diff --git a/docs/articles/OldFord_PotableReuse.html b/docs/articles/OldFord_PotableReuse.html index c5690036..7bd0b430 100644 --- a/docs/articles/OldFord_PotableReuse.html +++ b/docs/articles/OldFord_PotableReuse.html @@ -8,8 +8,10 @@ WWTP Old Ford: public irrigation scenario • kwb.qmra - - + + + + @@ -100,7 +108,7 @@

WWTP Old Ford: public irrigation scenario

Michael Rustler

-

05 Juni, 2018

+

26 June, 2018

@@ -138,7 +146,7 @@ 

#### DEFINE DIRECTORY ################
 confDir <- dir(scenarios_dir,full.names = TRUE)[2]
 confDir
-
## [1] "C:\\Users\\mrustl.KWB\\AppData\\Local\\Temp\\RtmpoTpDGb/scenarios/oldFord_prior_potableReuse"
+
## [1] "C:\\Users\\mrustl.KWB\\AppData\\Local\\Temp\\Rtmp4Q6dO2/scenarios/oldFord_prior_potableReuse"

@@ -657,7 +665,7 @@

## Simulated exposure: volume per event ## Replicate 365000 times constant value 1.000000 
## Joining, by = c("PathogenGroup", "eventID", "repeatID")
-
## Warning: Paket 'bindrcpp' wurde unter R Version 3.4.4 erstellt
+
## Warning: package 'bindrcpp' was built under R version 3.4.4
## Joining, by = c("eventID", "repeatID")
## 
 ## ### STEP 4: DOSE RESPONSE #################################################
@@ -689,7 +697,7 @@ 

 ##   ..$ events:'data.frame':   1095000 obs. of  6 variables:
 ##   .. ..$ repeatID     : int [1:1095000] 1 1 1 1 1 1 1 1 1 1 ...
 ##   .. ..$ eventID      : int [1:1095000] 1 2 3 4 5 6 7 8 9 10 ...
-##   .. ..$ inflow       : num [1:1095000] 447152 537387 436318 510017 389743 ...
+##   .. ..$ inflow       : num [1:1095000] 917947 80710 637611 837167 412221 ...
 ##   .. ..$ PathogenID   : int [1:1095000] 3 3 3 3 3 3 3 3 3 3 ...
 ##   .. ..$ PathogenName : chr [1:1095000] "Campylobacter jejuni" "Campylobacter jejuni" "Campylobacter jejuni" "Campylobacter jejuni" ...
 ##   .. ..$ PathogenGroup: chr [1:1095000] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ...
@@ -706,7 +714,7 @@ 

 ##   ..$ events_long        :'data.frame':  12045000 obs. of  8 variables:
 ##   .. ..$ repeatID           : int [1:12045000] 1 1 1 1 1 1 1 1 1 1 ...
 ##   .. ..$ eventID            : int [1:12045000] 1 1 1 1 2 2 2 2 3 3 ...
-##   .. ..$ logreduction       : num [1:12045000] 0.459 0.459 0.459 0.459 0.109 ...
+##   .. ..$ logreduction       : num [1:12045000] 0.0931 0.0931 0.0931 0.0931 0.1184 ...
 ##   .. ..$ TreatmentID        : int [1:12045000] 16 16 16 16 16 16 16 16 16 16 ...
 ##   .. ..$ PathogenGroup      : chr [1:12045000] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ...
 ##   .. ..$ TreatmentSchemeID  : int [1:12045000] 1 2 3 4 1 2 3 4 1 2 ...
@@ -719,16 +727,16 @@ 

 ##   .. ..$ TreatmentSchemeID  : int [1:12045000] 0 1 2 2 3 3 3 4 4 4 ...
 ##   .. ..$ TreatmentSchemeName: chr [1:12045000] "0" "1st" "1st-2nd" "1st-2nd" ...
 ##   .. ..$ TreatmentName      : chr [1:12045000] "None" "Primary treatment" "Primary treatment" "Secondary treatment" ...
-##   .. ..$ 16                 : num [1:12045000] NA 0.459 0.459 NA NA ...
-##   .. ..$ 17                 : num [1:12045000] NA NA NA 1.45 NA ...
-##   .. ..$ 19                 : num [1:12045000] NA NA NA NA 3.53 ...
+##   .. ..$ 16                 : num [1:12045000] NA 0.0931 0.0931 NA NA ...
+##   .. ..$ 17                 : num [1:12045000] NA NA NA 2.42 NA ...
+##   .. ..$ 19                 : num [1:12045000] NA NA NA NA 5.61 ...
 ##   .. ..$ 20                 : num [1:12045000] NA NA NA NA NA ...
 ##   .. ..$ 21                 : num [1:12045000] 0 NA NA NA NA NA NA NA NA NA ...
 ##   ..$ schemes_events_wide:'data.frame':  12045000 obs. of  7 variables:
 ##   .. ..$ eventID      : int [1:12045000] 1 1 1 1 1 1 1 1 1 1 ...
 ##   .. ..$ PathogenGroup: chr [1:12045000] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ...
 ##   .. ..$ scheme_0     : num [1:12045000] 0 NA NA NA NA NA NA NA NA NA ...
-##   .. ..$ scheme_1     : num [1:12045000] NA 0.459 0.459 NA NA ...
+##   .. ..$ scheme_1     : num [1:12045000] NA 0.0931 0.0931 NA NA ...
 ##   .. ..$ scheme_2     : num [1:12045000] NA NA NA NA NA NA NA NA NA NA ...
 ##   .. ..$ scheme_3     : num [1:12045000] NA NA NA NA NA NA NA NA NA NA ...
 ##   .. ..$ scheme_4     : num [1:12045000] NA NA NA NA NA NA NA NA NA NA ...
@@ -813,21 +821,21 @@ 

