Threshold Model", "topics": [ "dLTM_grid" ] }, { "page": "DMC", "title": "Diffusion Model for Conflict Tasks", "topics": [ "dDMC", "DMC", "pDMC", "rDMC" ] }, { "page": "dPAM_grid", "title": "Generate Grid for PDF of Piecewise Attention Model", "topics": [ "dPAM_grid" ] }, { "page": "dRDMC_grid", "title": "Generate Grid for PDF of the Revised Diffusion Model of Conflict Tasks", "topics": [ "dRDMC_grid" ] }, { "page": "dRTM_grid", "title": "Generate Grid for PDF of the Rational Threshold Model", "topics": [ "dRTM_grid" ] }, { "page": "dSDDM_grid", "title": "Generate Grid for PDF of the Simple Drift Diffusion Model", "topics": [ "dSDDM_grid" ] }, { "page": "dSDPM_grid", "title": "Generate Grid for PDF of the Sequential Dual Process Model", "topics": [ "dSDPM_grid" ] }, { "page": "dSSP_grid", "title": "Generate Grid for PDF of the Shrinking Spotlight Model", "topics": [ "dSSP_grid" ] }, { "page": "dUGM_grid", "title": "Generate Grid for PDF of the Urgency Gating Model", "topics": [ "dUGM_grid" ] }, { "page": "dUGMF_grid", "title": "Generate Grid for PDF of the Urgency Gating Model With Flip", "topics": [ "dUGMF_grid" ] }, { "page": "dWDSTP_grid", "title": "Generate Grid for PDF of the Weibull Dual-Stage Two-Phase Model of Selective Attention", "topics": [ "dWDSTP_grid" ] }, { "page": "dWTM_grid", "title": "Generate Grid for PDF of the Weibull Threshold Model", "topics": [ "dWTM_grid" ] }, { "page": "ETM", "title": "Exponential Threshold Model", "topics": [ "dETM", "ETM", "pETM", "rETM" ] }, { "page": "LIM", "title": "Leaky Integration Model", "topics": [ "dLIM", "LIM", "pLIM", "rLIM" ] }, { "page": "LIMF", "title": "Leaky Integration Model With Flip", "topics": [ "dLIMF", "LIMF", "pLIMF", "rLIMF" ] }, { "page": "LTM", "title": "Linear Threshold Model", "topics": [ "dLTM", "LTM", "pLTM", "rLTM" ] }, { "page": "PAM", "title": "Piecewise Attention Model", "topics": [ "dPAM", "PAM", "pPAM", "rPAM" ] }, { "page": "RDMC", "title": "Revised Diffusion Model of Conflict Tasks", "topics": [ "dRDMC", "pRDMC", "RDMC", "rRDMC" ] }, { "page": "RTM", "title": "Rational Threshold Model", "topics": [ "dRTM", "pRTM", "rRTM", "RTM" ] }, { "page": "SDDM", "title": "Simple Drift Diffusion Model", "topics": [ "dSDDM", "pSDDM", "rSDDM", "SDDM" ] }, { "page": "SDPM", "title": "Sequential Dual Process Model", "topics": [ "dSDPM", "pSDPM", "rSDPM", "SDPM" ] }, { "page": "SSP", "title": "Shrinking Spotlight Model", "topics": [ "dSSP", "pSSP", "rSSP", "SSP" ] }, { "page": "UGM", "title": "Urgency Gating Model", "topics": [ "dUGM", "pUGM", "rUGM", "UGM" ] }, { "page": "UGMF", "title": "Urgency Gating Model With Flip", "topics": [ "dUGMF", "pUGMF", "rUGMF", "UGMF" ] }, { "page": "WDSTP", "title": "Weibull Dual-Stage Two-Phase Model of Selective Attention", "topics": [ "dWDSTP", "pWDSTP", "rWDSTP", "WDSTP" ] }, { "page": "WTM", "title": "Weibull Threshold Model", "topics": [ "dWTM", "pWTM", "rWTM", "WTM" ] } ], "_readme": "https://github.com/raphaelhartmann/ream/raw/HEAD/README.md", "_rundeps": [], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "guideline.Rmd", "filename": "guideline.html", "title": "ream: guideline", "author": "Raphael Hartmann and Matthew Murrow", "engine": "knitr::rmarkdown", "headings": [ "R Package to Calculate the PDF and CDF of Evidence Accumulation Models", "Overview", "0 Preparation", "1 Random Sampling", "2 Calculating the PDF and CDF", "3 Fitting a Model to Data", "4. Implement your custom EAM", "4.1 Option 1: use R or Rcpp functions", "4.1.1 Define R or Rcpp functions", "4.1.2 Register the functions for ream", "4.1.3 Run the new implementation of LIM and compare it to LIM", "4.1.4 Using Rcpp instead", "4.2.2 Register the functions for ream", "4.2.3 Run the new implementation of LIM and compare it to LIM", "4.3 Option 3: change the package", "4.3.1 Get the source code", "4.3.2 Get your system ready", "4.3.3 What source files to modify", "4.3.4 How to modify the necessary class methods", "4.3.5 Recompile the R package", "4.3.6 Some notes", "References" ], "created": "2025-12-16 12:38:16", "modified": "2025-12-16 16:27:46", "commits": 2 } ], "_score": 