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-4.6-any)phylosamp_1.0.1.tgz(r-4.5-any)
phylosamp_1.0.1.tar.gz(r-4.7-any)phylosamp_1.0.1.tar.gz(r-4.6-any)
phylosamp_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phylosamp/json (API)

# 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

6.88 score 13 stars 39 scripts 276 downloads 1 mentions 57 exports 3 dependencies

Last updated from:d43c73bfa1. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK152
source / vignettesOK181
linux-release-x86_64OK163
macos-release-arm64OK229
macos-oldrel-arm64OK156
windows-develOK126
windows-releaseOK156
windows-oldrelOK124
wasm-releaseOK113

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:clilifecyclerlang

Estimating sample size for transmission linkage from the false discovery rate
Rendered fromL2_SampleSize.Rmdusingknitr::rmarkdown

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

Estimating the probability of detecting a variant
Variant detection | Variant prevalence | Other sampling scenarios
Rendered fromV3_ProbCrossSectional.Rmdusingknitr::rmarkdown

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

Estimating bias in observed variant prevalence
Sample size calculations
Rendered fromV1_CoefficientDetectionBias.Rmdusingknitr::rmarkdown

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

Estimating the linkage false discovery rate from sample size
Important Note
Rendered fromL1_FalseDiscoveryRate.Rmdusingknitr::rmarkdown

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

Estimating the probability of detecting a variant
Variant prevalence
Rendered fromV5_ProbDetectPeriodic.Rmdusingknitr::rmarkdown

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

Estimating the sample size needed for variant monitoring
Variant detection | Variant prevalence | Other sampling scenarios
Rendered fromV2_SampleSizeCrossSectional.Rmdusingknitr::rmarkdown

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

Estimating the sample size needed for variant monitoring
Variant detection | Variant prevalence | Other sampling scenarios
Rendered fromV4_SampleSizePeriodic.Rmdusingknitr::rmarkdown

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

Estimating the sensitivity and specificity of a linkage criteria
1. The mutation rate of the pathogen | 2. The distribution of generations between cases
Rendered fromL3_SensitivitySpecificity.Rmdusingknitr::rmarkdown

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

Illustrative examples for evaluating transmission linkage
Calculating sensitivity and specificity for an Ebola-like pathogen | Optimal values for an Ebola-like pathogen | Calculating sensitivity and specificity for a faster-spreading, slower mutating pathogen | Optimal values for a faster-spreading, slower mutating pathogen | Calculating the false discovery rate of genetic distance as a linkage criteria
Rendered fromL4_IllustrativeExamples.Rmdusingknitr::rmarkdown

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

Variant surveillance example
Guidance for determining variant-specific parameters | The coefficient of detection ratio | Sample size calculations | Estimating the probability of detection
Rendered fromV6_IllustrativeExample.Rmdusingknitr::rmarkdown

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