add DB v0.5 (2018-09-23), changes by Patrick

README.md

@@ -1,3 +1,42 @@
+# v0.5
+
+Based on v0.4 (changes by Patrick):
+
+tbl_inflow Added new parameters to allow for stochastic distribution parameters to be entered
+"distribution"= the type of stochastic distribution to describe uncertainty about mean concentration
+"alpha" "beta" = the parameters of this distribution, assuming that no more than two parameter distributions will be used. e.g. with normal distribution alpha is the mean and beta is the standard deviation
+Michael: align naming of distributon type with R or make sure R can translate it. Also allow for input of these parameters through the .csv file
+Check: entered now as lognormal, entered values as normal distributed over log concentration (mean=min+max/2 stdev=mean-min in log values)
+
+tbl_inflow Changed Field size of min, max, alpha, beta to "Double" to allow for digits in the values (concentrations <1/l)
+
+tbl_waterSource: changed field names for consistency and added descriptions of water sources 
+
+tbl_pathogen: added "viruses" "bacteria" and "protozoa" since this is the level that selections are made
+all other pathogens were removed from this table for this level assessment
+I saved original table: "Copy Of tbl_pathogen"
+
+tbl_doseResponse: added viruses (rotavirus) bacteria (campy) protozoa (crypto) 
+Note: need to check which one was chosen by Michael since there are multiple D-R for some organisms
+
+tbl_health: changed to viruses (rotavirus) bacteria (campy) protozoa (crypto)
+
+Note: Why is tbl_pathogen:tbl_doseResponse a one to many? each pathogenID has a single dose response. So these don't need to be in separate tables
+Note: Log removal is now based on pathogen type, however it should be per pathogen (adenovirus different from enterovirus etc. althogh some will be the same due to lack of detail)
+Note: the front end selects data from databases based on user selection. It then combines all relevant information from databases in csv files for the R-tool. For the front end it keeps other data to store the scenario and later on make graphs etc.
+
+tbl_exposure changed name to "tbl_ingestion" since exposure is generally used for the pathogens and we want to show that exposure as output. e.g. WHO QMRAdoc "magnitude and frequency of exposure to reference pathogens via the defined exposure pathways and hazardous
+events" although the term isn't used consistently (e.g. Table A5.4)
+
+Michael: the .csv file "exposure" is very different from "tbl_exposure". Please clarify what should be sent from the front end to the R-tool:
+- is the number of events per year a value or a distribution?
+- is the volume per event a value or a distribution?
+- where do we set the number of repetitions (Monte Carlo simulation)?
+
+
+Note that we allow only one intended use, for other applications the user needs to do a separate run of the model
+
+
 # v0.4
 
