Description
Dose response data
Dose Infected Non-infected Total
1000 8 8 16
1E+07 16 0 16
1E+09 16 0 16

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 3.07e-05 7.15e-06 2 3.84 
0.998 		5.99 
1
Beta Poisson 2.36e-05 1 3.84 
0.996
Exponential is preferred to beta-Poisson; cannot reject good fit for exponential.

 

Optimized k parameter for the exponential model, from 10000 bootstrap iterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
k 6.93E-04 2.08E-04 2.88E-04 3.75E-04 1.16E-03 1.39E-03 1.67E-03
ID50/LD50/ETC* 1E+03 4.14E+02 5.00E+02 5.96E+02 1.85E+03 2.41E+03 3.34E+03
*Not a parameter of the exponential model; however, it facilitates comparison with other models.

 

Parameter histogram for Exponential model (uncertainty of the parameter)

Exponential model plot, with confidence bounds around optimized model

# of Doses
3.00
Μodel
exponential
LD50/ID50
1000
Dose Units
CFU
Response
infection
Exposure Route
oral
Contains Preferred Model
k
6.93E-04
Agent Strain
sub sp. Paratuberculosis Bovine
Experiment ID
262
Host type
deer
Description
humans/ echovirus-12 strain 
Dose infected Non-infected Total
330 15 35 50
1000 9 11 20
3300 19 7 26
1E+04 12 0 12

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 7.39 4.18 3 3.84 
0.041 		7.81 
0.0605
Beta Poisson 3.21 2 5.99 
0.201
Beta-Poisson fits better than exponential; cannot reject good fit for beta-Poisson.

 

Optimized parameters for the beta-Poisson model, from 10000 bootstrap iterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
α 1.06E+00 3.07E-01 4.04E-01 4.69E-01 1.23E+01 6.22E+02 3.74E+04
N50 9.22E+02 4.68E+02 5.59E+02 6.15E+02 1.37E+03 1.49E+03 1.73E+03

 

Parameter scatter plot for beta Poisson model ellipses signify the 0.9, 0.95 and 0.99 confidence of the parameters.

beta Poisson model plot, with confidence bounds around optimized model

# of Doses
4.00
Μodel
beta-Poisson
N50
9.22E+02
LD50/ID50
9.22E+02
Dose Units
PFU
Response
infection
Exposure Route
oral
Contains Preferred Model
a
1.06E+00
Agent Strain
strain 12
Experiment ID
256 (excluding the outliers of exp 112)
Host type
human
Description
hamsters/scrapie strain 263K model data 
Dose Dead Survived Total
200 0 40 40
2000 1 79 80
2E+04 9 71 80
2E+05 58 22 80
2E+06 29 1 30

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 14.5 12.6 4 3.84 
0.000382 		9.49 
0.00576
Beta Poisson 1.92 3 7.81 
0.589
Beta-Poisson fits better than exponential; cannot reject good fit for beta-Poisson.

 

Optimized parameters for the beta-Poisson model, from 10000 bootstrap iterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
α 1.76E+00 7.48E-01 8.76E-01 9.66E-01 1.44E+04 1.73E+04 2.08E+04
N50 1.04E+05 7.05E+04 7.83E+04 8.22E+04 1.34E+05 1.40E+05 1.55E+05

 

Parameter scatter plot for beta Poisson model ellipses signify the 0.9, 0.95 and 0.99 confidence of the parameters.

beta Poisson model plot, with confidence bounds around optimized model

# of Doses
5.00
Μodel
beta-Poisson
N50
1.04E+05
LD50/ID50
1.04E+05
Dose Units
LD50 i.c.
Response
death
Exposure Route
oral
Contains Preferred Model
a
1.76E+00
Agent Strain
scrapie strain 263k
Experiment ID
250
Host type
hamsters
Description
Human/Salmonella newportmodel data ]
Dose Infected Non-infected Total
152000 3 3 6
385000 6 2 8
1350000 6 0 6

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 0.16 -3.32e-05 2 3.84 
1 		5.99 
0.923
Beta Poisson 0.16 1 3.84 
0.689
Exponential is preferred to beta-Poisson; cannot reject good fit for exponential.