 ##   ..$ PathogenGroup          : chr [1:5475000] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ...
 ##   ..$ eventID                : int [1:5475000] 1 1 1 1 1 2 2 2 2 2 ...
 ##   ..$ repeatID               : int [1:5475000] 1 1 1 1 1 1 1 1 1 1 ...
-##   ..$ logreduction           : num [1:5475000] 0 0.459 1.906 5.44 7.834 ...
-##   ..$ inflow                 : num [1:5475000] 447152 447152 447152 447152 447152 ...
+##   ..$ logreduction           : num [1:5475000] 0 0.0931 2.5132 8.1274 13.5012 ...
+##   ..$ inflow                 : num [1:5475000] 917947 917947 917947 917947 917947 ...
 ##   ..$ PathogenID             : int [1:5475000] 3 3 3 3 3 3 3 3 3 3 ...
 ##   ..$ PathogenName           : chr [1:5475000] "Campylobacter jejuni" "Campylobacter jejuni" "Campylobacter jejuni" "Campylobacter jejuni" ...
-##   ..$ effluent               : num [1:5475000] 4.47e+05 1.55e+05 5.55e+03 1.62 6.56e-03 ...
+##   ..$ effluent               : num [1:5475000] 9.18e+05 7.41e+05 2.82e+03 6.84e-03 2.89e-08 ...
 ##   ..$ volume_perEvent        : int [1:5475000] 1 1 1 1 1 1 1 1 1 1 ...
-##   ..$ exposure_perEvent      : num [1:5475000] 4.47e+05 1.55e+05 5.55e+03 1.62 6.56e-03 ...
-##   ..$ dose_perEvent          : int [1:5475000] 445988 155299 5598 0 0 536374 417690 5580 0 0 ...
-##   ..$ infectionProb_per_event: num [1:5475000] 0.796 0.762 0.616 0 0 ...
+##   ..$ exposure_perEvent      : num [1:5475000] 9.18e+05 7.41e+05 2.82e+03 6.84e-03 2.89e-08 ...
+##   ..$ dose_perEvent          : int [1:5475000] 917917 740831 2794 0 0 80135 61487 264 0 0 ...
+##   ..$ infectionProb_per_event: num [1:5475000] 0.816 0.81 0.576 0 0 ...
 ##   ..$ infection_to_illness   : num [1:5475000] 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 ...
 ##   ..$ dalys_per_case         : num [1:5475000] 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 ...
 ##   ..$ ReferenceName          : chr [1:5475000] "WHO (2011): Drinking water guideline, Table 7.4" "WHO (2011): Drinking water guideline, Table 7.4" "WHO (2011): Drinking water guideline, Table 7.4" "WHO (2011): Drinking water guideline, Table 7.4" ...
 ##   ..$ ReferenceLink          : chr [1:5475000] "http://apps.who.int/iris/bitstream/10665/44584/1/9789241548151_eng.pdf#page=155" "http://apps.who.int/iris/bitstream/10665/44584/1/9789241548151_eng.pdf#page=155" "http://apps.who.int/iris/bitstream/10665/44584/1/9789241548151_eng.pdf#page=155" "http://apps.who.int/iris/bitstream/10665/44584/1/9789241548151_eng.pdf#page=155" ...
-##   ..$ illnessProb_per_event  : num [1:5475000] 0.239 0.229 0.185 0 0 ...
-##   ..$ dalys_per_event        : num [1:5475000] 0.0011 0.00105 0.00085 0 0 ...
+##   ..$ illnessProb_per_event  : num [1:5475000] 0.245 0.243 0.173 0 0 ...
+##   ..$ dalys_per_event        : num [1:5475000] 0.001126 0.001118 0.000794 0 0 ...
 ##   ..- attr(*, "vars")= chr [1:4] "TreatmentSchemeID" "TreatmentSchemeName" "PathogenGroup" "eventID"
 ##   ..- attr(*, "labels")='data.frame':    5475 obs. of  4 variables:
 ##   .. ..$ TreatmentSchemeID  : int [1:5475] 0 0 0 0 0 0 0 0 0 0 ...
@@ -948,14 +956,14 @@ 

 ##   ..$ PathogenName       : chr [1:15000] "Campylobacter jejuni" "Rotavirus" "Cryptosporidium parvum" "Campylobacter jejuni" ...
 ##   ..$ PathogenGroup      : chr [1:15000] "Bacteria" "Viruses" "Protozoa" "Bacteria" ...
 ##   ..$ events             : int [1:15000] 365 365 365 365 365 365 365 365 365 365 ...
-##   ..$ inflow_median      : num [1:15000] 494555 2672 4973 494555 2672 ...
-##   ..$ logreduction_median: num [1:15000] 0 0 0 0.2678 0.0502 ...
+##   ..$ inflow_median      : num [1:15000] 482058 2294 5000 482058 2294 ...
+##   ..$ logreduction_median: num [1:15000] 0 0 0 0.2496 0.0486 ...
 ##   ..$ volume_sum         : int [1:15000] 365 365 365 365 365 365 365 365 365 365 ...
-##   ..$ exposure_sum       : num [1:15000] 1.82e+08 9.60e+05 1.79e+06 1.04e+08 8.58e+05 ...
-##   ..$ dose_sum           : int [1:15000] 181833941 959284 1795208 103510665 860033 728036 2214557 78406 83751 106 ...
+##   ..$ exposure_sum       : num [1:15000] 1.77e+08 8.65e+05 1.83e+06 1.04e+08 7.77e+05 ...
+##   ..$ dose_sum           : int [1:15000] 176852764 865606 1829451 103609235 778360 737684 2174748 71010 94326 112 ...
 ##   ..$ infectionProb_sum  : num [1:15000] 1 1 1 1 1 ...
 ##   ..$ illnessProb_sum    : num [1:15000] 1 1 1 1 1 ...
-##   ..$ dalys_sum          : num [1:15000] 0.396 2.247 0.381 0.386 2.238 ...
+##   ..$ dalys_sum          : num [1:15000] 0.395 2.239 0.383 0.386 2.23 ...
 ##   ..- attr(*, "vars")= chr [1:5] "repeatID" "TreatmentSchemeID" "TreatmentSchemeName" "PathogenID" ...
 ##   ..- attr(*, "drop")= logi TRUE

Thus the user has access to all results.

@@ -1085,14 +1093,14 @@

Campylobacter jejuni Bacteria 365 -494555.023 +482058.389 0.0000000 365 -1.818511e+08 -181833941 +1.768543e+08 +176852764 1.0000000 1.0000000 -0.3960481 +0.3954151 1 @@ -1102,14 +1110,14 @@

Rotavirus Viruses 365 -2671.992 +2293.630 0.0000000 365 -9.599605e+05 -959284 +8.654389e+05 +865606 1.0000000 1.0000000 -2.2473266 +2.2391351 1 @@ -1119,14 +1127,14 @@

Cryptosporidium parvum Protozoa 365 -4973.285 +4999.568 0.0000000 365 -1.794275e+06 -1795208 +1.829787e+06 +1829451 1.0000000 1.0000000 -0.3810995 +0.3829863 1 @@ -1136,14 +1144,14 @@

Campylobacter jejuni Bacteria 365 -494555.023 -0.2678000 +482058.389 +0.2496297 365 -1.035111e+08 -103510665 +1.036035e+08 +103609235 1.0000000 1.0000000 -0.3859880 +0.3858960 1 @@ -1153,14 +1161,14 @@

