Merge pull request #77 from mrc-ide/nipah_workflow

Creates initial Nipah workflow

Author: sangeetabhatia03

nipah_workflow.R

@@ -45,3 +45,11 @@ orderly_run("nipah_latex_tables", list(pathogen="NIPAH"))
 orderly_run("nipah_transmission", list(pathogen="NIPAH"))
 
 orderly_run("nipah_severity", list(pathogen="NIPAH"))
+
+orderly_run("nipah_delays", list(pathogen="NIPAH"))
+
+orderly_run("nipah_summary", list(pathogen="NIPAH"))
+
+orderly_run("nipah_supp_tables", list(pathogen="NIPAH"))
+
+orderly_run("nipah_risk_factors", list(pathogen="NIPAH"))

priority-pathogens.Rproj

@@ -0,0 +1,26 @@
+Year,Cases,Death,CFR
+2001,13,9,69.23%
+2002,0,0,0.00%
+2003,12,8,66.67%
+2004,67,50,74.63%
+2005,12,11,91.67%
+2006,0,0,0.00%
+2007,18,9,50.00%
+2008,11,7,63.64%
+2009,4,1,25.00%
+2010,18,16,88.89%
+2011,43,37,86.05%
+2012,17,12,70.59%
+2013,31,25,80.65%
+2014,37,16,43.24%
+2015,15,11,73.33%
+2016,0,0,0.00%
+2017,3,2,66.67%
+2018,4,2,50.00%
+2019,8,7,87.50%
+2020,7,5,71.43%
+2021,2,0,0.00%
+2022,3,2,66.67%
+2023,13,10,76.92%
+2024,5,5,100.00%
+2025,4,4,100.00%