 Based on v0.3

qmra-db_accdb/tbl_doseResponse.csv

@@ -1,38 +1,4 @@
 "PathogenID","Bestfitmodel","k","alpha","N50","Hosttype","Doseunits","Route","Response","ReferenceID"
-1,"exponential",1.65e-05,NA,NA,"guinea pig","spores","inhalation","death",9
-2,"beta-Poisson",NA,0.328,5430,"C57BL/6 mice and diabetic rat","CFU","intranasal,intraperitoneal","death",22
-3,"beta-Poisson",NA,0.144,890,"human","CFU","oral (in milk)","infection",2
-4,"beta-Poisson",NA,0.357,4.93e+08,"C57BL/1OScN mice","PFU","intraperitoneal","death",41
-5,"exponential",0.000218,NA,NA,"pig","CFU","oral (in food)","shedding in feces",4
-6,"beta-Poisson",NA,0.155,2110000,"human","CFU","oral (in milk)","positive stool isolation",10
-7,"exponential",0.0473,NA,NA,"monkeys","CFU","inhalation","death",6
-8,"exponential",0.0599,NA,NA,"guinea pig","CFU","inhalation","infection",28
-9,"exponential",1.15e-05,NA,NA,"C57B1/6J mice","CFU","oral","death",13
-10,"beta-Poisson",NA,0.253,277,"C57Bl/6J mice","CFU","oral","infection",12
-11,"beta-Poisson",NA,0.0422,1.78e+09,"pooled","CFU","oral","stillbirths",36
-12,"exponential",0.000693,NA,NA,"deer","CFU","oral","infection",30
-13,"beta-Poisson",NA,0.19,18500,"white rabbit","CFU","contact lens","corneal ulceration",21
-14,"exponential",0.000105,NA,NA,"Swiss webster mice (5day old)","CFU","injected in eyelids","death",14
-15,"beta-Poisson",NA,0.777,21.3,"Pooled data","CFU",NA,"morbidity",34
-16,"beta-Poisson",NA,0.175,1110000,"human","CFU","oral, in milk","disease",16
-17,"beta-Poisson",NA,0.318,37100,"human","CFU","oral, with eggnog","positive stool culture",24
-18,"beta-Poisson",NA,0.389,16800,"human","CFU","oral, with eggnog","infection",23
-19,"beta-Poisson",NA,0.21,49.8,"mice","CFU","intraperitoneal","death",27
-20,"exponential",3.97e-06,NA,NA,"human","CFU","oral","infection",25
-21,"beta-Poisson",NA,0.265,1480,"human","CFU","oral (in milk)","positive stool isolation",11
-22,"exponential",7.64e-08,NA,NA,"human","CFU/cm2","subcutaneous","infection",33
-23,"beta-Poisson",NA,0.25,243,"human","CFU","oral (with NaHCO3)","infection",17
-24,"exponential",0.00163,NA,NA,"mice","CFU","intranasal","death",20
-25,"exponential",0.607,NA,NA,"human","TCID50","inhalation","infection",5
-26,"beta-Poisson",NA,1.06,922,"human","PFU","oral","infection",35
-27,"exponential",0.00374,NA,NA,"pig","PFU","oral","infection",3
-28,"beta-Poisson",NA,0.581,945000,"human","TCID50","intranasal","infection",29
-29,"exponential",2.95,NA,NA,"guinea pig","PFU","subcutaneous","death",18
-30,"exponential",0.491,NA,NA,"human","PD50 (mouse paralytic doses)","oral (capsule)","alimentary infection",19
-31,"beta-Poisson",NA,0.221,1.81,"human","TCID50 doses","intranasal","infection",15
-32,"beta-Poisson",NA,0.253,6.17,"human","FFU","oral","infection",37
-33,"exponential",0.00246,NA,NA,"mice hACE-2 and A/J","PFU","intranasal","death",7
-34,"exponential",0.0572,NA,NA,"human","oocysts","oral","infection",26
-35,"beta-Poisson",NA,0.101,341,"human","Cysts","oral","infection",31
-36,"exponential",0.0199,NA,NA,"human","Cysts","oral","infection",32
-37,"exponential",3.42e-07,NA,NA,"mice","no of trophozoites","intravenous","death",1
+39,"beta-Poisson",NA,0.144,890,"human","CFU","oral (in milk)","infection",2
+38,"beta-Poisson",NA,0.253,6.17,"human","FFU","oral","infection",37
+40,"exponential",0.0572,NA,NA,"human","oocysts","oral","infection",26

qmra-db_accdb/tbl_health.csv

@@ -1,4 +1,4 @@
 "PathogenID","ReferenceID","infection_to_illness","dalys_per_case"
-3,38,0.3,0.0046
-32,38,0.5,0.014
-34,38,0.7,0.0015
+39,38,0.3,0.0046
+38,38,0.5,0.014
+40,38,0.7,0.0015

qmra-db_accdb/tbl_inflow.csv

@@ -1,8 +1,5 @@
-"PathogenID","ReferenceID","WaterSourceID","min","max"
-3,39,8,100,1e+06
-6,39,8,1000000,1e+10
-23,39,8,100,1e+06
-27,39,8,1,1000
-32,39,8,50,5000
-34,39,8,1,10000
-36,39,8,1,10000
+"PathogenID","ReferenceID","WaterSourceID","min","max","distribution","alpha","beta"
+39,39,8,100,1e+06,"lognormal",10000,100
+6,39,8,1e+06,1e+10,"lognormal",1e+08,100
+40,39,8,1,10000,"lognormal",31.6,31.6
+38,39,8,1,1000,"lognormal",31.6,31.6

qmra-db_accdb/tbl_exposure.csv → qmra-db_accdb/tbl_ingestion.csv

@@ -1,7 +1,7 @@
 "WaterUseID","WaterUseName","WaterUseDescription","events_perYear","litres_perEvent","ReferenceID"
 1,"irrigation, unrestricted",NA,NA,NA,NA
 2,"domestic use, car washing",NA,NA,NA,NA
-7,"irrigation, public",NA,50,0.001,NA
 3,"irrigation, restricted",NA,NA,NA,NA
 4,"domestic use, toilet flushing",NA,1000,1e-05,NA
 5,"drinking water",NA,365,1,NA
+7,"irrigation, public",NA,50,0.001,NA