Rotavirus Viruses 365 -2671.992 -0.0502211 +2293.630 +0.0486245 365 -8.584255e+05 -860033 +7.766945e+05 +778360 1.0000000 1.0000000 -2.2384652 +2.2296912 1 @@ -1170,14 +1178,14 @@

Cryptosporidium parvum Protozoa 365 -4973.285 -0.5114650 +4999.568 +0.4905561 365 -7.268409e+05 -728036 +7.382405e+05 +737684 1.0000000 1.0000000 -0.3784575 +0.3806089 1 @@ -1187,14 +1195,14 @@

Campylobacter jejuni Bacteria 365 -494555.023 -2.2832195 +482058.389 +2.2796193 365 -2.213746e+06 -2214557 +2.173946e+06 +2174748 1.0000000 1.0000000 -0.2716946 +0.2725962 1 @@ -1204,14 +1212,14 @@

Rotavirus Viruses 365 -2671.992 -1.2831768 +2293.630 +1.2509413 365 -7.802607e+04 -78406 +7.047213e+04 +71010 1.0000000 1.0000000 -1.8750911 +1.8673308 1 @@ -1221,14 +1229,14 @@

Cryptosporidium parvum Protozoa 365 -4973.285 -1.4963317 +4999.568 +1.4902524 365 -8.389713e+04 -83751 +9.427079e+04 +94326 1.0000000 1.0000000 -0.3507002 +0.3461806 1 @@ -1238,14 +1246,14 @@

Campylobacter jejuni Bacteria 365 -494555.023 -7.0838192 +482058.389 +7.0256899 365 -1.171063e+02 -106 -0.8038235 -0.3798779 -0.0021781 +1.145329e+02 +112 +0.8451686 +0.4236382 +0.0025185 1 @@ -1255,14 +1263,14 @@

Rotavirus Viruses 365 -2671.992 -5.5020433 +2293.630 +5.6159475 365 -3.081156e+01 -31 -0.9995577 -0.9699217 -0.0451909 +2.589215e+01 +33 +0.9998781 +0.9837517 +0.0533956 1 @@ -1272,10 +1280,10 @@

Cryptosporidium parvum Protozoa 365 -4973.285 -7.4963317 +4999.568 +7.4902524 365 -8.389710e-02 +9.427080e-02 0 0.0000000 0.0000000 @@ -1289,14 +1297,14 @@

Campylobacter jejuni Bacteria 365 -494555.023 -11.2045868 +482058.389 +11.0894174 365 -1.832132e-01 -0 -0.0000000 -0.0000000 -0.0000000 +1.100879e-01 +1 +0.0183515 +0.0055055 +0.0000253 1 @@ -1306,14 +1314,14 @@

Rotavirus Viruses 365 -2671.992 -7.4064595 +2293.630 +7.5545833 365 -4.593275e-01 -0 -0.0000000 -0.0000000 -0.0000000 +6.632673e-01 +1 +0.2633623 +0.1316812 +0.0018435 1 @@ -1323,10 +1331,10 @@

Cryptosporidium parvum Protozoa 365 -4973.285 -8.2533495 +4999.568 +8.1904208 365 -2.251630e-02 +2.741630e-02 0 0.0000000 0.0000000 @@ -1339,7 +1347,7 @@

6 Export results

-

E.g. Write reports for all configurations in a folder e.g. /scenarios (here: C:.KWB/scenarios):

+

E.g. Write reports for all configurations in a folder e.g. /scenarios (here: C:.KWB4Q6dO2/scenarios):

@@ -1387,6 +1395,20 @@

- - + + diff --git a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-10-1.png index 7ee07eb2..f56bb5bc 100644 Binary files a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-11-1.png b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-11-1.png index 1df94903..bfccd1ad 100644 Binary files a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-11-1.png and b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-11-1.png differ diff --git a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-12-1.png b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-12-1.png index 4fea436a..bb2a4a56 100644 Binary files a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-12-1.png and b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-12-1.png differ diff --git a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-14-1.png b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-14-1.png index 4b3d384a..b31057fb 100644 Binary files a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-14-1.png and b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-14-1.png differ diff --git a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-15-1.png index 18a397fa..dbd77300 100644 Binary files a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-15-1.png and b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-15-1.png differ diff --git a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-16-1.png b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-16-1.png index a5400b3b..3e7d3e8d 100644 Binary files a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-16-1.png and b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-16-1.png differ diff --git a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-17-1.png b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-17-1.png index d910fd85..e0e8544a 100644 Binary files a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-17-1.png and b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-17-1.png differ diff --git a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-18-1.png b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-18-1.png index f8b5be85..653b9cae 100644 Binary files a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-18-1.png and b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-18-1.png differ diff --git a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-19-1.png b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-19-1.png index 05cbeeb2..bb4fef86 100644 Binary files a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-19-1.png and b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-19-1.png differ diff --git a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-9-1.png b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-9-1.png index 715ac804..14c0cd4e 100644 Binary files a/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-9-1.png and b/docs/articles/OldFord_PotableReuse_files/figure-html/unnamed-chunk-9-1.png differ diff --git a/docs/articles/OldFord_PublicIrrigation.html b/docs/articles/OldFord_PublicIrrigation.html index 61b496d7..39f3e9d0 100644 --- a/docs/articles/OldFord_PublicIrrigation.html +++ b/docs/articles/OldFord_PublicIrrigation.html @@ -8,8 +8,10 @@ WWTP Old Ford: public irrigation scenario • kwb.qmra - - + + + + @@ -100,7 +108,7 @@

WWTP Old Ford: public irrigation scenario

Michael Rustler

-

05 Juni, 2018

+

26 June, 2018

@@ -135,7 +143,7 @@ 

#### DEFINE DIRECTORY ################
 confDir <- dir(scenarios_dir,full.names = TRUE)[1]
 confDir
-
## [1] "C:\\Users\\mrustl.KWB\\AppData\\Local\\Temp\\Rtmp8a13Gu/scenarios/oldFord_prior_irrigationPublic"
+
## [1] "C:\\Users\\mrustl.KWB\\AppData\\Local\\Temp\\RtmpCO5qI7/scenarios/oldFord_prior_irrigationPublic"

