{ "_id": "6a12afc4acfb0bcc41d193aa", "Package": "phylosamp", "Type": "Package", "Title": "Sample Size Calculations for Molecular and Phylogenetic Studies", "Version": "1.0.1", "Date": "2023-04-25", "Authors@R": "c(person(\"Shirlee\", \"Wohl\", role=c(\"aut\", \"ctb\"), email=\"swohl@scripps.edu\"),\nperson(\"Elizabeth C\", \"Lee\", role=c(\"aut\", \"ctb\"), email=\"elizabeth.c.lee@jhu.edu\"),\nperson(\"Lucy\", \"D'Agostino McGowan\", role=c(\"aut\", \"ctb\"), email = \"lucydagostino@gmail.com\",\ncomment = c(ORCID = \"0000-0002-6983-2759\")),\nperson(\"John R\", \"Giles\", role=c(\"aut\", \"ctb\"), email=\"jrgiles@uw.edu\"),\nperson(\"Justin\", \"Lessler\", role=c(\"aut\", \"cre\"), email=\"jlessler@unc.edu\"))", "Maintainer": "Justin Lessler ", "Description": "Implements novel tools for estimating sample sizes needed\nfor phylogenetic studies, including studies focused on\nestimating the probability of true pathogen transmission\nbetween two cases given phylogenetic linkage and studies\nfocused on tracking pathogen variants at a population level.\nMethods described in Wohl, Giles, and Lessler (2021) and in\nWohl, Lee, DiPrete, and Lessler (2023).", "License": "GPL-2", "URL": "https://github.com/HopkinsIDD/phylosamp", "BugReports": "https://github.com/HopkinsIDD/phylosamp/issues", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "Repository": "https://hopkinsidd.r-universe.dev", "Date/Publication": "2023-05-23 22:02:12 UTC", "RemoteUrl": "https://github.com/hopkinsidd/phylosamp", "RemoteRef": "HEAD", "RemoteSha": "d43c73bfa108ed03cb5e6330518fd5b3fc1d74c2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-24 07:54:10 UTC", "User": "root" }, "Author": "Shirlee Wohl [aut, ctb],\nElizabeth C Lee [aut, ctb],\nLucy D'Agostino McGowan [aut, ctb] (ORCID:\n),\nJohn R Giles [aut, ctb],\nJustin Lessler [aut, cre]", "MD5sum": 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Lessler", "email": "jlessler@unc.edu", "login": "jlessler", "description": "", "uuid": 4983095 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "cli", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "cowplot", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "purrr", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "hopkinsidd", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "phylogenetics", "sampling" ], "_stars": 13, "_contributors": [ { "user": "eclee25", "count": 68, "uuid": 5208766 }, { "user": 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"falsediscoveryrate", "gen_dists", "gendist_distribution", "gendist_roc_format", "gendist_sensspec_cutoff", "get_optim_roc", "obs_pairs_mtml", "obs_pairs_mtsl", "obs_pairs_stsl", "optim_roc_threshold", "prob_trans_mtml", "prob_trans_mtsl", "prob_trans_stsl", "relR_power", "relR_power_simulated", "relR_samplesize", "relR_samplesize_basic", "relR_samplesize_ci", "samplesize", "sens_spec_calc", "sens_spec_roc", "translink_expected_links_obs", "translink_expected_links_obs_mtml", "translink_expected_links_obs_mtsl", "translink_expected_links_obs_stsl", "translink_expected_links_true", "translink_expected_links_true_mtml", "translink_expected_links_true_mtsl", "translink_expected_links_true_stsl", "translink_fdr", "translink_prob_transmit", "translink_prob_transmit_mtml", "translink_prob_transmit_mtsl", "translink_prob_transmit_stsl", "translink_samplesize", "translink_tdr", "true_pairs", "true_pairs_mtml", "true_pairs_mtsl", "true_pairs_stsl", "truediscoveryrate", "varfreq_cdf_logistic", "varfreq_expected_mbias", "varfreq_freq_logistic", "varfreq_obs_freq", "vartrack_cod_ratio", "vartrack_prob_detect", "vartrack_prob_detect_cont", "vartrack_prob_detect_xsect", "vartrack_prob_prev", "vartrack_prob_prev_xsect", "vartrack_samplesize_detect", "vartrack_samplesize_detect_cont", "vartrack_samplesize_detect_xsect", "vartrack_samplesize_prev", "vartrack_samplesize_prev_xsect" ], "_datasets": [ { "name": "genDistSim", "title": "Simulations of the genetic distance distribution", "object": "genDistSim", "class": [ "data.frame" ], "fields": [ "R", "gens", "X1", "X2", "X3", "X4", "X5", "X6", "X7", "X8", "X9", "X10", "X11", "X12", "X13", "X14", "X15", "X16", "X17", "X18", "X19", "X20", "X21", "X22", "X23", "X24", "X25", "X26", "X27", "X28", "X29", "X30", "X31", "X32", "X33", "X34", "X35", "X36", "X37", "X38", "X39", "X40", "X41", "X42", "X43", "X44", "X45", "X46", "X47", "X48", "X49", "X50", "X51", "X52" ], "rows": 168, "table": true, "tojson": true } ], "_help": [ { "page": "exp_links", "title": "Calculate