qmra-db_accdb/tbl_logRemoval.csv

@@ -1,60 +1,60 @@
 "TreatmentID","min","max","ReferenceID","PathogenGroupID"
 1,0.2,2,40,1
-1,1,2,40,3
 1,0.1,3.4,40,2
+1,1,2,40,3
 2,0.6,2.6,40,3
 3,2,2.8,40,3
 4,1,4,40,1
-4,0,2,40,3
 4,2,4,40,2
+4,0,2,40,3
 5,0.2,4.4,40,1
-5,0.4,3.3,40,3
 5,0,3.5,40,2
+5,0.4,3.3,40,3
 6,1,7,40,1
-6,2.3,7,40,3
 6,1,6.5,40,2
+6,2.3,7,40,3
 7,0.2,2.3,40,1
-7,3,6.7,40,3
 7,1,1.7,40,2
+7,3,6.7,40,3
 8,2,6,40,1
-8,0.3,5,40,3
 8,0.25,4,40,2
+8,0.3,5,40,3
 9,2,6,40,1
-9,1,2,40,3
 9,2.1,8.3,40,2
+9,1,2,40,3
 10,0.2,2.3,40,1
 11,0.7,2.2,40,1
 11,1.4,2.3,40,3
 12,2,2,40,1
-12,2,2,40,3
 12,2,2,40,2
+12,2,2,40,3
 13,2,2,40,1
-13,2,2,40,3
 13,2,2,40,2
+13,2,2,40,3
 14,2,2,40,1
-14,2,2,40,3
 14,2,2,40,2
+14,2,2,40,3
 15,4,4,40,1
-15,4,4,40,3
 15,4,4,40,2
+15,4,4,40,3
 16,0,0.5,8,1
-16,0,1,8,3
 16,0,0.1,8,2
+16,0,1,8,3
 17,1,3,8,1
-17,0.5,1.5,8,3
 17,0.5,2,8,2
+17,0.5,1.5,8,3
 18,0,1,8,1
-18,1.5,2.5,8,3
 18,0.5,3,8,2
+18,1.5,2.5,8,3
 19,3.5,6,8,1
-19,6,6,8,3
 19,2.5,6,8,2
+19,6,6,8,3
 20,2,6,8,1
-20,0,1.5,8,3
 20,1,3,8,2
-21,6,6,8,1
+20,0,1.5,8,3
 21,6,6,6,2
 21,6,6,6,3
+21,6,6,8,1
 22,2,6,8,1
 22,3,6,8,2
 23,1.5,2.5,8,1

