pathogenflows v0.0.0.9004
pathogenflows is a package that predicts the flow of pathogens through sanitation systems
Installation
The latest version of pathogenflows can be installed from github (if you don’t have the package devtools, you will need to install it first):
# install.packages("devtools")
devtools::install_github('mverbyla/pathogenflows')
About
The pathogenflows package contains two functions that can be used to predict pathogen flows throughout sanitation systems.
The getLoadings function allows you to predict annual loadings of water pathogens from onsite sanitation system technologies used in a given region of the world.
The getLRV function allows you to predict the overall log10 reduction value for viral, bacterial, protozoan, or helminth pathogens by a custom wastewater treatment plant, specified using the K2P Sketcher Tool.
getLoadings
Inputs:
The getloadings function requires the following two inputs:
- onsiteData
- pathogenType
The input onsiteData should refer to the web address of a data input file from the K2P Data Portal (data.waterpathogens.org). This file must be in a very specific format. An example file can be found here.
The input pathogenType should be equal to either one of the following strings: c("Virus","Bacteria","Protozoa","Helminth").
Outputs:
The function outputs a list with a dataframe for each subregion, where each subregion’s dataframe contains the following estimated annual loadings and calculated reduction values:
| Variable | Pathogen Loadings | Description |
|---|---|---|
subregion |
Subregion | The subregion of interest |
id |
ID | String ID for the sanitation technology category |
sanitationTechnology |
Sanitation technology | A description of the sanitation technology |
percentage |
Percentage | Percentage of the population in a subregion using that particular sanitation technology |
excreted |
Excreted | Number of pathogens excreted per year |
toGroundwater |
To groundwater | Number of pathogens emitted to groundwater each year |
toSurface |
To the surface | Number of pathogens emitted to the surface each year |
inSubsurface |
Retained in subsurface | Number of pathogens retained in the subsurface each year |
decayed |
Decayed/inactivated | Number of pathogens inactivated per year |
fecalSludge |
Conveyed in fecal sludge to treatment | Number of pathogens conveyed each year to treatment in fecal sludge |
sewerage |
Conveyed in sewerage to treatment | Number of pathogens conveyed each year to treatment in sewerage |
stillViable |
Still viable | Total number of pathogens that remain viable (stillViable + decayed = excreted) |
onsiteLRV |
Onsite log reduction value | The base 10 logarithmic reduction of pathogens achieved by onsite sanitation (Onsite_LRV = log10(excreted/stillViable)) |
getLRV
Inputs:
The getLRV function requires the following two inputs:
- sketch
- pathogenType
- inFecalSludge
- inSewage
The input sketch should refer to a JSON file that describes the wastewater or fecal sludge treatment plant. This file must be in a very specific format. An example file can be found here. A file like this can be created using the K2P Sketcher Tool.
The input pathogenType should be equal to either one of the following strings: c("Virus","Bacteria","Protozoa","Helminth").
The input inFecalSludge should be a number value that represents the number of pathogens conveyed each year in fecal sludge to the treatment plant. The getLoadings function can be used to estimate this value for a given service area of interest, but if this value is unknown, you can just leave it blank and the function will calculate the log reduction value and the relative portion of pathogens discharged in liquid effluent vs. sludge.
The input inSewage should be a number value that represents the number of pathogens conveyed each year in fecal sludge to the treatment plant. The getLoadings function can be used to estimate this value for a given service area of interest, but if this value is unknown, you can just leave it blank and the function will calculate the log reduction value and the relative portion of pathogens discharged in liquid effluent vs. sludge.
Outputs:
The function outputs a dataframe with the following values:
dataframe goes here
Examples
Here is an example output.
