Package: phylosamp 1.0.1

Justin Lessler

phylosamp: Sample Size Calculations for Molecular and Phylogenetic Studies

Implements novel tools for estimating sample sizes needed for phylogenetic studies, including studies focused on estimating the probability of true pathogen transmission between two cases given phylogenetic linkage and studies focused on tracking pathogen variants at a population level. Methods described in Wohl, Giles, and Lessler (2021) and in Wohl, Lee, DiPrete, and Lessler (2023).

Authors:Shirlee Wohl [aut, ctb], Elizabeth C Lee [aut, ctb], Lucy D'Agostino McGowan [aut, ctb], John R Giles [aut, ctb], Justin Lessler [aut, cre]

phylosamp_1.0.1.tar.gz
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phylosamp_1.0.1.tgz(r-4.4-any)phylosamp_1.0.1.tgz(r-4.3-any)
phylosamp_1.0.1.tar.gz(r-4.5-noble)phylosamp_1.0.1.tar.gz(r-4.4-noble)
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phylosamp.pdf |phylosamp.html✨
phylosamp/json (API)
NEWS

Peer review:

Bug tracker:https://github.com/hopkinsidd/phylosamp/issues

On CRAN:

phylogeneticssampling

57 exports 12 stars 1.92 score 4 dependencies 1 mentions 25 scripts 313 downloads

Last updated 1 years agofrom:d43c73bfa1. Checks:OK: 7. Indexed: yes.

Exports:exp_linksfalsediscoveryrategen_distsgendist_distributiongendist_roc_formatgendist_sensspec_cutoffget_optim_rocobs_pairs_mtmlobs_pairs_mtslobs_pairs_stsloptim_roc_thresholdprob_trans_mtmlprob_trans_mtslprob_trans_stslrelR_powerrelR_power_simulatedrelR_samplesizerelR_samplesize_basicrelR_samplesize_cisamplesizesens_spec_calcsens_spec_roctranslink_expected_links_obstranslink_expected_links_obs_mtmltranslink_expected_links_obs_mtsltranslink_expected_links_obs_stsltranslink_expected_links_truetranslink_expected_links_true_mtmltranslink_expected_links_true_mtsltranslink_expected_links_true_stsltranslink_fdrtranslink_prob_transmittranslink_prob_transmit_mtmltranslink_prob_transmit_mtsltranslink_prob_transmit_stsltranslink_samplesizetranslink_tdrtrue_pairstrue_pairs_mtmltrue_pairs_mtsltrue_pairs_stsltruediscoveryratevarfreq_cdf_logisticvarfreq_expected_mbiasvarfreq_freq_logisticvarfreq_obs_freqvartrack_cod_ratiovartrack_prob_detectvartrack_prob_detect_contvartrack_prob_detect_xsectvartrack_prob_prevvartrack_prob_prev_xsectvartrack_samplesize_detectvartrack_samplesize_detect_contvartrack_samplesize_detect_xsectvartrack_samplesize_prevvartrack_samplesize_prev_xsect

Dependencies:cligluelifecyclerlang