expected number of links in a sample", "concept": [ "obs_pairs" ], "topics": [ "exp_links" ] }, { "page": "falsediscoveryrate", "title": "Calculate false discovery rate of a sample", "concept": [ "discovery_rate" ], "topics": [ "falsediscoveryrate" ] }, { "page": "gen_dists", "title": "Calculate genetic distance distribution", "concept": [ "mutrate_functions" ], "topics": [ "gen_dists" ] }, { "page": "gendist_distribution", "title": "Calculate genetic distance distribution", "concept": [ "genetic distance functions" ], "topics": [ "gendist_distribution" ] }, { "page": "gendist_roc_format", "title": "Make ROC curve from sensitivity and specificity", "concept": [ "ROC functions", "genetic distance functions" ], "topics": [ "gendist_roc_format" ] }, { "page": "gendist_sensspec_cutoff", "title": "Calculate sensitivity and specificity of a genetic distance cutoff", "concept": [ "genetic distance functions" ], "topics": [ "gendist_sensspec_cutoff" ] }, { "page": "genDistSim", "title": "Simulations of the genetic distance distribution", "topics": [ "genDistSim" ] }, { "page": "get_optim_roc", "title": "Find optimal ROC threshold", "concept": [ "mutrate_functions" ], "topics": [ "get_optim_roc" ] }, { "page": "obs_pairs_mtml", "title": "Expected number of observed pairs assuming multiple-transmission and multiple-linkage", "concept": [ "obs_pairs" ], "topics": [ "obs_pairs_mtml" ] }, { "page": "obs_pairs_mtsl", "title": "Expected number of observed pairs assuming multiple-transmission and single-linkage", "concept": [ "obs_pairs" ], "topics": [ "obs_pairs_mtsl" ] }, { "page": "obs_pairs_stsl", "title": "Expected number of observed pairs assuming single-transmission and single-linkage", "concept": [ "obs_pairs" ], "topics": [ "obs_pairs_stsl" ] }, { "page": "optim_roc_threshold", "title": "Find optimal ROC threshold", "concept": [ "ROC functions" ], "topics": [ "optim_roc_threshold" ] }, { "page": "prob_trans_mtml", "title": "Probability of transmission assuming multiple-transmission and multiple-linkage", "concept": [ "prob_trans" ], "topics": [ "prob_trans_mtml" ] }, { "page": "prob_trans_mtsl", "title": "Probability of transmission assuming multiple-transmission and single-linkage", "concept": [ "prob_trans" ], "topics": [ "prob_trans_mtsl" ] }, { "page": "prob_trans_stsl", "title": "Probability of transmission assuming single-transmission and single-linkage", "concept": [ "prob_trans" ], "topics": [ "prob_trans_stsl" ] }, { "page": "relR_power", "title": "Calculate power for detecting differential transmission given a sample size", "topics": [ "relR_power" ] }, { "page": "relR_power_simulated", "title": "Simulate power for detecting differential transmission", "topics": [ "relR_power_simulated" ] }, { "page": "relR_samplesize", "title": "Calculate sample size needed to detect differential transmission", "topics": [ "relR_samplesize" ] }, { "page": "relR_samplesize_basic", "title": "Calculate simple derived sample size for detecting differential transmission", "topics": [ "relR_samplesize_basic" ] }, { "page": "relR_samplesize_ci", "title": "Calculate sample size for detecting differential transmission with uncertainty bounds", "topics": [ "relR_samplesize_ci" ] }, { "page": "relR_samplesize_linkerr", "title": "Calculate sample size for detecting differential transmission correcting for sensitivity and specificity", "topics": [ "relR_samplesize_linkerr" ] }, { "page": "relR_samplesize_opterr", "title": "Function to calculate the error in estimated sample size for use in optimize function", "topics": [ "relR_samplesize_opterr" ] }, { "page": "relR_samplesize_simsolve", "title": "Calculate optimized sample size for detecting differential transmission", "topics": [ "relR_samplesize_simsolve" ] }, { "page": "relR_samplesize_solve", "title": "Calculate optimal sample size for detecting differential transmission with imperfect specificity", "topics": [ "relR_samplesize_solve" ] }, { "page": "samplesize", "title": "Calculate sample size", "concept": [ "inverse_functions" ], "topics": [ "samplesize" ] }, { "page": "sens_spec_calc", "title": "Calculate sensitivity and specificity", "concept": [ "mutrate_functions" ], "topics": [ "sens_spec_calc" ] }, { "page": "sens_spec_roc", "title": "Make ROC from sensitivity and specificity", "concept": [ "mutrate_functions" ], "topics": [ "sens_spec_roc" ] }, { "page": "translink_expected_links_obs", "title": "Calculate expected number of transmission links in a sample", "concept": [ "transmission linkage functions" ], "topics": [ "translink_expected_links_obs" ] }, { "page": "translink_expected_links_obs_mtml", "title": "Calculate expected number of observed pairs assuming multiple-transmission and multiple-linkage", "concept": [ "transmission linkage functions" ], "topics": [ "translink_expected_links_obs_mtml" ] }, { "page": "translink_expected_links_obs_mtsl", "title": "Calculate expected number of observed pairs assuming multiple-transmission and single-linkage", "concept": [ "transmission linkage functions" ], "topics": [ "translink_expected_links_obs_mtsl" ] }, { "page": "translink_expected_links_obs_stsl", "title": "Calculate expected number of observed pairs assuming single-transmission and single-linkage", "concept": [ "transmission linkage functions" ], "topics": [ "translink_expected_links_obs_stsl" ] }, { "page": "translink_expected_links_true", "title": "Calculate expected number of true transmission pairs", "concept": [ "transmission linkage functions" ], "topics": [ "translink_expected_links_true" ] }, { "page": "translink_expected_links_true_mtml", "title": "Calculate expected number of true transmission pairs assuming multiple-transmission and multiple-linkage", "concept": [ "transmission linkage functions" ], "topics": [ "translink_expected_links_true_mtml" ] }, { "page": "translink_expected_links_true_mtsl", "title": "Calculate expected number of true transmission pairs assuming multiple-transmission and single-linkage", "concept": [ "transmission linkage functions" ], "topics": [ "translink_expected_links_true_mtsl" ] }, { "page": "translink_expected_links_true_stsl", "title": "Calculate expected number of true transmission pairs assuming single-transmission and single-linkage", "concept": [ "transmission linkage functions" ], "topics": [ "translink_expected_links_true_stsl" ] }, { "page": "translink_fdr", "title": "Calculate false discovery rate of identifying transmission pairs in a sample", "concept": [ "transmission linkage functions" ], "topics": [ "translink_fdr" ] }, { "page": "translink_prob_transmit", "title": "Calculate probability of transmission", "concept": [ "transmission linkage functions" ], "topics": [ "translink_prob_transmit" ] }, { "page": "translink_prob_transmit_mtml", "title": "Calculate probability of transmission assuming multiple-transmission and multiple-linkage", "concept": [ "transmission linkage functions" ], "topics": [ "translink_prob_transmit_mtml" ] }, { "page": "translink_prob_transmit_mtsl", "title": "Calculate probability of transmission assuming multiple-transmission and single-linkage", "concept": [ "transmission linkage functions" ], "topics": [ "translink_prob_transmit_mtsl" ] }, { "page": "translink_prob_transmit_stsl", "title": "Calculate probability of transmission assuming single-transmission and single-linkage", "concept": [ "transmission linkage functions" ], "topics": [ "translink_prob_transmit_stsl" ] }, { "page": "translink_samplesize", "title": "Calculate sample size needed to identify true transmission links", "concept": [ "transmission linkage functions" ], "topics": [ "translink_samplesize" ] }, { "page": "translink_tdr", "title": "Calculate true discovery rate of identifying transmission pairs", "concept": [ "transmission linkage functions" ], "topics": [ "translink_tdr" ] }, { "page": "true_pairs", "title": "Calculate expected number of true transmission pairs", "concept": [ "true_pairs" ], "topics": [ "true_pairs" ] }, { "page": "true_pairs_mtml", "title": "Expected number of true transmission pairs assuming multiple-transmission and multiple-linkage", "concept": [ "true_pairs" ], "topics": [ "true_pairs_mtml" ] }, { "page": "true_pairs_mtsl", "title": "Expected number of true transmission pairs assuming multiple-transmission and single-linkage", "concept": [ "true_pairs" ], "topics": [ "true_pairs_mtsl" ] }, { "page": "true_pairs_stsl", "title": "Expected number of true transmission pairs assuming single-transmission and single-linkage", "concept": [ "true_pairs" ], "topics": [ "true_pairs_stsl" ] }, { "page": "truediscoveryrate", "title": "Calculate true discovery rate of a sample", "concept": [ "discovery_rate" ], "topics": [ "truediscoveryrate" ] }, { "page": "varfreq_cdf_logistic", "title": "Calculate cumulative observed variant prevalence at time t given logistic growth", "concept": [ "logistic growth functions", "variant frequency functions" ], 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