@@ -653,7 +661,7 @@

## Simulated exposure: volume per event ## Replicate 50000 times constant value 0.001000 
## Joining, by = c("PathogenGroup", "eventID", "repeatID")
-
## Warning: Paket 'bindrcpp' wurde unter R Version 3.4.4 erstellt
+
## Warning: package 'bindrcpp' was built under R version 3.4.4
## Joining, by = c("eventID", "repeatID")
## 
 ## ### STEP 4: DOSE RESPONSE #################################################
@@ -685,7 +693,7 @@ 

 ##   ..$ events:'data.frame':   150000 obs. of  6 variables:
 ##   .. ..$ repeatID     : int [1:150000] 1 1 1 1 1 1 1 1 1 1 ...
 ##   .. ..$ eventID      : int [1:150000] 1 2 3 4 5 6 7 8 9 10 ...
-##   .. ..$ inflow       : num [1:150000] 930972 658790 133159 601524 692630 ...
+##   .. ..$ inflow       : num [1:150000] 542287 606840 211180 414027 796748 ...
 ##   .. ..$ PathogenID   : int [1:150000] 3 3 3 3 3 3 3 3 3 3 ...
 ##   .. ..$ PathogenName : chr [1:150000] "Campylobacter jejuni" "Campylobacter jejuni" "Campylobacter jejuni" "Campylobacter jejuni" ...
 ##   .. ..$ PathogenGroup: chr [1:150000] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ...
@@ -702,7 +710,7 @@ 

 ##   ..$ events_long        :'data.frame':  1650000 obs. of  8 variables:
 ##   .. ..$ repeatID           : int [1:1650000] 1 1 1 1 1 1 1 1 1 1 ...
 ##   .. ..$ eventID            : int [1:1650000] 1 1 1 1 2 2 2 2 3 3 ...
-##   .. ..$ logreduction       : num [1:1650000] 0.434 0.434 0.434 0.434 0.409 ...
+##   .. ..$ logreduction       : num [1:1650000] 0.153 0.153 0.153 0.153 0.299 ...
 ##   .. ..$ TreatmentID        : int [1:1650000] 16 16 16 16 16 16 16 16 16 16 ...
 ##   .. ..$ PathogenGroup      : chr [1:1650000] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ...
 ##   .. ..$ TreatmentSchemeID  : int [1:1650000] 1 2 3 4 1 2 3 4 1 2 ...
@@ -715,16 +723,16 @@ 

 ##   .. ..$ TreatmentSchemeID  : int [1:1650000] 0 1 2 2 3 3 3 4 4 4 ...
 ##   .. ..$ TreatmentSchemeName: chr [1:1650000] "0" "1st" "1st-2nd" "1st-2nd" ...
 ##   .. ..$ TreatmentName      : chr [1:1650000] "None" "Primary treatment" "Primary treatment" "Secondary treatment" ...
-##   .. ..$ 16                 : num [1:1650000] NA 0.434 0.434 NA NA ...
-##   .. ..$ 17                 : num [1:1650000] NA NA NA 2.63 NA ...
-##   .. ..$ 19                 : num [1:1650000] NA NA NA NA 5.66 ...
+##   .. ..$ 16                 : num [1:1650000] NA 0.153 0.153 NA NA ...
+##   .. ..$ 17                 : num [1:1650000] NA NA NA 1.19 NA ...
+##   .. ..$ 19                 : num [1:1650000] NA NA NA NA 3.6 ...
 ##   .. ..$ 20                 : num [1:1650000] NA NA NA NA NA ...
 ##   .. ..$ 21                 : num [1:1650000] 0 NA NA NA NA NA NA NA NA NA ...
 ##   ..$ schemes_events_wide:'data.frame':  1650000 obs. of  7 variables:
 ##   .. ..$ eventID      : int [1:1650000] 1 1 1 1 1 1 1 1 1 1 ...
 ##   .. ..$ PathogenGroup: chr [1:1650000] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ...
 ##   .. ..$ scheme_0     : num [1:1650000] 0 NA NA NA NA NA NA NA NA NA ...
-##   .. ..$ scheme_1     : num [1:1650000] NA 0.434 0.434 NA NA ...
+##   .. ..$ scheme_1     : num [1:1650000] NA 0.153 0.153 NA NA ...
 ##   .. ..$ scheme_2     : num [1:1650000] NA NA NA NA NA NA NA NA NA NA ...
 ##   .. ..$ scheme_3     : num [1:1650000] NA NA NA NA NA NA NA NA NA NA ...
 ##   .. ..$ scheme_4     : num [1:1650000] NA NA NA NA NA NA NA NA NA NA ...
@@ -809,21 +817,21 @@ 

 ##   ..$ PathogenGroup          : chr [1:750000] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ...
 ##   ..$ eventID                : int [1:750000] 1 1 1 1 1 2 2 2 2 2 ...
 ##   ..$ repeatID               : int [1:750000] 1 1 1 1 1 1 1 1 1 1 ...
-##   ..$ logreduction           : num [1:750000] 0 0.434 3.066 8.727 11.572 ...
-##   ..$ inflow                 : num [1:750000] 930972 930972 930972 930972 930972 ...
+##   ..$ logreduction           : num [1:750000] 0 0.153 1.346 4.945 9.608 ...
+##   ..$ inflow                 : num [1:750000] 542287 542287 542287 542287 542287 ...
 ##   ..$ PathogenID             : int [1:750000] 3 3 3 3 3 3 3 3 3 3 ...
 ##   ..$ PathogenName           : chr [1:750000] "Campylobacter jejuni" "Campylobacter jejuni" "Campylobacter jejuni" "Campylobacter jejuni" ...
-##   ..$ effluent               : num [1:750000] 9.31e+05 3.43e+05 7.99e+02 1.75e-03 2.49e-06 ...
+##   ..$ effluent               : num [1:750000] 5.42e+05 3.81e+05 2.45e+04 6.16 1.34e-04 ...
 ##   ..$ volume_perEvent        : num [1:750000] 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 ...
-##   ..$ exposure_perEvent      : num [1:750000] 9.31e+02 3.43e+02 7.99e-01 1.75e-06 2.49e-09 ...
-##   ..$ dose_perEvent          : int [1:750000] 932 365 0 0 0 701 271 1 0 0 ...
-##   ..$ infectionProb_per_event: num [1:750000] 0.503 0.432 0 0 0 ...
+##   ..$ exposure_perEvent      : num [1:750000] 5.42e+02 3.81e+02 2.45e+01 6.16e-03 1.34e-07 ...
+##   ..$ dose_perEvent          : int [1:750000] 514 363 23 0 0 621 326 17 0 0 ...
+##   ..$ infectionProb_per_event: num [1:750000] 0.459 0.432 0.185 0 0 ...
 ##   ..$ infection_to_illness   : num [1:750000] 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 ...
 ##   ..$ dalys_per_case         : num [1:750000] 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 ...
 ##   ..$ ReferenceName          : chr [1:750000] "WHO (2011): Drinking water guideline, Table 7.4" "WHO (2011): Drinking water guideline, Table 7.4" "WHO (2011): Drinking water guideline, Table 7.4" "WHO (2011): Drinking water guideline, Table 7.4" ...
 ##   ..$ ReferenceLink          : chr [1:750000] "http://apps.who.int/iris/bitstream/10665/44584/1/9789241548151_eng.pdf#page=155" "http://apps.who.int/iris/bitstream/10665/44584/1/9789241548151_eng.pdf#page=155" "http://apps.who.int/iris/bitstream/10665/44584/1/9789241548151_eng.pdf#page=155" "http://apps.who.int/iris/bitstream/10665/44584/1/9789241548151_eng.pdf#page=155" ...
-##   ..$ illnessProb_per_event  : num [1:750000] 0.151 0.13 0 0 0 ...
-##   ..$ dalys_per_event        : num [1:750000] 0.000695 0.000597 0 0 0 ...
+##   ..$ illnessProb_per_event  : num [1:750000] 0.1378 0.1296 0.0556 0 0 ...
+##   ..$ dalys_per_event        : num [1:750000] 0.000634 0.000596 0.000256 0 0 ...
 ##   ..- attr(*, "vars")= chr [1:4] "TreatmentSchemeID" "TreatmentSchemeName" "PathogenGroup" "eventID"
 ##   ..- attr(*, "labels")='data.frame':    750 obs. of  4 variables:
 ##   .. ..$ TreatmentSchemeID  : int [1:750] 0 0 0 0 0 0 0 0 0 0 ...
@@ -944,14 +952,14 @@ 

