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phylosamp  

Sample Size Calculations for Molecular and Phylogenetic Studies
View on CRAN: Click here


Download and install phylosamp package within the R console
Install from CRAN:
install.packages("phylosamp")

Install from Github:
library("remotes")
install_github("cran/phylosamp")

Install by package version:
library("remotes")
install_version("phylosamp", "1.0.1")



Attach the package and use:
library("phylosamp")
Maintained by
Justin Lessler
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-11-22
Latest Update: 2023-05-23
Description:
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).
How to cite:
Justin Lessler (2021). phylosamp: Sample Size Calculations for Molecular and Phylogenetic Studies. R package version 1.0.1, https://cran.r-project.org/web/packages/phylosamp. Accessed 07 Nov. 2024.
Previous versions and publish date:
0.1.6 (2021-11-22 10:40)
Other packages that cited phylosamp R package
View phylosamp citation profile
Other R packages that phylosamp depends, imports, suggests or enhances
Complete documentation for phylosamp
Functions, R codes and Examples using the phylosamp R package
Some associated functions: exp_links . falsediscoveryrate . genDistSim . 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 . phylosamp-package . prob_trans_mtml . prob_trans_mtsl . prob_trans_stsl . relR_power . relR_power_simulated . relR_samplesize . relR_samplesize_basic . relR_samplesize_ci . relR_samplesize_linkerr . relR_samplesize_opterr . relR_samplesize_simsolve . relR_samplesize_solve . 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 . 
Some associated R codes: exp_links.R . falsediscoveryrate.R . genDistSim.R . gen_dists.R . gendist_distribution.R . gendist_roc_format.R . gendist_sensspec_cutoff.R . get_optim_roc.R . obs_pairs_mtml.R . obs_pairs_mtsl.R . obs_pairs_stsl.R . optim_roc_threshold.R . phylosamp-package.R . prob_trans_mtml.R . prob_trans_mtsl.R . prob_trans_stsl.R . relR_power.R . relR_power_simulated.R . relR_samplesize.R . relR_samplesize_basic.R . relR_samplesize_ci.R . relR_samplesize_linkerr.R . relR_samplesize_simsolve.R . relR_samplesize_solve.R . samplesize.R . sens_spec_calc.R . sens_spec_roc.R . translink_expected_links_obs.R . translink_expected_links_obs_mtml.R . translink_expected_links_obs_mtsl.R . translink_expected_links_obs_stsl.R . translink_expected_links_true.R . translink_expected_links_true_mtml.R . translink_expected_links_true_mtsl.R . translink_expected_links_true_stsl.R . translink_fdr.R . translink_prob_transmit.R . translink_prob_transmit_mtml.R . translink_prob_transmit_mtsl.R . translink_prob_transmit_stsl.R . translink_samplesize.R . translink_tdr.R . true_pairs.R . true_pairs_mtml.R . true_pairs_mtsl.R . true_pairs_stsl.R . truediscoveryrate.R . utils.R . varfreq_cdf_logistic.R . varfreq_expected_mbias.R . varfreq_freq_logistic.R . varfreq_obs_freq.R . vartrack_cod_ratio.R . vartrack_prob_detect.R . vartrack_prob_detect_cont.R . vartrack_prob_detect_xsect.R . vartrack_prob_prev.R . vartrack_prob_prev_xsect.R . vartrack_samplesize_detect.R . vartrack_samplesize_detect_cont.R . vartrack_samplesize_detect_xsect.R . vartrack_samplesize_prev.R . vartrack_samplesize_prev_xsect.R .  Full phylosamp package functions and examples
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