qmra-db_accdb/tbl_pathogen.csv

@@ -1,38 +1,5 @@
 "PathogenID","PathogenName","PathogenDescription","PathogenGroupID"
-1,"Bacillus anthracis",NA,1
-2,"Burkholderia pseudomallei",NA,1
-3,"Campylobacter jejuni",NA,1
-4,"Coxiella burnetii",NA,1
-5,"Escherichia coli enterohemorrhagic (EHEC)",NA,1
 6,"Escherichia coli",NA,1
-7,"Francisella tularensis",NA,1
-8,"Legionella pneumophila",NA,1
-9,"Listeria monocytogenes (Death as response)",NA,1
-10,"Listeria monocytogenes (Infection)",NA,1
-11,"Listeria monocytogenes (Stillbirths)",NA,1
-12,"Mycobacterium avium",NA,1
-13,"Pseudomonas aeruginosa (Contact lens)",NA,1
-14,"Pseudomonas aeruginosa (bacterimia)",NA,1
-15,"Rickettsia rickettsi",NA,1
-16,"Salmonella Typhi",NA,1
-17,"Salmonella anatum",NA,1
-18,"Salmonella meleagridis",NA,1
-19,"Salmonella nontyphoid",NA,1
-20,"Salmonella serotype newport",NA,1
-21,"Shigella",NA,1
-22,"Staphylococcus aureus",NA,1
-23,"Vibrio cholerae",NA,1
-24,"Yersinia pestis",NA,1
-25,"Adenovirus",NA,2
-26,"Echovirus",NA,2
-27,"Enteroviruses",NA,2
-28,"Influenza",NA,2
-29,"Lassa virus",NA,2
-30,"Poliovirus",NA,2
-31,"Rhinovirus",NA,2
-32,"Rotavirus",NA,2
-33,"SARS",NA,2
-34,"Cryptosporidium parvum",NA,3
-35,"Endamoeba coli",NA,3
-36,"Giardia duodenalis",NA,3
-37,"Naegleria fowleri",NA,3
+38,"Viruses","Viruses are the smallest waterborne pathogens. They cannot replicate themselves, but they are replicated by the human (or animal) they infect. They are generally very host-specific, so generally only human viruses can infect other humans. Well-known waterborne viral diseases are gastroenteritis with symptoms of diarrhoea, vomiting or fever (norovirus), hepatitis A and E (hepatitis virus). Polio appears to have been eradicated since 2012",2
+39,"Bacteria","Bacteria are single-celled organisms. They can replicate very rapidly under favourable conditions. Most pathogenic bacteria replicate only inside infected humans or animals, but some can also replicate outside the host�s body. Bacterial pathogens are not very host-specific. Zoonotic bacteria can infect both animals and humans. Well-known bacterial diseases are typhoid (Salmonella typhi), cholera (Vibrio cholerae), gastroenteritis with symptoms of diarrhoea, vomiting or fever (Campylobacter, E. coli  O157:H7) and dysentery (Shigella). The bacteria E. coli and enterococcus are generally used to monitor water quality by analysis of water samples in a laboratory. These bacteria are present in large numbers in faeces of warm-blooded animals, so detection in the water indicates recent faecal contamination of the water. The organisms themselves are not infectious to humans.",1
+40,"Protozoa","Protozoa are single-celled organisms, slightly larger than most bacteria. They can form (oo)cysts that are very resistant to environmental conditions and to chlorine and other disinfectants. This makes them of special concern. Giardia and Cryptosporidium are protozoa that are known to cause outbreaks of disease even in chlorinated systems. Shedding of the protozoa Cryptosporidium by young calves has been an important cause of water contamination in many cases. Infections with Entamoeba histolytica have also been reported in tropical regions.",3

qmra-db_accdb/tbl_treatment.csv

@@ -1,6 +1,4 @@
 "TreatmentID","TreatmentName","TreatmentGroup","TreatmentDescription"
-27,"Ultrafiltration","Filtration",NA
-28,"Nanofiltration","Filtration",NA
 1,"Conventional clarification","Coagulation, flocculation and sedimentation",NA
 2,"Dissolved air flotation","Coagulation, flocculation and sedimentation",NA
 3,"High-rate clarification","Coagulation, flocculation and sedimentation",NA
@@ -32,3 +30,5 @@ Wetlands, surface flow",NA,NA
 25,"UV radiation
 UV","Primary disinfection",NA
 26,"Microfiltration","Filtration",NA
+27,"Ultrafiltration","Filtration",NA
+28,"Nanofiltration","Filtration",NA

qmra-db_accdb/tbl_waterSource.csv

@@ -1,9 +1,9 @@
 "WaterSourceID","WaterSourceName","WaterSourceDescription"
-1,"sewage, treated",NA
-2,"surface water",NA
-3,"surface water, contaminated",NA
-4,"surface water, protected",NA
-5,"harvesting, rainwater",NA
-6,"harvesting, stormwater",NA
-7,"drinking water",NA
-8,"sewage, raw",NA
+1,"treated wastewater","Municipal sewage that has received secondary, so including activated sludge"
+2,"surface water, general","Rivers, lakes, ponds. Select this categogy if no indication of the level of contamination is known"
+3,"surface water, contaminated","Rivers, lakes, ponds that are prone to discharge of treated or untreated wastewater or other sources of fecal contamination are known (e.g. cattle accessing the water, runoff from agricultural land)"
+4,"surface water, protected","Rivers, lakes, ponds where the absence of pollution is actively managed, e.g. in protcted catchments"
+5,"rainwater, rooftop harvesting","Rainwater collected from rooftops or other surface areas which are kept relatively clean"
+6,"rainwater, stormwater harvesting","Rainwater collected from roads or other surfaces which are likely to be contaminated"
+7,"drinking water","Drinking water which is perceived as clean, e.g. protected groundwater wells"
+8,"raw sewage","Municipal sewage that has not received any treatment or only minimal treatment e.g. sedimentation"