 ##   ..$ PathogenName       : chr [1:15000] "Campylobacter jejuni" "Rotavirus" "Cryptosporidium parvum" "Campylobacter jejuni" ...
 ##   ..$ PathogenGroup      : chr [1:15000] "Bacteria" "Viruses" "Protozoa" "Bacteria" ...
 ##   ..$ events             : int [1:15000] 50 50 50 50 50 50 50 50 50 50 ...
-##   ..$ inflow_median      : num [1:15000] 515929 2569 4602 515929 2569 ...
-##   ..$ logreduction_median: num [1:15000] 0 0 0 0.2547 0.0493 ...
+##   ..$ inflow_median      : num [1:15000] 492968 2587 4992 492968 2587 ...
+##   ..$ logreduction_median: num [1:15000] 0 0 0 0.2526 0.0539 ...
 ##   ..$ volume_sum         : num [1:15000] 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 ...
-##   ..$ exposure_sum       : num [1:15000] 26227 120 238 14877 108 ...
-##   ..$ dose_sum           : int [1:15000] 26516 123 258 14832 115 83 291 6 10 0 ...
+##   ..$ exposure_sum       : num [1:15000] 24187 132 256 13917 118 ...
+##   ..$ dose_sum           : int [1:15000] 24299 130 261 13991 110 85 407 4 14 0 ...
 ##   ..$ infectionProb_sum  : num [1:15000] 1 1 1 1 1 ...
-##   ..$ illnessProb_sum    : num [1:15000] 0.999 1 1 0.998 1 ...
-##   ..$ dalys_sum          : num [1:15000] 0.0301 0.1026 0.0125 0.0266 0.1028 ...
+##   ..$ illnessProb_sum    : num [1:15000] 0.999 1 1 0.997 1 ...
+##   ..$ dalys_sum          : num [1:15000] 0.0287 0.1058 0.0127 0.0255 0.0956 ...
 ##   ..- attr(*, "vars")= chr [1:5] "repeatID" "TreatmentSchemeID" "TreatmentSchemeName" "PathogenID" ...
 ##   ..- attr(*, "drop")= logi TRUE

Thus the user has access to all results.

@@ -1081,14 +1089,14 @@

Campylobacter jejuni Bacteria 50 -515929.330 +492968.236 0.0000000 0.05 -2.622694e+04 -26516 +2.418714e+04 +24299 1.0000000 -0.9991202 -0.0301061 +0.9987516 +0.0286771 1 @@ -1098,14 +1106,14 @@

Rotavirus Viruses 50 -2568.744 +2586.973 0.0000000 0.05 -1.196306e+02 -123 +1.320160e+02 +130 1.0000000 -0.9997302 -0.1026083 +0.9997911 +0.1057595 1 @@ -1115,14 +1123,14 @@

Cryptosporidium parvum Protozoa 50 -4601.948 +4991.803 0.0000000 0.05 -2.383780e+02 -258 -0.9999996 -0.9999298 -0.0125002 +2.557190e+02 +261 +0.9999997 +0.9999401 +0.0127429 1 @@ -1132,14 +1140,14 @@

Campylobacter jejuni Bacteria 50 -515929.330 -0.2547373 +492968.236 +0.2525687 0.05 -1.487671e+04 -14832 +1.391705e+04 +13991 1.0000000 -0.9978814 -0.0265516 +0.9972782 +0.0255144 1 @@ -1149,14 +1157,14 @@

Rotavirus Viruses 50 -2568.744 -0.0493129 +2586.973 +0.0539353 0.05 -1.080021e+02 -115 +1.182406e+02 +110 1.0000000 -0.9997280 -0.1028465 +0.9995131 +0.0955771 1 @@ -1166,14 +1174,14 @@

Cryptosporidium parvum Protozoa 50 -4601.948 -0.5287657 +4991.803 +0.5238862 0.05 -8.315339e+01 -83 -0.9913275 -0.9594864 -0.0044712 +9.524696e+01 +85 +0.9922650 +0.9627496 +0.0046029 1 @@ -1183,14 +1191,14 @@

Campylobacter jejuni Bacteria 50 -515929.330 -2.3388704 +492968.236 +2.0990841 0.05 -2.976659e+02 -291 -0.9554119 -0.5876341 -0.0039923 +4.191294e+02 +407 +0.9777965 +0.6587275 +0.0048304 1 @@ -1200,14 +1208,14 @@

Rotavirus Viruses 50 -2568.744 -1.3334035 +2586.973 +1.4350078 0.05 -9.717874e+00 -6 -0.8103794 -0.5327144 -0.0098663 +6.983935e+00 +4 +0.6505560 +0.3802394 +0.0061792 1 @@ -1217,14 +1225,14 @@