The following shows the use of the getLoadings function for data from Kampala, Uganda, grouping the data by ‘region’ and showing results for the ‘Virus’ group.
getLoadings(onsiteData,pathogenType="Virus")
> loadings
$Central
id sanitationTechnology percentage excreted toGroundwater toSurface inSubsurface decayed fecalSludge sewerage stillViable onsiteLRV
1 flushSewer Flush / pour flush to piped sewer system 0.263426061 9.142680e+15 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 9.14268e+15 9.142680e+15 0.00
2 flushSeptic Flush / pour flush to septic tank 0.202395075 7.023540e+15 5.618832e+14 1.174215e+13 5.056949e+15 1.389521e+15 3.444403e+12 0.00000e+00 5.770698e+14 1.09
3 flushPit Flush / pour flush to pit latrine 0.057237316 1.987380e+15 1.589904e+14 3.322557e+12 1.430914e+15 3.931788e+14 9.746279e+11 0.00000e+00 1.632876e+14 1.09
4 flushOpen Flush / pour flush to open drain 0.012221734 4.245600e+14 0.000000e+00 4.245600e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 4.245600e+14 0.00
5 flushUnknown Flush / pour flush to don't know where 0.007753772 2.708400e+14 0.000000e+00 2.708400e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 2.708400e+14 0.00
6 pitSlab Dry pit latrine with slab 0.410974140 1.425936e+16 0.000000e+00 1.191960e+14 0.000000e+00 1.410520e+16 3.496455e+13 0.00000e+00 1.541605e+14 1.97
7 pitNoSlab Dry pit latrine without slab / open pit 0.024476960 8.491200e+14 0.000000e+00 7.097912e+12 0.000000e+00 8.399400e+14 2.082078e+12 0.00000e+00 9.179989e+12 1.97
8 compostingTwinSlab Composting toilet - twin pit with slab 0.000000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 NaN
9 compostingTwinNoSlab Composting toilet - twin pit without slab 0.000000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 NaN
10 compostingToilet Composting toilet - other 0.006835904 2.379000e+14 0.000000e+00 1.988639e+12 0.000000e+00 2.353280e+14 5.833408e+11 0.00000e+00 2.571980e+12 1.97
11 bucketLatrine Bucket toilet 0.000000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 NaN
12 containerBased Container-based sanitation 0.000000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 NaN
13 hangingToilet Hanging toilet / latrine 0.000000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 NaN
14 openDefecation No facility / bush / field 0.011578119 4.026000e+14 0.000000e+00 4.026000e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 4.026000e+14 0.00
15 other Other (specify) 0.003100918 1.061400e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 Inf
$Kawempe
id sanitationTechnology percentage excreted toGroundwater toSurface inSubsurface decayed fecalSludge sewerage stillViable onsiteLRV
1 flushSewer Flush / pour flush to piped sewer system 0.0368606218 6.738060e+15 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 6.73806e+15 6.738060e+15 0.00
2 flushSeptic Flush / pour flush to septic tank 0.1422744756 2.601162e+16 2.080930e+15 6.090085e+13 1.872837e+16 5.135254e+15 6.169477e+12 0.00000e+00 2.148000e+15 1.08
3 flushPit Flush / pour flush to pit latrine 0.0576012883 1.052982e+16 8.423856e+14 2.465340e+13 7.581470e+15 2.078813e+15 2.497479e+12 0.00000e+00 8.695365e+14 1.08
4 flushOpen Flush / pour flush to open drain 0.0016795832 3.074400e+14 0.000000e+00 3.074400e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 3.074400e+14 0.00
5 flushUnknown Flush / pour flush to don't know where 0.0052484696 9.589200e+14 0.000000e+00 9.589200e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 9.589200e+14 0.00
6 pitSlab Dry pit latrine with slab 0.7361309305 1.345855e+17 0.000000e+00 1.575521e+15 0.000000e+00 1.328504e+17 1.596060e+14 0.00000e+00 1.735127e+15 1.89
7 pitNoSlab Dry pit latrine without slab / open pit 0.0144161741 2.635200e+15 0.000000e+00 3.084889e+13 0.000000e+00 2.601226e+15 3.125105e+12 0.00000e+00 3.397399e+13 1.89
8 compostingTwinSlab Composting toilet - twin pit with slab 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 NaN
9 compostingTwinNoSlab Composting toilet - twin pit without slab 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 NaN
