The advent of fast computational algorithms for phylogenetic comparative methods allows for consi... more The advent of fast computational algorithms for phylogenetic comparative methods allows for considering multiple hypotheses concerning the co-adaptation of traits and also for studying if it is possible to distinguish between such models based on contemporary species measurements. Here we demonstrate how one can perform a study with multiple competing hypotheses using mvSLOUCH by analysing two data sets, one concerning feeding styles and oral morphology in ungulates, and the other concerning fruit evolution in Ferula (Apiaceae). We also perform simulations to determine if it is possible to distinguish between various adaptive hypotheses. We find that Akaike’s information criterion corrected for small sample size has the ability to distinguish between most pairs of considered models. However, in some cases there seems to be bias towards Brownian motion or simpler Ornstein–Uhlenbeck models. We also find that measurement error and forcing the sign of the diagonal of the drift matrix fo...
The American Journal of Tropical Medicine and Hygiene
Plasmodium falciparum sporozoite (PfSPZ) direct venous inoculation (DVI) using cryopreserved, inf... more Plasmodium falciparum sporozoite (PfSPZ) direct venous inoculation (DVI) using cryopreserved, infectious PfSPZ (PfSPZ Challenge [Sanaria, Rockville, Maryland]) is an established controlled human malaria infection model. However, to evaluate new chemical entities with potential blood-stage activity, more detailed data are needed on safety, tolerability, and parasite clearance kinetics for DVI of PfSPZ Challenge with established schizonticidal antimalarial drugs. This open-label, phase Ib study enrolled 16 malaria-naïve healthy adults in two cohorts (eight per cohort). Following DVI of 3,200 PfSPZ (NF54 strain), parasitemia was assessed by quantitative polymerase chain reaction (qPCR) from day 7. The approved antimalarial artemether-lumefantrine was administered at a qPCR-defined target parasitemia of ≥ 5,000 parasites/mL of blood. The intervention was generally well tolerated, with two grade 3 adverse events of neutropenia, and no serious adverse events. All 16 participants developed...
Added function PCMTreeInsertTipsOrSingletons. Added possibility to specify metaI as a character s... more Added function PCMTreeInsertTipsOrSingletons. Added possibility to specify metaI as a character string (function name) rather. So far, it was only possible to specify this as a function object or as the list resulting from calling the function on the tree, data and PCM model. Added an operator + for PCMTree objects. This is analogical to the operator + for phylo objects but maintains the edge.part and part.regime members (experimental). Removed argument parametrizations from PCMGenerateModelTypes. Now it's possible to specify the type of parametrization (all/default) separately for each model type. Added automatic generation of White noise model types. Improved man pages.
An example R-package using the SPLITT library to calculate the likelihood of a phylogenetic mixed... more An example R-package using the SPLITT library to calculate the likelihood of a phylogenetic mixed model (PMM).
R-package executing in a parallel a user-defined function on each line of a data.table and storin... more R-package executing in a parallel a user-defined function on each line of a data.table and storing the result into a new column. The package automates the generation of a job-submission script for executing on a cluster.
The advent of fast computational algorithms for phylogenetic comparative methods allows for consi... more The advent of fast computational algorithms for phylogenetic comparative methods allows for considering multiple hypotheses concerning the co-adaptation of traits and also for studying if it is possible to distinguish between such models based on contemporary species measurements. Here we demonstrate how one can perform a study with multiple competing hypotheses using mvSLOUCH by analysing two data sets, one concerning feeding styles and oral morphology in ungulates, and the other concerning fruit evolution in Ferula (Apiaceae). We also perform simulations to determine if it is possible to distinguish between various adaptive hypotheses. We find that Akaike’s information criterion corrected for small sample size has the ability to distinguish between most pairs of considered models. However, in some cases there seems to be bias towards Brownian motion or simpler Ornstein–Uhlenbeck models. We also find that measurement error and forcing the sign of the diagonal of the drift matrix fo...
The American Journal of Tropical Medicine and Hygiene
Plasmodium falciparum sporozoite (PfSPZ) direct venous inoculation (DVI) using cryopreserved, inf... more Plasmodium falciparum sporozoite (PfSPZ) direct venous inoculation (DVI) using cryopreserved, infectious PfSPZ (PfSPZ Challenge [Sanaria, Rockville, Maryland]) is an established controlled human malaria infection model. However, to evaluate new chemical entities with potential blood-stage activity, more detailed data are needed on safety, tolerability, and parasite clearance kinetics for DVI of PfSPZ Challenge with established schizonticidal antimalarial drugs. This open-label, phase Ib study enrolled 16 malaria-naïve healthy adults in two cohorts (eight per cohort). Following DVI of 3,200 PfSPZ (NF54 strain), parasitemia was assessed by quantitative polymerase chain reaction (qPCR) from day 7. The approved antimalarial artemether-lumefantrine was administered at a qPCR-defined target parasitemia of ≥ 5,000 parasites/mL of blood. The intervention was generally well tolerated, with two grade 3 adverse events of neutropenia, and no serious adverse events. All 16 participants developed...
Added function PCMTreeInsertTipsOrSingletons. Added possibility to specify metaI as a character s... more Added function PCMTreeInsertTipsOrSingletons. Added possibility to specify metaI as a character string (function name) rather. So far, it was only possible to specify this as a function object or as the list resulting from calling the function on the tree, data and PCM model. Added an operator + for PCMTree objects. This is analogical to the operator + for phylo objects but maintains the edge.part and part.regime members (experimental). Removed argument parametrizations from PCMGenerateModelTypes. Now it's possible to specify the type of parametrization (all/default) separately for each model type. Added automatic generation of White noise model types. Improved man pages.
An example R-package using the SPLITT library to calculate the likelihood of a phylogenetic mixed... more An example R-package using the SPLITT library to calculate the likelihood of a phylogenetic mixed model (PMM).
R-package executing in a parallel a user-defined function on each line of a data.table and storin... more R-package executing in a parallel a user-defined function on each line of a data.table and storing the result into a new column. The package automates the generation of a job-submission script for executing on a cluster.
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