 

Optimized k parameter for the exponential model, from 10000 bootstrap iterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
k 3.97E-06 1.75E-06 2.16E-06 2.32E-06 7.36E-06 9.04E-06 1.27E-05
ID50/LD50/ETC* 1.74E+05 5.45E+04 7.67E+04 9.41E+04 2.98E+05 3.20E+05 3.97E+05
*Not a parameter of the exponential model; however, it facilitates comparison with other models.

 

Parameter histogram for exponential model (uncertainty of the parameter)

Exponential model plot, with confidence bounds around optimized model

# of Doses
3.00
Μodel
exponential
LD50/ID50
1.74E+05
Dose Units
CFU
Response
infection
Exposure Route
oral
Contains Preferred Model
k
3.97E-06
Agent Strain
*Salmonella newport*
Experiment ID
235
Host type
human
Description
Moredunn isolate data 
Dose Infected Non-infected Total
100 2 2 4
300 2 3 5
1000 1 2 3
3000 3 1 4

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 7.37 6.16 3 3.84 
0.0131 		7.81 
0.0611
Beta Poisson 1.21 2 5.99 
0.546
Beta-Poisson fits better than exponential; cannot reject good fit for beta-Poisson.

 

Optimized parameters for the beta-Poisson model, from 10000 bootstrap iterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
α 1.14E-01 9.79E-04 9.81E-04 9.82E-04 1.17E+03 2.25E+03 5.52E+03
N50 4.55E+02 2.13E-09 2.19E-06 1.55E-05 5.62E+05 3.59E+09 1.43E+16

Parameter scatter plot for beta Poisson model ellipses signify the 0.9, 0.95 and 0.99 confidence of the parameters.

beta Poisson model plot, with confidence bounds around optimized model.

# of Doses
4.00
Μodel
beta-Poisson
N50
4.55E+02
LD50/ID50
4.55E+02
Dose Units
oocysts
Response
infection
Exposure Route
oral
Contains Preferred Model
a
1.14E-01
Agent Strain
Moredun isolate
Experiment ID
183
Host type
human
Description
TU502 data 
Dose Diarrhea Not diarrhea Total
10 2 3 5
30 3 2 5
100 5 2 7
500 3 1 4

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 11.6 11.5 3 3.84 
0.000708 		7.81 
0.00894
Beta Poisson 0.119 2 5.99 
0.942
Beta-Poisson fits better than exponential; cannot reject good fit for beta-Poisson.

 

Optimized parameters for the beta-Poisson model, from 10000 bootstrap iterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
α 2.7E-01 9.83E-04 9.85E-04 2.03E-03 6.60E+00 6.70E+02 3.19E+03
N50 1.68E+01 3.41E-16 9.86E-09 1.68E-06 7.15E+01 9.76E+01 6.59E+02

Parameter scatter plot for beta Poisson model ellipses signify the 0.9, 0.95 and 0.99 confidence of the parameters.

beta Poisson model plot, with confidence bounds around optimized model.

# of Doses
4.00
Μodel
beta-Poisson
N50
1.68E+01
LD50/ID50
1.68E+01
Dose Units
oocysts
Response
diarrhea
Exposure Route
oral
Contains Preferred Model
a
2.7E-01
Agent Strain
*C. hominis*, TU502
Experiment ID
181
Host type
human
Description
UCP isolate 
Dose Infected Non-infected Total
500 3 2 5
1000 2 1 3
5000 2 3 5
1E+04 4 0 4

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 11.5 6.99 3 3.84 
0.0082 		7.81 
0.00945
Beta Poisson 4.48 2 5.99 
0.107
Beta-Poisson fits better than exponential; cannot reject good fit for beta-Poisson.