Cryptosporidium parvum Protozoa 50 -4601.948 -1.4960981 +4991.803 +1.4668059 0.05 -9.396315e+00 -10 -0.4356045 -0.3262063 -0.0005740 +1.286309e+01 +14 +0.5510304 +0.4255310 +0.0008108 1 @@ -1234,10 +1242,10 @@

Campylobacter jejuni Bacteria 50 -515929.330 -7.3362377 +492968.236 +6.9103207 0.05 -4.732200e-03 +3.093380e-02 0 0.0000000 0.0000000 @@ -1251,10 +1259,10 @@

Rotavirus Viruses 50 -2568.744 -5.7132764 +2586.973 +5.6110209 0.05 -3.782300e-03 +2.324800e-03 0 0.0000000 0.0000000 @@ -1268,10 +1276,10 @@

Cryptosporidium parvum Protozoa 50 -4601.948 -7.4960981 +4991.803 +7.4668059 0.05 -9.400000e-06 +1.290000e-05 0 0.0000000 0.0000000 @@ -1285,10 +1293,10 @@

Campylobacter jejuni Bacteria 50 -515929.330 -11.1772568 +492968.236 +10.4708477 0.05 -1.460000e-05 +1.580000e-05 0 0.0000000 0.0000000 @@ -1302,10 +1310,10 @@

Rotavirus Viruses 50 -2568.744 -7.6992149 +2586.973 +7.4802662 0.05 -1.270000e-04 +7.710000e-05 0 0.0000000 0.0000000 @@ -1319,10 +1327,10 @@

Cryptosporidium parvum Protozoa 50 -4601.948 -8.2763468 +4991.803 +8.3472254 0.05 -2.300000e-06 +2.200000e-06 0 0.0000000 0.0000000 @@ -1335,7 +1343,7 @@

6 Export results

-

E.g. Write reports for all configurations in a folder e.g. /scenarios (here: C:.KWB8a13Gu/scenarios):

+

E.g. Write reports for all configurations in a folder e.g. /scenarios (here: C:.KWB5qI7/scenarios):

@@ -1379,6 +1387,20 @@

- - + + diff --git a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-10-1.png index 72c39783..0161e21a 100644 Binary files a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-11-1.png b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-11-1.png index cb7e8b01..44e38416 100644 Binary files a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-11-1.png and b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-11-1.png differ diff --git a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-12-1.png b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-12-1.png index 3f25621d..38269ca3 100644 Binary files a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-12-1.png and b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-12-1.png differ diff --git a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-14-1.png b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-14-1.png index f67100cb..ed99ba89 100644 Binary files a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-14-1.png and b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-14-1.png differ diff --git a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-15-1.png index 4f01a6bf..4e15b209 100644 Binary files a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-15-1.png and b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-15-1.png differ diff --git a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-16-1.png b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-16-1.png index b6d43a88..0bfe65e4 100644 Binary files a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-16-1.png and b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-16-1.png differ diff --git a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-17-1.png b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-17-1.png index ffaa840c..6c87751c 100644 Binary files a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-17-1.png and b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-17-1.png differ diff --git a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-18-1.png b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-18-1.png index 1352bc0f..f928529d 100644 Binary files a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-18-1.png and b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-18-1.png differ diff --git a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-19-1.png b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-19-1.png index 2daabec9..d04e508e 100644 Binary files a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-19-1.png and b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-19-1.png differ diff --git a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-9-1.png b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-9-1.png index 55f6c109..396dc48e 100644 Binary files a/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-9-1.png and b/docs/articles/OldFord_PublicIrrigation_files/figure-html/unnamed-chunk-9-1.png differ diff --git a/docs/articles/doseresponse_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/doseresponse_files/figure-html/unnamed-chunk-5-1.png index bfd1b1da..db955e8d 100644 Binary files a/docs/articles/doseresponse_files/figure-html/unnamed-chunk-5-1.png and b/docs/articles/doseresponse_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/docs/articles/usage.html b/docs/articles/usage.html index c5fd4a3e..8b4c7e56 100644 --- a/docs/articles/usage.html +++ b/docs/articles/usage.html @@ -590,7 +590,7 @@

26 June, 2018

## ..$ events:'data.frame': 10950 obs. of 6 variables: ## .. ..$ repeatID : int [1:10950] 1 1 1 1 1 1 1 1 1 1 ... ## .. ..$ eventID : int [1:10950] 1 2 3 4 5 6 7 8 9 10 ... -## .. ..$ inflow : num [1:10950] 1670 5410 3294 9668 8601 ... +## .. ..$ inflow : num [1:10950] 2216 6146 3016 9300 9451 ... ## .. ..$ PathogenID : int [1:10950] 3 3 3 3 3 3 3 3 3 3 ... ## .. ..$ PathogenName : chr [1:10950] "Campylobacter jejuni and Campylobacter coli" "Campylobacter jejuni and Campylobacter coli" "Campylobacter jejuni and Campylobacter coli" "Campylobacter jejuni and Campylobacter coli" ... ## .. ..$ PathogenGroup: chr [1:10950] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ... @@ -607,7 +607,7 @@

26 June, 2018

## ..$ events_long :'data.frame': 54750 obs. of 8 variables: ## .. ..$ repeatID : int [1:54750] 1 1 1 1 1 1 1 1 1 1 ... ## .. ..$ eventID : int [1:54750] 1 2 3 4 5 6 7 8 9 10 ... -## .. ..$ logreduction : num [1:54750] 1.029 1.305 0.468 0.529 0.364 ... +## .. ..$ logreduction : num [1:54750] 0.852 0.97 1.632 0.472 0.607 ... ## .. ..$ TreatmentID : int [1:54750] 1 1 1 1 1 1 1 1 1 1 ... ## .. ..$ PathogenGroup : chr [1:54750] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ... ## .. ..$ TreatmentSchemeID : int [1:54750] 2 2 2 2 2 2 2 2 2 2 ... @@ -620,10 +620,10 @@