4.8750612633917, "_indexed": true, "_nocasepkg": "ream", "_universes": [ "raphaelhartmann" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0-11", "date": "2026-05-23T15:13:34.000Z", "distro": "noble", "arch": "aarch64", "commit": "939e18895b215ec52294a441ba2bf201f20bc31b", "fileid": "a2770cff1a8ddf6a8dffd2d08931edd970d7f0a597a0e8681df42526bf3e3fd6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raphaelhartmann/actions/runs/26336145133" }, { "r": "4.7.0", "os": "linux", "version": "1.0-11", "date": "2026-05-23T15:14:14.000Z", "distro": "noble", "arch": "x86_64", "commit": "939e18895b215ec52294a441ba2bf201f20bc31b", "fileid": "199ce455dfbe4cbae3ffaeea20af8b74840a935bde1b9f82e61384ec6252c1da", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raphaelhartmann/actions/runs/26336145133" }, { "r": "4.6.0", "os": "linux", "version": "1.0-11", "date": "2026-05-23T15:13:30.000Z", "distro": "noble", "arch": "aarch64", "commit": "939e18895b215ec52294a441ba2bf201f20bc31b", "fileid": "8e07a6535bf8e6ccd4dee0a1c3531f2549a33c9723357d3d007e6cfb20d50f73", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raphaelhartmann/actions/runs/26336145133" }, { "r": "4.6.0", "os": "linux", "version": "1.0-11", "date": "2026-05-23T15:13:29.000Z", "distro": "noble", "arch": "x86_64", "commit": "939e18895b215ec52294a441ba2bf201f20bc31b", "fileid": "7d250cc127843765fd62f2b946fa62f466ef8157d968c9a10c27fcffdeae07a3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raphaelhartmann/actions/runs/26336145133" }, { "r": "4.5.3", "os": "mac", "version": "1.0-11", "date": "2026-05-23T15:12:59.000Z", "arch": "aarch64", "commit": "939e18895b215ec52294a441ba2bf201f20bc31b", "fileid": "f348faace2f4d8c9fa73002c4e012a49b1b40e378008642b4286236f836b905d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raphaelhartmann/actions/runs/26336145133" }, { "r": "4.5.3", "os": "mac", "version": "1.0-11", "date": "2026-05-23T15:15:01.000Z", "arch": "x86_64", "commit": "939e18895b215ec52294a441ba2bf201f20bc31b", "fileid": "6eb46b6c9292c0fd6954d19fc12fe8da10f92ae35f4c04398621fa122fe2cfd0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raphaelhartmann/actions/runs/26336145133" }, { "r": "4.6.0", "os": "mac", "version": "1.0-11", "date": "2026-05-23T15:12:54.000Z", "arch": "aarch64", "commit": "939e18895b215ec52294a441ba2bf201f20bc31b", "fileid": "ce3cefe93d8012244a4d7d9946440f22459b915d75e04787602ff1dc43bfdc7e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raphaelhartmann/actions/runs/26336145133" }, { "r": "4.6.0", "os": "mac", "version": "1.0-11", "date": "2026-05-23T15:14:26.000Z", "arch": "x86_64", "commit": "939e18895b215ec52294a441ba2bf201f20bc31b", "fileid": "c024a0903840f8951355e471c3e61f80c5e60f82b96fef405d316039559b4cce", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raphaelhartmann/actions/runs/26336145133" }, { "r": "4.6.0", "os": "wasm", "version": "1.0-11", "date": "2026-05-23T15:13:24.000Z", "arch": "emscripten", "commit": "939e18895b215ec52294a441ba2bf201f20bc31b", "fileid": "f9cfb7955cdd107d1f96025e75c72e430a25648d2b8f954226fcf34d3152ca58", "status": "success", "buildurl": "https://github.com/r-universe/raphaelhartmann/actions/runs/26336145133" }, { "r": "4.7.0", "os": "win", "version": "1.0-11", "date": "2026-05-23T15:12:55.000Z", "arch": "x86_64", "commit": "939e18895b215ec52294a441ba2bf201f20bc31b", "fileid": "5e2675034eaba756a746d3459616e621306189e1d1cb3dbaa70e87304a342cb8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raphaelhartmann/actions/runs/26336145133" }, { "r": "4.5.3", "os": "win", "version": "1.0-11", "date": "2026-05-23T15:12:47.000Z", "arch": "x86_64", "commit": "939e18895b215ec52294a441ba2bf201f20bc31b", "fileid": "7d782bd65dff5a0b9a9ff011a25793fddbcbf26b6f065fb9c549223998148a35", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raphaelhartmann/actions/runs/26336145133" }, { "r": "4.6.0", "os": "win", "version": "1.0-11", "date": "2026-05-23T15:12:51.000Z", "arch": "x86_64", "commit": "939e18895b215ec52294a441ba2bf201f20bc31b", "fileid": "47595b41d4d591baaf71692f65e717e6f57dfa597f51c7fa3f8a7ba225f137b7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raphaelhartmann/actions/runs/26336145133" } ] }