10 compostingToilet Composting toilet - other 0.0003306902 5.856000e+13 0.000000e+00 6.855309e+11 0.000000e+00 5.780502e+13 6.944677e+10 0.00000e+00 7.549776e+11 1.89
11 bucketLatrine Bucket toilet 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 NaN
12 containerBased Container-based sanitation 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 NaN
13 hangingToilet Hanging toilet / latrine 0.0001060999 1.830000e+13 0.000000e+00 1.830000e+13 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 1.830000e+13 0.00
14 openDefecation No facility / bush / field 0.0045986602 8.418000e+14 0.000000e+00 8.418000e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 8.418000e+14 0.00
15 other Other (specify) 0.0007456240 1.354200e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 Inf
$Makindye
id sanitationTechnology percentage excreted toGroundwater toSurface inSubsurface decayed fecalSludge sewerage stillViable onsiteLRV
1 flushSewer Flush / pour flush to piped sewer system 2.857037e-02 6.042660e+15 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 6.04266e+15 6.042660e+15 0.00
2 flushSeptic Flush / pour flush to septic tank 2.592807e-01 5.484510e+16 4.387608e+15 1.243115e+14 3.948847e+16 1.083015e+16 1.455793e+13 0.00000e+00 4.526477e+15 1.08
3 flushPit Flush / pour flush to pit latrine 8.254003e-02 1.745820e+16 1.396656e+15 3.957064e+13 1.256990e+16 3.447435e+15 4.634057e+12 0.00000e+00 1.440861e+15 1.08
4 flushOpen Flush / pour flush to open drain 3.821692e-03 8.088600e+14 0.000000e+00 8.088600e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 8.088600e+14 0.00
5 flushUnknown Flush / pour flush to don't know where 1.747709e-02 3.696600e+15 0.000000e+00 3.696600e+15 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 3.696600e+15 0.00
6 pitSlab Dry pit latrine with slab 5.746897e-01 1.215669e+17 0.000000e+00 1.377714e+15 0.000000e+00 1.200278e+17 1.613419e+14 0.00000e+00 1.539055e+15 1.90
7 pitNoSlab Dry pit latrine without slab / open pit 2.428971e-02 5.138640e+15 0.000000e+00 5.823603e+13 0.000000e+00 5.073584e+15 6.819933e+12 0.00000e+00 6.505597e+13 1.90
8 compostingTwinSlab Composting toilet - twin pit with slab 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 NaN
9 compostingTwinNoSlab Composting toilet - twin pit without slab 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 NaN
10 compostingToilet Composting toilet - other 1.400786e-03 2.964600e+14 0.000000e+00 3.359771e+12 0.000000e+00 2.927068e+14 3.934577e+11 0.00000e+00 3.753229e+12 1.90
11 bucketLatrine Bucket toilet 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 NaN
12 containerBased Container-based sanitation 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 NaN
13 hangingToilet Hanging toilet / latrine 3.447166e-05 7.320000e+12 0.000000e+00 7.320000e+12 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 7.320000e+12 0.00
14 openDefecation No facility / bush / field 6.082428e-03 1.288320e+15 0.000000e+00 1.288320e+15 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 1.288320e+15 0.00
15 other Other (specify) 1.834099e-03 3.879600e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000e+00 0.000000e+00 Inf
$Nakawa
id sanitationTechnology percentage excreted toGroundwater toSurface inSubsurface decayed fecalSludge sewerage stillViable onsiteLRV
1 flushSewer Flush / pour flush to piped sewer system 0.0986066974 1.716174e+16 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.716174e+16 1.716174e+16 0.00
2 flushSeptic Flush / pour flush to septic tank 0.2822786268 4.912818e+16 3.930254e+15 1.180298e+14 3.537229e+16 9.697091e+15 1.051516e+13 0.000000e+00 4.058799e+15 1.08
3 flushPit Flush / pour flush to pit latrine 0.0659452582 1.147776e+16 9.182208e+14 2.757517e+13 8.263987e+15 2.265520e+15 2.456644e+12 0.000000e+00 9.482526e+14 1.08
4 flushOpen Flush / pour flush to open drain 0.0027246677 4.758000e+14 0.000000e+00 4.758000e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 4.758000e+14 0.00