26 June, 2018

## .. ..$ TreatmentSchemeID : int [1:54750] 1 1 2 2 2 1 1 2 2 2 ... ## .. ..$ TreatmentSchemeName: chr [1:54750] "Berlin (BF + Slow sand)" "Berlin (BF + Slow sand)" "Depth & surface filtration" "Depth & surface filtration" ... ## .. ..$ TreatmentName : chr [1:54750] "Bank filtration" "Slow sand filtration" "Conventional clarification" "Granular high-rate filtration" ... -## .. ..$ 1 : num [1:54750] NA NA 1.03 NA NA ... -## .. ..$ 5 : num [1:54750] NA NA NA 2.7 NA ... -## .. ..$ 8 : num [1:54750] NA 5.59 NA NA NA ... -## .. ..$ 9 : num [1:54750] 4.76 NA NA NA NA ... +## .. ..$ 1 : num [1:54750] NA NA 0.852 NA NA ... +## .. ..$ 5 : num [1:54750] NA NA NA 0.266 NA ... +## .. ..$ 8 : num [1:54750] NA 3.46 NA NA NA ... +## .. ..$ 9 : num [1:54750] 3.52 NA NA NA NA ... ## .. ..$ 15 : num [1:54750] NA NA NA NA 4 NA NA NA NA 4 ... ## ..$ schemes_events_wide:'data.frame': 54750 obs. of 4 variables: ## .. ..$ eventID : int [1:54750] 1 1 1 1 1 1 1 1 1 1 ... @@ -663,7 +663,7 @@

26 June, 2018

## .. ..$ events:'data.frame': 3650 obs. of 3 variables: ## .. .. ..$ repeatID : int [1:3650] 1 1 1 1 1 1 1 1 1 1 ... ## .. .. ..$ eventID : int [1:3650] 1 2 3 4 5 6 7 8 9 10 ... -## .. .. ..$ volume_perEvent: num [1:3650] 2.49 1.11 1.76 2.28 1.05 ... +## .. .. ..$ volume_perEvent: num [1:3650] 1.03 1.27 1.06 2.49 1.9 ... ## .. ..$ paras :'data.frame': 1 obs. of 6 variables: ## .. .. ..$ type : Factor w/ 1 level "triangle": 1 ## .. .. ..$ repeatings: int 10 @@ -710,19 +710,19 @@

26 June, 2018

## ..$ PathogenGroup : chr [1:21900] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ... ## ..$ eventID : int [1:21900] 1 1 2 2 3 3 4 4 5 5 ... ## ..$ repeatID : int [1:21900] 1 1 1 1 1 1 1 1 1 1 ... -## ..$ logreduction : num [1:21900] 10.36 7.73 8.57 8.52 7.82 ... -## ..$ inflow : num [1:21900] 1670 1670 5410 5410 3294 ... +## ..$ logreduction : num [1:21900] 6.98 5.12 8.91 7.07 9.19 ... +## ..$ inflow : num [1:21900] 2216 2216 6146 6146 3016 ... ## ..$ PathogenID : int [1:21900] 3 3 3 3 3 3 3 3 3 3 ... ## ..$ PathogenName : chr [1:21900] "Campylobacter jejuni and Campylobacter coli" "Campylobacter jejuni and Campylobacter coli" "Campylobacter jejuni and Campylobacter coli" "Campylobacter jejuni and Campylobacter coli" ... -## ..$ effluent : num [1:21900] 7.37e-08 3.13e-05 1.46e-05 1.62e-05 4.98e-05 ... -## ..$ volume_perEvent : num [1:21900] 2.49 2.49 1.11 1.11 1.76 ... -## ..$ exposure_perEvent : num [1:21900] 1.83e-07 7.78e-05 1.62e-05 1.80e-05 8.75e-05 ... -## ..$ dose_perEvent : int [1:21900] 0 0 0 0 0 0 0 0 0 1 ... -## ..$ infectionProb_per_event: num [1:21900] 0 0 0 0 0 ... +## ..$ effluent : num [1:21900] 2.31e-04 1.69e-02 7.50e-06 5.21e-04 1.93e-06 ... +## ..$ volume_perEvent : num [1:21900] 1.03 1.03 1.27 1.27 1.06 ... +## ..$ exposure_perEvent : num [1:21900] 2.38e-04 1.74e-02 9.52e-06 6.62e-04 2.04e-06 ... +## ..$ dose_perEvent : int [1:21900] 0 0 0 0 0 0 0 0 0 0 ... +## ..$ infectionProb_per_event: num [1:21900] 0 0 0 0 0 0 0 0 0 0 ... ## ..$ infection_to_illness : num [1:21900] 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 ... ## ..$ dalys_per_case : num [1:21900] 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 0.0046 ... -## ..$ illnessProb_per_event : num [1:21900] 0 0 0 0 0 ... -## ..$ dalys_per_event : num [1:21900] 0 0 0 0 0 ... +## ..$ illnessProb_per_event : num [1:21900] 0 0 0 0 0 0 0 0 0 0 ... +## ..$ dalys_per_event : num [1:21900] 0 0 0 0 0 0 0 0 0 0 ... ## ..- attr(*, "vars")= chr [1:4] "TreatmentSchemeID" "TreatmentSchemeName" "PathogenGroup" "eventID" ## ..- attr(*, "labels")='data.frame': 2190 obs. of 4 variables: ## .. ..$ TreatmentSchemeID : int [1:2190] 1 1 1 1 1 1 1 1 1 1 ... @@ -843,14 +843,14 @@

26 June, 2018

## ..$ PathogenName : chr [1:60] "Campylobacter jejuni and Campylobacter coli" "Rotavirus" "Giardia duodenalis" "Campylobacter jejuni and Campylobacter coli" ... ## ..$ PathogenGroup : chr [1:60] "Bacteria" "Viruses" "Protozoa" "Bacteria" ... ## ..$ events : int [1:60] 365 365 365 365 365 365 365 365 365 365 ... -## ..$ inflow_median : num [1:60] 4894 4749 4790 4894 4749 ... -## ..$ logreduction_median: num [1:60] 8.03 7.38 3.84 7.39 7.54 ... -## ..$ volume_sum : num [1:60] 621 621 621 621 621 ... -## ..$ exposure_sum : num [1:60] 1.87 160.51 6992.19 4.18 4.15 ... -## ..$ dose_sum : int [1:60] 0 144 6893 7 4 0 4 95 4487 2 ... -## ..$ infectionProb_sum : num [1:60] 0 1 1 0.12 0.706 ... -## ..$ illnessProb_sum : num [1:60] 0 0.3151 1 0.0851 0.0312 ... -## ..$ dalys_sum : num [1:60] 0 0.005265 0.025218 0.000406 0.000442 ... +## ..$ inflow_median : num [1:60] 4533 4768 5409 4533 4768 ... +## ..$ logreduction_median: num [1:60] 8.04 7.54 4.09 7.38 7.32 ... +## ..$ volume_sum : num [1:60] 618 618 618 618 618 ... +## ..$ exposure_sum : num [1:60] 3.42 88.95 4990.57 2.81 4.95 ... +## ..$ dose_sum : int [1:60] 5 90 4902 4 5 1 2 93 4413 3 ... +## ..$ infectionProb_sum : num [1:60] 0.0865 1 1 0.0714 0.7831 ... +## ..$ illnessProb_sum : num [1:60] 0.0612 0.2189 1 0.0504 0.0389 ... +## ..$ dalys_sum : num [1:60] 0.000288 0.003436 0.02144 0.000236 0.000553 ... ## ..- attr(*, "vars")= chr [1:5] "repeatID" "TreatmentSchemeID" "TreatmentSchemeName" "PathogenID" ... ## ..- attr(*, "drop")= logi TRUE

