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]

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

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

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

Datasets:
  • genDistSim - Simulations of the genetic distance distribution

On CRAN:

Conda:

phylogeneticssampling

6.65 score 12 stars 25 scripts 216 downloads 1 mentions 57 exports 4 dependencies

Last updated 2 years agofrom:d43c73bfa1. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 24 2025
R-4.5-winOKFeb 24 2025
R-4.5-macOKFeb 24 2025
R-4.5-linuxOKFeb 24 2025
R-4.4-winOKFeb 24 2025
R-4.4-macOKFeb 24 2025
R-4.3-winOKFeb 24 2025
R-4.3-macOKFeb 24 2025

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

Estimating bias in observed variant prevalence

Rendered fromV1_CoefficientDetectionBias.Rmdusingknitr::rmarkdownon Feb 24 2025.

Last update: 2023-02-14
Started: 2023-02-14

Estimating sample size for transmission linkage from the false discovery rate

Rendered fromL2_SampleSize.Rmdusingknitr::rmarkdownon Feb 24 2025.

Last update: 2023-05-23
Started: 2023-02-14

Estimating the linkage false discovery rate from sample size

Rendered fromL1_FalseDiscoveryRate.Rmdusingknitr::rmarkdownon Feb 24 2025.

Last update: 2023-02-14
Started: 2023-02-14

Estimating the probability of detecting a variant

Rendered fromV3_ProbCrossSectional.Rmdusingknitr::rmarkdownon Feb 24 2025.

Last update: 2023-05-23
Started: 2023-02-14

Estimating the probability of detecting a variant

Rendered fromV5_ProbDetectPeriodic.Rmdusingknitr::rmarkdownon Feb 24 2025.

Last update: 2023-02-14
Started: 2023-02-14

Estimating the sample size needed for variant monitoring

Rendered fromV2_SampleSizeCrossSectional.Rmdusingknitr::rmarkdownon Feb 24 2025.

Last update: 2023-02-14
Started: 2023-02-14

Estimating the sample size needed for variant monitoring

Rendered fromV4_SampleSizePeriodic.Rmdusingknitr::rmarkdownon Feb 24 2025.

Last update: 2023-02-14
Started: 2023-02-14

Estimating the sensitivity and specificity of a linkage criteria

Rendered fromL3_SensitivitySpecificity.Rmdusingknitr::rmarkdownon Feb 24 2025.

Last update: 2023-02-14
Started: 2023-02-14

Illustrative examples for evaluating transmission linkage

Rendered fromL4_IllustrativeExamples.Rmdusingknitr::rmarkdownon Feb 24 2025.

Last update: 2023-02-14
Started: 2023-02-14

Variant surveillance example

Rendered fromV6_IllustrativeExample.Rmdusingknitr::rmarkdownon Feb 24 2025.