5 flushUnknown Flush / pour flush to don't know where 0.0160243516 2.788920e+15 0.000000e+00 2.788920e+15 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 2.788920e+15 0.00
6 pitSlab Dry pit latrine with slab 0.4979572900 8.666880e+16 0.000000e+00 1.041103e+15 0.000000e+00 8.553495e+16 9.275086e+13 0.000000e+00 1.133854e+15 1.88
7 pitNoSlab Dry pit latrine without slab / open pit 0.0274612361 4.779960e+15 0.000000e+00 5.741896e+13 0.000000e+00 4.717426e+15 5.115398e+12 0.000000e+00 6.253436e+13 1.88
8 compostingTwinSlab Composting toilet - twin pit with slab 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 NaN
9 compostingTwinNoSlab Composting toilet - twin pit without slab 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 NaN
10 compostingToilet Composting toilet - other 0.0005598630 9.882000e+13 0.000000e+00 1.187069e+12 0.000000e+00 9.752718e+13 1.057548e+11 0.000000e+00 1.292824e+12 1.88
11 bucketLatrine Bucket toilet 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 NaN
12 containerBased Container-based sanitation 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 NaN
13 hangingToilet Hanging toilet / latrine 0.0006785063 1.171200e+14 0.000000e+00 1.171200e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.171200e+14 0.00
14 openDefecation No facility / bush / field 0.0069327567 1.207800e+15 0.000000e+00 1.207800e+15 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.207800e+15 0.00
15 other Other (specify) 0.0008310225 1.427400e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 Inf
$Rubaga
id sanitationTechnology percentage excreted toGroundwater toSurface inSubsurface decayed fecalSludge sewerage stillViable onsiteLRV
1 flushSewer Flush / pour flush to piped sewer system 4.654201e-03 9.808800e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 9.8088e+14 9.808800e+14 0.00
2 flushSeptic Flush / pour flush to septic tank 1.646388e-01 3.463824e+16 2.771059e+15 7.774515e+13 2.493953e+16 6.840419e+15 9.483889e+12 0.0000e+00 2.858288e+15 1.08
3 flushPit Flush / pour flush to pit latrine 8.954142e-02 1.883802e+16 1.507042e+15 4.228173e+13 1.356337e+16 3.720164e+15 5.157816e+12 0.0000e+00 1.554481e+15 1.08
4 flushOpen Flush / pour flush to open drain 1.799026e-03 3.769800e+14 0.000000e+00 3.769800e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.0000e+00 3.769800e+14 0.00
5 flushUnknown Flush / pour flush to don't know where 1.079161e-02 2.269200e+15 0.000000e+00 2.269200e+15 0.000000e+00 0.000000e+00 0.000000e+00 0.0000e+00 2.269200e+15 0.00
6 pitSlab Dry pit latrine with slab 6.888292e-01 1.449214e+17 0.000000e+00 1.626372e+15 0.000000e+00 1.430966e+17 1.983961e+14 0.0000e+00 1.824768e+15 1.90
7 pitNoSlab Dry pit latrine without slab / open pit 3.100959e-02 6.522120e+15 0.000000e+00 7.319413e+13 0.000000e+00 6.439997e+15 8.928724e+12 0.0000e+00 8.212286e+13 1.90
8 compostingTwinSlab Composting toilet - twin pit with slab 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000e+00 0.000000e+00 NaN
9 compostingTwinNoSlab Composting toilet - twin pit without slab 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000e+00 0.000000e+00 NaN
10 compostingToilet Composting toilet - other 5.664655e-04 1.207800e+14 0.000000e+00 1.355447e+12 0.000000e+00 1.192592e+14 1.653467e+11 0.0000e+00 1.520794e+12 1.90
11 bucketLatrine Bucket toilet 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000e+00 0.000000e+00 NaN
12 containerBased Container-based sanitation 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000e+00 0.000000e+00 NaN
13 hangingToilet Hanging toilet / latrine 2.013197e-05 3.660000e+12 0.000000e+00 3.660000e+12 0.000000e+00 0.000000e+00 0.000000e+00 0.0000e+00 3.660000e+12 0.00
14 openDefecation No facility / bush / field 3.735057e-03 7.869000e+14 0.000000e+00 7.869000e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.0000e+00 7.869000e+14 0.00
15 other Other (specify) 4.392258e-03 9.223200e+14 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000e+00 0.000000e+00 Inf
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