references

.gitignore

@@ -11,3 +11,4 @@ output
 *.out
 *.docx
 fetch
+*.sif

manuscript/manuscript.Rmd

@@ -24,18 +24,17 @@ config <- yaml::read_yaml(params$config_file)
 Assessments of global functional outcome such as the Glasgow Outcome Scale (GOS)
 and the Glasgow Outcome Scale extended (GOSe) capture 
 meaningful differences across the full spectrum of recovery,
-and have popularity as endpoints in TBI studies (Horton et al 2018).
+and have popularity as endpoints in TBI studies @horton2018randomized.
 However, missing outcome data is a common problem in TBI research, 
 and for longitudinal studies completion rates at six months can be 
-lower than 70% (Richter et al).
+lower than 70% @richter2019handling.
 Imputation of patient outcomes is gradually gaining acceptance in the TBI
 field as a method of dealing with missing data in studies.
 This is important since it is well known that complete-case analyses may
 introduce bias or reduce power [REFERENCE].
 Recent longitudinal studies have successfully employed techniques for both
-single (Clifton et al., 2011; Silver et al 2006; Skolnick et al 2014) and
-multiple imputation (Bulger et al, 2010, Kirkness et al 2006;
-Wright et al, 2014; Robertson et al, 2014).
+single @clifton2011 @silver2006 @skolnick2014 and
+multiple imputation @bulger2010 @kirkness2006 @wright2014 @robertson2014.
 The advantage of multiple imputation over single imputation clearly lies in the
 fact that the uncertainty about imputed values can be properly accounted for 
 in a subsequent statistical analysis.
@@ -73,7 +72,8 @@ or - based on the findings presented in this manuscript - fit a custom
 imputation model to adjust for different covariates or obtain multiply
 imputed values.
 
-We propose three different model-based approaches - a mixed-effects model, a Gaussian process regression, and a multi-state model - for imputing GOSe 
+We propose three different model-based approaches - a mixed-effects model, 
+a Gaussian process regression, and a multi-state model - for imputing GOSe 
 longitudinally each of which we fit in a version including baseline covariates
 and without.
 

manuscript/references.bib

+@article{horton2018randomized,
+  title={Randomized controlled trials in adult traumatic brain injury: A systematic review on the use and reporting of clinical outcome assessments},
+  author={Horton, Lindsay and Rhodes, Jonathan and Wilson, Lindsay},
+  journal={Journal of neurotrauma},
+  volume={35},
+  number={17},
+  pages={2005--2014},
+  year={2018},
+  publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
+}
+
+@article{richter2019handling,
+  title={Handling missing outcome data in traumatic brain injury research-a systematic review},
+  author={Richter, Sophie and Stevenson, Susan and Newman, Tom and Wilson, Lindsay and Menon, David and Maas, Andrew and Nieboer, Daan and Lingsma, Hester and Steyerberg, Ewout and Newcombe, Virginia},
+  year={2019},
+  publisher={Mary Ann Liebert Inc.}
+}
+
+@article{white2010bias,
+  title={Bias and efficiency of multiple imputation compared with complete-case analysis for missing covariate values},
+  author={White, Ian R and Carlin, John B},
+  journal={Statistics in medicine},
+  volume={29},
+  number={28},
+  pages={2920--2931},
+  year={2010},
+  publisher={Wiley Online Library}
+}
+
+@article{clifton2011,
+  title={Very early hypothermia induction in patients with severe brain injury (the National Acute Brain Injury Study: Hypothermia II): a randomised trial},
+  author={Clifton, Guy L and Valadka, Alex and Zygun, David and Coffey, Christopher S and Drever, Pamala and Fourwinds, Sierra and Janis, L Scott and Wilde, Elizabeth and Taylor, Pauline and Harshman, Kathy and others},
+  journal={The Lancet Neurology},
+  volume={10},
+  number={2},
+  pages={131--139},
+  year={2011},
+  publisher={Elsevier}
+}
+
+@article{silver2006,
+  title={Effects of rivastigmine on cognitive function in patients with traumatic brain injury},
+  author={Silver, JM and Koumaras, B and Chen, M and Mirski, D and Potkin, SG and Reyes, P and Warden, D and Harvey, Philip D and Arciniegas, D and Katz, DI and others},
+  journal={Neurology},
+  volume={67},
+  number={5},
+  pages={748--755},
+  year={2006},
+  publisher={AAN Enterprises}
+}
+
+@article{skolnick2014,
+  title={A clinical trial of progesterone for severe traumatic brain injury},
+  author={Skolnick, Brett E and Maas, Andrew I and Narayan, Raj K and Van Der Hoop, Roland Gerritsen and MacAllister, Thomas and Ward, John D and Nelson, Neta R and Stocchetti, Nino},
+  journal={New England Journal of Medicine},
+  volume={371},
+  number={26},
+  pages={2467--2476},
+  year={2014},
+  publisher={Mass Medical Soc}
+}
+
+@article{bulger2010,
+  title={Out-of-hospital hypertonic resuscitation following severe traumatic brain injury: a randomized controlled trial},
+  author={Bulger, Eileen M and May, Susanne and Brasel, Karen J and Schreiber, Martin and Kerby, Jeffrey D and Tisherman, Samuel A and Newgard, Craig and Slutsky, Arthur and Coimbra, Raul and Emerson, Scott and others},
+  journal={Jama},
+  volume={304},
+  number={13},
+  pages={1455--1464},
+  year={2010},
+  publisher={American Medical Association}
+}
+
+@article{kirkness2006,
+  title={Effect of continuous display of cerebral perfusion pressure on outcomes in patients with traumatic brain injury},
+  author={Kirkness, Catherine J and Burr, Robert L and Cain, Kevin C and Newell, David W and Mitchell, Pamela H},
+  journal={American journal of critical care},
+  volume={15},
+  number={6},
+  pages={600--609},
+  year={2006},
+  publisher={AACN}
+}
+
+@article{wright2014,
+  title={Very early administration of progesterone for acute traumatic brain injury},
+  author={Wright, David W and Yeatts, Sharon D and Silbergleit, Robert and Palesch, Yuko Y and Hertzberg, Vicki S and Frankel, Michael and Goldstein, Felicia C and Caveney, Angela F and Howlett-Smith, Harriet and Bengelink, Erin M and others},
+  journal={New England Journal of Medicine},
+  volume={371},
+  number={26},
+  pages={2457--2466},
+  year={2014},
+  publisher={Mass Medical Soc}
+}
+
+@article{robertson2014,
+  title={Effect of erythropoietin and transfusion threshold on neurological recovery after traumatic brain injury: a randomized clinical trial},
+  author={Robertson, Claudia S and Hannay, H Julia and Yamal, Jos{\'e}-Miguel and Gopinath, Shankar and Goodman, J Clay and Tilley, Barbara C and Baldwin, Athena and Lara, Lucia Rivera and Saucedo-Crespo, Hector and Ahmed, Osama and others},
+  journal={Jama},
+  volume={312},
+  number={1},
+  pages={36--47},
+  year={2014},
+  publisher={American Medical Association}
+}
+
+
 @article{msm2011,
 author = {Jackson, Christopher H.},
 doi = {10.18637/jss.v038.i08},