Package: LTFHPlus 2.2.0

Emil Michael Pedersen

LTFHPlus: Implementation of LT-FH++

Implementation of LT-FH++, an extension of the liability threshold family history (LT-FH) model. LT-FH++ uses a Gibbs sampler for sampling from the truncated multivariate normal distribution and allows for flexible family structures. LT-FH++ was first described in Pedersen, Emil M., et al. (2022) <doi:10.1016/j.ajhg.2022.01.009> as an extension to LT-FH with more flexible family structures, and again as the age-dependent liability threshold (ADuLT) model Pedersen, Emil M., et al. (2023) <https://www.nature.com/articles/s41467-023-41210-z> as an alternative to traditional time-to-event genome-wide association studies, where family history was not considered.

Authors:Emil Michael Pedersen [aut, cre], Florian Privé [aut, ths], Bjarni Jóhann Vilhjálmsson [ths], Esben Agerbo [ths], Jette Steinbach [aut], Lucas Rasmussen [ctb]

LTFHPlus_2.2.0.tar.gz
LTFHPlus_2.2.0.zip(r-4.7-x86_64)LTFHPlus_2.2.0.zip(r-4.7-arm64)LTFHPlus_2.2.0.zip(r-4.6-x86_64)LTFHPlus_2.2.0.zip(r-4.6-arm64)LTFHPlus_2.2.0.zip(r-4.5-x86_64)
LTFHPlus_2.2.0.tgz(r-4.6-x86_64)LTFHPlus_2.2.0.tgz(r-4.6-arm64)LTFHPlus_2.2.0.tgz(r-4.5-x86_64)LTFHPlus_2.2.0.tgz(r-4.5-arm64)
LTFHPlus_2.2.0.tar.gz(r-4.7-arm64)LTFHPlus_2.2.0.tar.gz(r-4.7-x86_64)LTFHPlus_2.2.0.tar.gz(r-4.6-arm64)LTFHPlus_2.2.0.tar.gz(r-4.6-x86_64)
LTFHPlus_2.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
LTFHPlus/json (API)

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

Bug tracker:https://github.com/emilmip/ltfhplus/issues

Pkgdown/docs site:https://emilmip.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

4.90 score 11 stars 36 scripts 328 downloads 34 exports 49 dependencies

Last updated from:958e8a6817. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK183
linux-devel-x86_64OK190
source / vignettesOK221
linux-release-arm64OK169
linux-release-x86_64OK184
macos-release-arm64OK133
macos-release-x86_64OK283
macos-oldrel-arm64OK183
macos-oldrel-x86_64OK409
windows-devel-arm64OK423
windows-devel-x86_64OK213
windows-release-arm64OK418
windows-release-x86_64OK140
windows-oldrel-x86_64OK158
wasm-releaseOK136

Exports:attach_attributesconstruct_covmatconstruct_covmat_multiconstruct_covmat_singleconvert_age_to_circonvert_age_to_threshconvert_cir_to_ageconvert_formatconvert_liability_to_aooconvert_observed_to_liability_scalecorrect_positive_definiteestimate_gen_liability_ltfhestimate_liabilityestimate_liability_multiestimate_liability_singlefamilywise_attach_attributesget_all_combsget_family_graphsget_generationsget_kinshipget_relatednessget_relationsgraph_based_covariance_constructiongraph_based_covariance_construction_multigraph_to_triolabel_relativesprepare_graphprepare_LTFHPlus_inputRelation_per_proband_plotrtmvnorm.gibbssimulate_under_LTMsimulate_under_LTM_multisimulate_under_LTM_singletruncated_normal_cdf

Dependencies:batchmeansclicodetoolscpp11data.tabledigestdplyrfarverfuturefuture.applygenericsggplot2globalsgluegmmgtableigraphisobandjsonlitelabelinglatticelifecyclelistenvmagrittrMatrixmvtnormparallellypillarpkgconfigpurrrR6RColorBrewerRcpprlangS7sandwichscalesstringistringrtibbletidyrtidyselecttmvtnormutf8vctrsviridisLitewithrxgboostzoo

Readme and manuals

Help Manual

Help pageTopics
Attach attributes to a family graphsattach_attributes
Constructing a covariance matrix for a variable number of phenotypesconstruct_covmat
Constructing a covariance matrix for multiple phenotypesconstruct_covmat_multi
Constructing a covariance matrix for a single phenotypeconstruct_covmat_single
Convert age to cumulative incidence rateconvert_age_to_cir
Convert age to thresholdconvert_age_to_thresh
Convert cumulative incidence rate to ageconvert_cir_to_age
Attempts to convert the list entry input format to a long formatconvert_format
Convert liability to age of onsetconvert_liability_to_aoo
Convert the heritability on the observed scale to that on the liability scaleconvert_observed_to_liability_scale
Positive definite matricescorrect_positive_definite
Estimate genetic liability similar to LT-FHestimate_gen_liability_ltfh
Estimating the genetic or full liability for a variable number of phenotypesestimate_liability
Estimating the genetic or full liability for multiple phenotypesestimate_liability_multi
Estimating the genetic or full liabilityestimate_liability_single
Wrapper to attach attributes to family graphsfamilywise_attach_attributes
Fixing sex coding in trio infofixSexCoding
construct all combinations of input vectorget_all_combs
Automatically identify family members of degree nget_family_graphs
Compute Generational Distances and Kinship Coefficients from a Family Graphget_generations
Construct kinship matrix from graphget_kinship
Relatedness between a pair of family membersget_relatedness
Compute and Label Pairwise Relationships Across Multiple Family Graphsget_relations
Constructing covariance matrix from local family graphgraph_based_covariance_construction
Constructing covariance matrix from local family graph for multi trait analysisgraph_based_covariance_construction_multi
Convert from igraph to trio informationgraph_to_trio
Label Pairwise Relationships Based on Generational Distance and Kinship Coefficientlabel_relatives
Construct graph from register informationprepare_graph
Prepares input for 'estimate_liability'prepare_LTFHPlus_input
Plot the (Average) Number of Relatives per Proband by Relationship TypeRelation_per_proband_plot
Gibbs Sampler for the truncated multivariate normal distributionrtmvnorm.gibbs
Simulate under the liability threshold model.simulate_under_LTM
Simulate under the liability threshold model (multiple phenotypes).simulate_under_LTM_multi
Simulate under the liability threshold model (single phenotype).simulate_under_LTM_single
CDF for truncated normal distribution.truncated_normal_cdf