 

Optimized parameters for the beta-Poisson model, from 10000 bootstrap iterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
α 1.45E-01 9.81E-04 4.63E-03 9.53E-03 1.27E+00 1.46E+02 9.10E+02
N50 1.79E+02 2.74E-13 7.60E-10 4.54E-09 2.62E+03 3.22E+03 6.10E+03

Parameter scatter plot for beta Poisson model ellipses signify the 0.9, 0.95 and 0.99 confidence of the parameters.

beta Poisson model plot, with confidence bounds around optimized model

# of Doses
4.00
Μodel
beta-Poisson
N50
1.79E+02
LD50/ID50
1.79E+02
Dose Units
oocysts
Response
infection
Exposure Route
oral
Contains Preferred Model
a
1.45E-01
Agent Strain
UCP isolate
Experiment ID
141
Host type
human
Description
TAMU data 
Dose Infected Non-infected Total
10 2 1 3
30 2 1 3
100 3 0 3
500 5 0 5

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 1.07 0.21 3 3.84 
0.647 		7.81 
0.783
Beta Poisson 0.864 2 5.99 
0.649
Exponential is preferred to beta-Poisson; cannot reject good fit for exponential.

 

Optimized k parameter for the exponential model, from 10000 bootstrap iterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
k 5.72E-02 1.80E-02 1.92E-02 2.46E-02 2.65E+00 2.65E+00 2.65E+00
ID50/LD50/ETC* 1.21E+01 2.61E-01 2.61E-01 2.61E-01 2.82E+01 3.61E+01 3.84E+01
*Not a parameter of the exponential model; however, it facilitates comparison with other models.

Exponential model plot, with confidence bounds around optimized model

Parameter histogram for exponential model (uncertainty of the parameter)

 

 

# of Doses
4.00
Μodel
exponential
LD50/ID50
1.21E+01
Dose Units
oocysts
Response
infection
Exposure Route
oral
Contains Preferred Model
k
5.72E-02
Agent Strain
TAMU isolate
Experiment ID
140
Host type
human
Description
Iowa isolate data 
Dose Infected Not infected Total
30 2 3 5
100 4 4 8
300 2 1 3
500 5 1 6
1000 2 0 2
1E+04 3 0 3
1E+05 1 0 1
1E+06 1 0 1

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 3.07 2 7 3.84 
0.157 		14.1 
0.879
Beta Poisson 1.07 6 12.6 
0.983
Exponential is preferred to beta-Poisson; cannot reject good fit for exponential.

 

Optimized k parameter for the exponential model, from 10000 bootstrap iterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
k 5.26E-03 2.25E-03 2.75E-03 3.08E-03 1.03E-02 1.19E-02 1.60E-02
ID50/LD50/ETC* 1.32E+02 4.33E+01 5.80E+01 6.72E+01 2.25E+02 2.52E+02 3.08E+02
*Not a parameter of the exponential model; however, it facilitates comparison with other models.

Parameter histogram for exponential model (uncertainty of the parameter)

Exponential model plot, with confidence bounds around optimized model

# of Doses
8.00
Μodel
exponential
LD50/ID50
1.32E+02
Dose Units
oocysts
Response
infection
Exposure Route
oral
Contains Preferred Model
k
5.26E-03
Agent Strain
Iowa isolate
Experiment ID
139
Host type
human
Description
humans/ echovirus-12 strain 
Dose infected Non-infected Total
330 15 35 50
1000 9 11 20
3300 19 7 26
1E+04 12 0 12
33000 2 2 4
330000 2 1 3

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 122 110 5 3.84 
0 		11.1 
0
Beta Poisson 11.7 4 9.49 
0.0196
Neither the exponential nor beta-Poisson fits well; beta-Poisson is less bad.

 

Optimized parameters for the beta-Poisson model, from 10000 bootstrap iterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
α 3.74E-01 1.24E-01 1.81E-01 2.09E-01 7.79E-01 9.41E-01 2.01E+00
N50 1.01E+03 3.84E+02 5.32E+02 5.94E+02 1.75E+03 1.97E+03 2.54E+03

 

Parameter scatter plot for beta Poisson model ellipses signify the 0.9, 0.95 and 0.99 confidence of the parameters.

beta Poisson model plot, with confidence bounds around optimized model

# of Doses
6.00
Μodel
beta-Poisson
N50
1.01E+03
LD50/ID50
1.01E+03
Dose Units
PFU
Response
infection
Exposure Route
oral
Contains Preferred Model
a
3.74E-01
Agent Strain
strain 12
Experiment ID
112
Host type
human
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