infection

LD50/ID50

1.91E+03

Dose Units

no of trophozoites

Response

Exposure Route

eyes-cornea

Contains Preferred Model

Status

fitted

Read more about Acanthamoeba Experiment 2: Keratitis

3.63E-04

Agent Strain

Acanthamoeba Ac118

Experiment ID

Acanth_Cornea2

Host type

rat

Experiment Dataset

Dose (no. of organisms)	Positive Response	Negative Response	Total Subjects/Responses
10	0	8	8
100	0	16	16
1000	7	17	24
10000	10	0	10

Description

**Goodness of Fit and Model Selection**
Model	Deviance	Δ	Degrees of freedom	χ²_0.95,1 p-value	χ²_0.95,m-k p-value
Exponential	9.88	6.48	5	3.84 0.011	11.1 0.0788
beta Poisson	3.4	6.48	4	3.84 0.011	9.49 0.494
beta-Poisson fits better than exponential; can not reject good fit for beta-Poisson

**Bootstrapped Parameter Estimates**
Parameter	MLE Estimate	0.5%	2.5%	5%	95%	97.5%	99.5%
α	6.95E-01	2.69E-01	3.39E-01	3.78E-01	2.56E+0	2.28E+01	1.18E+03
N50	3.39E+03	3.58E+01	2.47E+02	4.67E+02	1.09E+04	1.26E+04	1.85E+04

Host

C57Bl/6J mice

# of Doses

6.00

Μodel

N50

277

Dose Units

Response

Exposure Route

oral

Contains Preferred Model

Status

fitted

Read more about Optimization Output for Exp. 292

0.253

Agent Strain

F5817

Experiment ID

292

Experiment Dataset

Dose (CFU)	Infected	Non-Infected	Total
5500	7	3	10
32400	7	3	10
55000	9	1	10
251000	10	0	10
550000	10	0	10
2820000	10	0	10

Description

**T3 Strain for serotype PEN 3 model data**
Dose	Infected	Non-infected	Total
1E+04	2	3	5
1E+05	4	1	5
1E+06	2	3	5
1E+07	3	2	5
1E+08	5	0	5

**Goodness of fit and model selection**
Model	Deviance	Δ	Degrees of freedom	χ²_0.95,1 p-value	χ²_0.95,m-k p-value
Exponential	45.6	40.2	4	3.84 2.25e-10	9.49 2.92e-09
Beta Poisson	5.41	40.2	3	3.84 2.25e-10	7.81 0.144
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
Parameter	MLE estimate	0.5%	2.5%	5%	95%	97.5%	99.5%
α	1.17E-01	1.06E-02	1.79E-02	2.48E-02	2.79E-01	3.29E-01	4.72E-01
N₅₀	3.14E+04	3.29E-09	2.55E-05	2.53E-02	4.21E+05	9.69E+05	3.68E+06

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

N50

3.14E+04

LD50/ID50

3.14E+04

Dose Units

Response

Exposure Route

Contains Preferred Model

Read more about Optimization Output for Exp. 186

1.17E-01

Agent Strain

type strain for serotype PEN 3

Experiment ID

186

Host type

mice

Description

**T2 Strain for serotype PEN 2 model data**
Dose	Infected	Non-infected	Total
1E+04	1	4	5
1E+05	3	2	5
1E+06	4	1	5
1E+07	4	1	5
1E+08	5	0	5

**Goodness of fit and model selection**
Model	Deviance	Δ	Degrees of freedom	χ²_0.95,1 p-value	χ²_0.95,m-k p-value
Exponential	25.4	24.5	4	3.84 7.59e-07	9.49 4.13e-05
Beta Poisson	0.969	24.5	3	3.84 7.59e-07	7.81 0.809
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
Parameter	MLE estimate	0.5%	2.5%	5%	95%	97.5%	99.5%
α	3.19E-01	8.29E-02	1.26E-01	1.49E-01	1.05E+01	5.53E+02	1.52E+03
N₅₀	6.68E+04	4.06E+02	5.55E+03	1.04E+04	3.58E+05	4.65E+05	8.48E+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

N50

6.68E+04

LD50/ID50

6.68E+04

Dose Units

Response

Exposure Route

Contains Preferred Model

Read more about Optimization Output for Exp. 185

3.19E-01

Agent Strain

type strain for serotype PEN 2

Experiment ID

185

Host type

mice

Description

**T1 Strain for serotype PEN 1 data**
Dose	Infected	Non-infected	Total
1	0	5	5
100	0	5	5
1E+04	0	5	5
1E+06	3	2	5
1E+08	5	0	5

**Goodness of fit and model selection**
Model	Deviance	Δ	Degrees of freedom	χ²_0.95,1 p-value	χ²_0.95,m-k p-value
Exponential	0.0918	-0.000599	4	3.84 1	9.49 0.999
Beta Poisson	0.0924	-0.000599	3	3.84 1	7.81 0.993
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
Parameter	MLE estimate	0.5%	2.5%	5%	95%	97.5%	99.5%
k	9.01E-07	4.61E-08	2.21E-07	2.21E-07	4.61E-06	4.61E-06	4.61E-06
ID50/LD50/ETC*	7.69E+05	1.51E+05	1.51E+05	1.51E+05	3.14E+06	3.14E+06	1.51E+07
*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