Thus the user has access to all

@@ -958,14 +958,14 @@

26 June, 2018

Campylobacter jejuni and Campylobacter coli Bacteria 365 -4893.987 -8.033334 -621.4861 -1.868014 -0 -0.0000000 -0.0000000 -0.0000000 +4532.811 +8.035069 +617.9005 +3.4190219 +5 +0.0865228 +0.0611605 +0.0002878 1 @@ -975,14 +975,14 @@

26 June, 2018

Rotavirus Viruses 365 -4748.882 -7.381241 -621.4861 -160.510613 -144 -0.9999999 -0.3150865 -0.0052653 +4767.988 +7.535198 +617.9005 +88.9485377 +90 +0.9999794 +0.2188515 +0.0034358 1 @@ -992,14 +992,14 @@

26 June, 2018

Giardia duodenalis Protozoa 365 -4789.970 -3.838076 -621.4861 -6992.193908 -6893 +5408.589 +4.090440 +617.9005 +4990.5679959 +4902 1.0000000 -1.0000000 -0.0252183 +0.9999999 +0.0214401 1 @@ -1009,14 +1009,14 @@

26 June, 2018

Campylobacter jejuni and Campylobacter coli Bacteria 365 -4893.987 -7.393566 -621.4861 -4.178734 -7 -0.1197426 -0.0851264 -0.0004060 +4532.811 +7.382850 +617.9005 +2.8097071 +4 +0.0714101 +0.0504026 +0.0002364 1 @@ -1026,14 +1026,14 @@

26 June, 2018

Rotavirus Viruses 365 -4748.882 -7.540869 -621.4861 -4.149484 -4 -0.7055472 -0.0312309 -0.0004424 +4767.988 +7.320194 +617.9005 +4.9468689 +5 +0.7830950 +0.0388850 +0.0005531 1 @@ -1043,14 +1043,14 @@

26 June, 2018

Giardia duodenalis Protozoa 365 -4789.970 -7.319157 -621.4861 -0.929711 -0 -0.0000000 -0.0000000 -0.0000000 +5408.589 +7.322425 +617.9005 +0.7126479 +1 +0.0197033 +0.0059110 +0.0000089 diff --git a/docs/articles/usage_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/usage_files/figure-html/unnamed-chunk-10-1.png index 210d507f..239ade00 100644 Binary files a/docs/articles/usage_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/usage_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/usage_files/figure-html/unnamed-chunk-11-1.png b/docs/articles/usage_files/figure-html/unnamed-chunk-11-1.png index 61a13efb..f8406d77 100644 Binary files a/docs/articles/usage_files/figure-html/unnamed-chunk-11-1.png and b/docs/articles/usage_files/figure-html/unnamed-chunk-11-1.png differ diff --git a/docs/articles/usage_files/figure-html/unnamed-chunk-12-1.png b/docs/articles/usage_files/figure-html/unnamed-chunk-12-1.png index 5729f8d5..fa71dfe8 100644 Binary files a/docs/articles/usage_files/figure-html/unnamed-chunk-12-1.png and b/docs/articles/usage_files/figure-html/unnamed-chunk-12-1.png differ diff --git a/docs/articles/usage_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/usage_files/figure-html/unnamed-chunk-13-1.png index 3b9fde92..b8d6ecd4 100644 Binary files a/docs/articles/usage_files/figure-html/unnamed-chunk-13-1.png and b/docs/articles/usage_files/figure-html/unnamed-chunk-13-1.png differ diff --git a/docs/articles/usage_files/figure-html/unnamed-chunk-14-1.png b/docs/articles/usage_files/figure-html/unnamed-chunk-14-1.png index b3c4adb0..f5bb6791 100644 Binary files a/docs/articles/usage_files/figure-html/unnamed-chunk-14-1.png and b/docs/articles/usage_files/figure-html/unnamed-chunk-14-1.png differ diff --git a/docs/articles/usage_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/usage_files/figure-html/unnamed-chunk-15-1.png index f6587e0c..6b22c3b1 100644 Binary files a/docs/articles/usage_files/figure-html/unnamed-chunk-15-1.png and b/docs/articles/usage_files/figure-html/unnamed-chunk-15-1.png differ diff --git a/docs/articles/usage_files/figure-html/unnamed-chunk-16-1.png b/docs/articles/usage_files/figure-html/unnamed-chunk-16-1.png index 4cc19113..30c18c87 100644 Binary files a/docs/articles/usage_files/figure-html/unnamed-chunk-16-1.png and b/docs/articles/usage_files/figure-html/unnamed-chunk-16-1.png differ diff --git a/docs/articles/usage_files/figure-html/unnamed-chunk-17-1.png b/docs/articles/usage_files/figure-html/unnamed-chunk-17-1.png index 071a148b..81c21a01 100644 Binary files a/docs/articles/usage_files/figure-html/unnamed-chunk-17-1.png and b/docs/articles/usage_files/figure-html/unnamed-chunk-17-1.png differ diff --git a/docs/articles/usage_files/figure-html/unnamed-chunk-18-1.png b/docs/articles/usage_files/figure-html/unnamed-chunk-18-1.png index 2485b126..d3b23f8e 100644 Binary files a/docs/articles/usage_files/figure-html/unnamed-chunk-18-1.png and b/docs/articles/usage_files/figure-html/unnamed-chunk-18-1.png differ diff --git a/docs/articles/usage_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/usage_files/figure-html/unnamed-chunk-8-1.png index ce0844ed..1d728a70 100644 Binary files a/docs/articles/usage_files/figure-html/unnamed-chunk-8-1.png and b/docs/articles/usage_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/docs/articles/usage_files/figure-html/unnamed-chunk-9-1.png b/docs/articles/usage_files/figure-html/unnamed-chunk-9-1.png index 41df4b19..db3d343e 100644 Binary files a/docs/articles/usage_files/figure-html/unnamed-chunk-9-1.png and b/docs/articles/usage_files/figure-html/unnamed-chunk-9-1.png differ