Package: LTFHPlus 2.1.1.9000

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) <https://pure.au.dk/ws/portalfiles/portal/353346245/> 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]

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

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

Peer review:

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

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

On CRAN:

26 exports 9 stars 1.96 score 41 dependencies 20 scripts 151 downloads

Last updated 3 months agofrom:64b7452f24. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 08 2024
R-4.5-win-x86_64OKSep 08 2024
R-4.5-linux-x86_64OKSep 08 2024
R-4.4-win-x86_64OKSep 08 2024
R-4.4-mac-x86_64OKSep 08 2024
R-4.4-mac-aarch64OKSep 08 2024
R-4.3-win-x86_64OKSep 08 2024
R-4.3-mac-x86_64OKSep 08 2024
R-4.3-mac-aarch64OKSep 08 2024

Exports:construct_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_singleget_all_combsget_kinshipget_relatednessgraph_based_covariance_constructiongraph_based_covariance_construction_multiprepare_graphprepare_LTFHPlus_inputrtmvnorm.gibbssimulate_under_LTMsimulate_under_LTM_multisimulate_under_LTM_singletruncated_normal_cdf

Dependencies:batchmeansclicodetoolscpp11data.tabledigestdplyrfansifuturefuture.applygenericsglobalsgluegmmigraphjsonlitelatticelifecyclelistenvmagrittrMatrixmvtnormparallellypillarpkgconfigpurrrR6Rcpprlangsandwichstringistringrtibbletidyrtidyselecttmvtnormutf8vctrswithrxgboostzoo

Readme and manuals

Help Manual

Help pageTopics
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
construct all combinations of input vectorget_all_combs
Construct kinship matrix from graphget_kinship
Relatedness between a pair of family membersget_relatedness
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
Construct graph from register informationprepare_graph
Prepares input for 'estimate_liability'prepare_LTFHPlus_input
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