In the fall of 2024, I graduated from my PhD on incubation time (infection to symptom onset) and latency time (infection to start-of-infectiousness) estimation in the beginning of an outbreak, with applications to SARS-CoV-2. The PhD project was supervised by Marta Fiocco (statistics department of the Mathematical Institute of Leiden University) and Ronald Geskus (Oxford University Clinical Research Unit, OUCRU) in Vietnam.
The thesis is openly available, as well as an interview (in Dutch or in English) about my work.
Academic papers
Research article (June 2024): Two biases in incubation time estimation related to exposure // Vera H. Arntzen, Marta Fiocco, Ronald B. Geskus. BMC Infectious Diseases.
Research article (April 2023): Towards robust and accurate estimates of the incubation time distribution, with focus on upper tail probabilities and SARS-CoV-2 infection // Vera H. Arntzen, Marta Fiocco, Nils Leitzinger, Ronald B. Geskus. Statistics in Medicine.
Research article (February 2023): A new inverse probability of selection weighted Cox model to deal with outcome-dependent sampling in survival analysis // Vera H. Arntzen, Marta Fiocco, Inge M.M. Lakeman, Maartje Nielsen, Mar Rodríguez-Girondo. Preprint.
Research article (December 2019): Multiple Sources of the Outbreak of Legionnaires’ Disease in Genesee County, Michigan, in 2014 and 2015 // Anya F. Smith , Anke Huss , Samuel Dorevitch , Leo Heijnen , Vera H. Arntzen , Megan Davies , Mirna Robert-Du Ry van Beest Holle , Yuki Fujita , Antonie M. Verschoor , Bernard Raterman , Frank Oesterholt , Dick Heederik , and Gertjan Medema. Environmental Health perspectives.
Research article (most work in 2017) Spatial analysis of methicillin-resistant Staphylococcus aureus carriage (MRSA) at hospital admission in a livestock dense region // Vera H. Arntzen, Sabiena G. Feenstra, Elisa Benincà, T.T.N. Le, Ellen M. Mascini, Marrigje H. Nabuurs-Franssen, Andreas Voss, Agi M. Marik, Eefje de Jong, Welmoed Silvis, Maarten J. Schijffelen, Peter Schneeberger, Joost Hopman, Hester Korthals Altes & Heiman F.L. Wertheim (contributed equally). Preprint.
R packages (software)
wcox
This package allows the user to calculate inverse probability of selection weights to correct for ascertainment bias in a specific situation: outcome dependently sampled (family) data (‘weighted cohort approach’). Weights can be included in a Cox proportional hazard model to obtain unbiased estimates of the effect of a (continuous) risk modifier on time-to-event. The package is joint work with Mar Rodríguez-Girondo and Marta Fiocco and is available from CRAN: install.packages(“wcox”) in R will install the software.
doublIn
This package provides convenient tools to estimate incubation and latency time of infectious diseases and is available from CRAN: install.packages(“doublIn”) in R will install the software. The software is suitable for doubly interval censored observations collected during the exponential growth or decay phase and allows for flexible choices regarding the shape of the distribution.
Miscelleneous
Master thesis (May 2020): Weighted Cox regression models to correct for outcome dependent sampling in clustered survival data Simulation study and application to familiar cancer studies // Vera H. Arntzen, Mar Rodríguez-Girondo and Marta Fiocco.
Article based on master course (June 2015) Dystonia and psychiatric disorders A pathofysiological connection? // Inge Roof, Noortje van Elderen and Vera Arntzen. Radboud Annals of Medical Students (RAMS).
Seminars
June 13th, 2023 Statistics group, Mathematical Institute When exactly? / Two overlooked biases in incubation time estimation
March 16th, 2023 Biostatistics seminar, University of Palermo, Siciliy, Italy When exactly? / Left truncation and differential recall in incubation time estimation
November 25th, 2022 Master Statistical science, Leiden Calculations for infectious diseases / The example of quarantine length
October 14th, 2021 Health focus group seminar, Leiden Estimating the incubation time of SARS-CoV-2 / Impact of distributional assumptions
September 30th, 2021 PhD Colloquium, Mathematical Institute, Leiden Introduction to my work
March 14th, 2021 Covid-19 modelling group, OUCRU, Vietnam Generation time and serial interval.
(?) Covid-19 modelling group, OUCRU, Vietnam Estimating incubation and latency time of an infectious disease.
(?) Statistics group, Mathematical Institute Estimating incubation and latency time of an infectious disease (II).
September 2nd, 2021 LUMC Statistics department, “MSTAT” meeting, Leiden Estimating the incubation time of SARS-CoV-2 / Impact of distributional assumptions
April 19th, 2021 Statistics group, Mathematical Institute Estimating incubation and latency time of an infectious disease.
September 21th, 2020 LUMC Statistics department, “Survival analysis” meeting, Leiden Weighted Cox to correct for outcome dependent sampling in clustered survival data.
June (?), 2020 Statistics group, Mathematical Institute Weighted Cox to correct for outcome dependent sampling in clustered survival data.
Conferences
Oral presentation
September 15th, 2023 SAfJR 2023 Survival Analysis for Junior Researchers, Reisenburg, Germany. When exactly / Two overlooked biases in SARS-CoV-2 incubation time estimation related to information regarding exposure
August 24th, 2023 CNC 2023 Channel Network Conference (International Biometric Society), Wageningen, the Netherlands. When exactly / Two overlooked biases in SARS-CoV-2 incubation time estimation related to information regarding exposure
July 14th, 2022 IBC 2022 International Biometric Society, Riga, Latvia. Estimation of incubation time in relation to quarantine length / The impact of distributional assumptions
August 23rd, 2022 ISCB 2022 International Society for Clinical Biostatistics, Newcastle, United Kingdom. Methods to estimate SARS-CoV-2 incubation time distribution in relation to length of quarantine period
July 19th, 2021 ISCB 2021 International Society for Clinical Biostatistics, online. Estimating the incubation time of SARS-CoV-2 / Impact of distributional assumptions
Poster presentation
November 29th, 2017 EPIDEMICS International Conference on Infectious Disease Dynamics, Sitges, Spain. Geographical clustering patterns of MRSA carriage in a livestock-dense region in the Netherlands
Teaching
2020, 2021, 2022 Leiden University College, Introduction to Statistics Introduction course in statistics for students with broad interests: lecturing, content creation, exercise class, tutoring and grading.
Vera Arntzen 