Last update: 2023-02-14
Started: 2023-02-14

Readme and manuals

Help Manual

Help pageTopics
Calculate expected number of links in a sampleexp_links
Calculate false discovery rate of a samplefalsediscoveryrate
Calculate genetic distance distributiongen_dists
Calculate genetic distance distributiongendist_distribution
Make ROC curve from sensitivity and specificitygendist_roc_format
Calculate sensitivity and specificity of a genetic distance cutoffgendist_sensspec_cutoff
Simulations of the genetic distance distributiongenDistSim
Find optimal ROC thresholdget_optim_roc
Expected number of observed pairs assuming multiple-transmission and multiple-linkageobs_pairs_mtml
Expected number of observed pairs assuming multiple-transmission and single-linkageobs_pairs_mtsl
Expected number of observed pairs assuming single-transmission and single-linkageobs_pairs_stsl
Find optimal ROC thresholdoptim_roc_threshold
Probability of transmission assuming multiple-transmission and multiple-linkageprob_trans_mtml
Probability of transmission assuming multiple-transmission and single-linkageprob_trans_mtsl
Probability of transmission assuming single-transmission and single-linkageprob_trans_stsl
Calculate power for detecting differential transmission given a sample sizerelR_power
Simulate power for detecting differential transmissionrelR_power_simulated
Calculate sample size needed to detect differential transmissionrelR_samplesize
Calculate simple derived sample size for detecting differential transmissionrelR_samplesize_basic
Calculate sample size for detecting differential transmission with uncertainty boundsrelR_samplesize_ci
Calculate sample size for detecting differential transmission correcting for sensitivity and specificityrelR_samplesize_linkerr
Function to calculate the error in estimated sample size for use in optimize functionrelR_samplesize_opterr
Calculate optimized sample size for detecting differential transmissionrelR_samplesize_simsolve
Calculate optimal sample size for detecting differential transmission with imperfect specificityrelR_samplesize_solve
Calculate sample sizesamplesize
Calculate sensitivity and specificitysens_spec_calc
Make ROC from sensitivity and specificitysens_spec_roc
Calculate expected number of transmission links in a sampletranslink_expected_links_obs
Calculate expected number of observed pairs assuming multiple-transmission and multiple-linkagetranslink_expected_links_obs_mtml
Calculate expected number of observed pairs assuming multiple-transmission and single-linkagetranslink_expected_links_obs_mtsl
Calculate expected number of observed pairs assuming single-transmission and single-linkagetranslink_expected_links_obs_stsl
Calculate expected number of true transmission pairstranslink_expected_links_true
Calculate expected number of true transmission pairs assuming multiple-transmission and multiple-linkagetranslink_expected_links_true_mtml
Calculate expected number of true transmission pairs assuming multiple-transmission and single-linkagetranslink_expected_links_true_mtsl
Calculate expected number of true transmission pairs assuming single-transmission and single-linkagetranslink_expected_links_true_stsl
Calculate false discovery rate of identifying transmission pairs in a sampletranslink_fdr
Calculate probability of transmissiontranslink_prob_transmit
Calculate probability of transmission assuming multiple-transmission and multiple-linkagetranslink_prob_transmit_mtml
Calculate probability of transmission assuming multiple-transmission and single-linkagetranslink_prob_transmit_mtsl
Calculate probability of transmission assuming single-transmission and single-linkagetranslink_prob_transmit_stsl
Calculate sample size needed to identify true transmission linkstranslink_samplesize
Calculate true discovery rate of identifying transmission pairstranslink_tdr
Calculate expected number of true transmission pairstrue_pairs
Expected number of true transmission pairs assuming multiple-transmission and multiple-linkagetrue_pairs_mtml
Expected number of true transmission pairs assuming multiple-transmission and single-linkagetrue_pairs_mtsl
Expected number of true transmission pairs assuming single-transmission and single-linkagetrue_pairs_stsl
Calculate true discovery rate of a sampletruediscoveryrate
Calculate cumulative observed variant prevalence at time t given logistic growthvarfreq_cdf_logistic
Calculate multiplicative bias (observed / actual) in variant prevalencevarfreq_expected_mbias
Calculate observed variant prevalence at time t given logistic growthvarfreq_freq_logistic
Calculate observed variant prevalencevarfreq_obs_freq
Calculate the coefficient of detection ratio for two variantsvartrack_cod_ratio
Calculate the probability of detecting a variant given a sample sizevartrack_prob_detect
Calculate probability of detecting a variant given a per-timestep sample size assuming periodic samplingvartrack_prob_detect_cont
Calculate probability of detecting a variant assuming cross-sectional samplingvartrack_prob_detect_xsect
Calculate confidence in a variant estimate given a sample sizevartrack_prob_prev
Calculate confidence in a variant estimate assuming cross-sectional samplingvartrack_prob_prev_xsect
Calculate sample size needed for variant detection given a desired probability of detectionvartrack_samplesize_detect
Calculate sample size needed for variant detection assuming periodic samplingvartrack_samplesize_detect_cont
Calculate sample size needed for variant detection assuming cross-sectional samplingvartrack_samplesize_detect_xsect
Calculate sample size needed for estimating variant prevalence given a desired confidencevartrack_samplesize_prev
Calculate sample size needed for variant prevalence estimation under cross-sectional samplingvartrack_samplesize_prev_xsect