5.00

Μodel

LD50/ID50

7.69E+05

Dose Units

Response

Exposure Route

Contains Preferred Model

Read more about Optimization Output for Exp. 184

9.01E-07

Agent Strain

type strain for serotype PEN 1

Experiment ID

184

Host type

mice

Description

**Strain A3249 Data**
Dose	Infected	Non-infected	Total
810	5	5	10
8100	6	4	10
91000	11	2	13
810000	8	3	11
1.1E+06	15	4	19
1.1E+08	5	0	5

**Goodness of fit and model selection**
Model	Deviance	Δ	Degrees of freedom	χ²_0.95,1 p-value	χ²_0.95,m-k p-value
Exponential	110	108	5	3.84 0	11.1 0
Beta Poisson	2.43	108	4	3.84 0	9.49 0.658
Beta-Poisson fits better than exponential; cannot reject good fit for beta-Poisson.

**Optimized parameters for the the beta-Poisson model, from 10000 bootstrap iterations**
Parameter	MLE estimate	Percentiles
Parameter	MLE estimate	0.5%	2.5%	5%	95%	97.5%	99.5%
α	1.44E-01	2.05E-02	3.61E-02	4.99E-02	2.66E-01	2.98E-01	3.71E-01
N₅₀	8.9E+02	6.54E-10	1.47E-04	8.11E-02	6.69E+03	8.97E+03	1.53E+04

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

N50

8.9E+02

LD50/ID50

8.9E+02

Dose Units

Response

Exposure Route

oral

Contains Preferred Model

Read more about Optimization Output for Exp. 106

1.44E-01

Agent Strain

strain A3249

Experiment ID

106

Host type

human

Description

Badenoch et al. (1990) studied the combined effect of Acanthamoeba Ac118 (a group III isolate) and the bacterium Corynebacterium xerosis on the corneas of female Porton rats. A constant dose of 10⁴ C. xerosis with increasing doses of Acanthamoeba spp. were injected into incisions in the rat corneas using a microsyringe (Badenoch et al. 1990).

The exponential model provided the best fit to the data.

Figure 1: Plot of the exponential model fit to Experiment 1 with upper and lower 95% and 99% confidence

Figure 2: Histogram of the 10,000 bootstrap replicates of k for the best fitting exponential model fit to Experiment 1

# of Doses

4.00

Μodel

LD50/ID50

6,886

Dose Units

no of trophozoites

Response

Exposure Route

eyes-cornea

Contains Preferred Model

Status

fitted

Resampled Parameters

Exponential_Bootstrap.csv

Read more about Acanthamoeba Experiment 1: Keratitis

1.01E-04

Agent Strain

Acanthamoeba Ac118

Experiment ID

Acanth_Cornea1

Host type

rat

Experiment Dataset

Dose (no. of organisms)	Positive Responses	Negative Responses	Total Subjects/Responses
10	0	8	8
100	0	16	16
1000	2	16	18
10000	5	3	8

Description

**Model data for rotavirus (OSU (ATCC VR892)) in the pig**
Dose	Infected	Non-infected	Total
0.9	0	3	3
9	0	3	3
90	5	1	6
900	3	0	3
2800	2	0	2
9000	3	0	3
56000	2	0	2
1.1E+07	2	0	2
2.2E+08	2	0	2
4.5E+09	2	0	2

**Goodness of fit and model selection**
Model	Deviance	Δ	Degrees of freedom	χ²_0.95,1 p-value	χ²_0.95,m-k p-value
Exponential	1.1	-0.0019	9	3.84 1	16.9 0.999
Beta Poisson	1.1	-0.0019	8	3.84 1	15.5 0.998
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
Parameter	MLE estimate	0.5%	2.5%	5%	95%	97.5%	99.5%
k	1.73E-02	4.64E-03	7.21E-03	7.21E-03	3.28E-02	3.28E-02	3.28E-02
ID50/LD50/ETC*	4E+01	2.11E+01	2.11E+01	2.11E+01	9.61E+01	9.61E+01	1.49E+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

10.00

Μodel

LD50/ID50

4E+01

Dose Units

particles

Response

Exposure Route

Contains Preferred Model

Read more about Optimization Output for Exp. 68

1.73E-02

Agent Strain

OSU (ATCC VR892)

Experiment ID

Host type

pig

Description

**Model data for rotavirus (CJN strain) in the human**
Dose	Symptoms and infection	No symptoms and infection	Total
9E-03	0	7	7
0.09	0	7	7
0.9	1	6	7
9	5	6	11
90	2	5	7
900	4	4	8
9000	3	4	7
9E+04	2	1	3

**Goodness of fit and model selection**
Model	Deviance	Δ	Degrees of freedom	χ²_0.95,1 p-value	χ²_0.95,m-k p-value
Exponential	103	99.5	7	3.84 0	14.1 0
Beta Poisson	3.14	99.5	6	3.84 0	12.6 0.791
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
Parameter	MLE estimate	0.5%	2.5%	5%	95%	97.5%	99.5%
α	7.28E-02	9.93E-04	9.95E-04	9.96E-04	1.32E-01	1.46E-01	1.83E-01
N₅₀	1.47E+03	6.55E-03	1.85E-02	4.58E-02	5.47E+06	1.82E+31	6.68E+122

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

8.00

Μodel

N50

1.47E+03

LD50/ID50

1.47E+03

Dose Units

FFU

Response