Description
mice (10day old, day2-21) /  Pseudomonas aeruginosa 
Dose Dead Survived Total
2.5 0 10 10
25 0 16 16
250 0 15 15
2500 2 11 13
25000 13 3 16
250000 14 3 17

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential

27.3

 23.1 5 3.84 
 1.54e-06 		11.1
5.01e-05
Beta Poisson

4.19

 4 9.49 
0.381
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 5.49E-01 2.38E-01 2.87E-01 3.17E-01 1.37E+00 1.13E+01 1.15E+04
N50 1.13E+04 4.53E+03 5.70E+03 6.34E+03 2.17E+04 2.46E+04 3.39E+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
beta-Poisson
N50
1.13E+04
LD50/ID50
1.13E+04
Dose Units
CFU
Response
death(after day 2-21)
Exposure Route
injected in eyelids
Contains Preferred Model
a
5.49E-01
Agent Strain
ATCC 19660
Experiment ID
284
Host type
Swiss webster mice(10day old)
Description
mice (10day old, day1) /  Pseudomonas aeruginosa 
Dose Dead Survived Total
2.5 0 10 10
25 0 16 16
250 0 15 15
2500 0 13 13
25000 12 4 16
250000 14 3 17

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential

21.1

 13.8 5 3.84 
0.000207 		11.1 
0.000783
Beta Poisson

7.32

 4 9.49 
0.12
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 6.73E-01 3.02E-01 3.62E-01 3.80E-01 1.55E+00 6.30E+03 1.06E+04
N50 1.93E+04 9.62E+03 1.12E+04 1.18E+04 3.42E+04 4.01E+04 5.18E+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
beta-Poisson
N50
1.93E+04
LD50/ID50
1.93E+04
Dose Units
CFU
Response
death(after day 1)
Exposure Route
injected in eyelids
Contains Preferred Model
a
6.73E-01
Agent Strain
ATCC 19660
Experiment ID
283
Host type
Swiss webster mice(10day old)
Description
mice (5day old) /  Pseudomonas aeruginosa 
Dose Dead Survived Total
2.5 0 13 13
25 0 14 14
250 0 12 12
2500 4 13 17
25000 15 0 15
250000 17 0 17

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential

2.17

-0.000196 

 5 3.84 
1 		11.1 
0.825
Beta Poisson

2.17

 4 9.49 
0.704
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 1.39E-04 8.87E-05 9.90E-05 9.90E-05 2.05E-04 2.36E-04 2.73E-04
ID50/LD50/ETC* 4.98E+03 2.54E+03 2.94E+03 3.38E+03 7.00E+03 7.00E+03 7.82E+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
6.00
Μodel
exponential
LD50/ID50
4.98E+03
Dose Units
CFU
Response
death(after day 21)
Exposure Route
injected in eyelids
Contains Preferred Model
k
1.39E-04
Agent Strain
ATCC 19660
Experiment ID
282
Host type
Swiss webster mice (5day old)
Description
mice (5day old) /  Pseudomonas aeruginosa 
Dose Dead Survived Total
2.5 0 13 13
25 0 14 14
250 0 12 12
2500 4 13 17
25000 13 2 15
250000 17 0 17

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential

0.802

 0.0885 5 3.84 
0.766 		11.1 
0.977
Beta Poisson

0.713

 4 9.49 
0.95
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 8.52E-05 4.21E-05 4.99E-05 5.50E-05 1.53E-04 1.57E-04 2.05E-04
ID50/LD50/ETC* 8.13E+03 3.38E+03 4.40E+03 4.54E+03 1.26E+04 1.39E+04 1.65E+04
*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
6.00
Μodel
exponential
LD50/ID50
8.13E+03
Dose Units
CFU
Response
death
Exposure Route
injected in eyelids
Contains Preferred Model
k
8.52E-05
Agent Strain
ATCC 19660
Experiment ID
281
Host type
Swiss webster mice (5day old)
Description

mice (5day old, day 1-21 pooled) /  Pseudomonas aeruginosa 
Dose Dead Survived Total
2.5 0 13 13
2.5 0 13 13
25 0 14 14
25 0 14 14
250 0 12 12
250 0 12 12
2500 4 13 17
2500 4 13 17
25000 13 2 15
25000 15 0 15
250000 17 0 17
250000 17 0 17

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential

4.36 

 -0.000549

   3.84 
1 		19.7
0.958
Beta Poisson

4.36

 10 18.3 
0.93
Exponential is preferred to beta-Poisson; cannot reject good fit for exponential.

 

Optimized k parameter for the exponential model, from 500 bootstrap iterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
k 1.05E-04 6.84E-05 7.49E-05 7.84E-05 1.48E-04 1.57E-04 1.73E-04
ID50/LD50/ETC* 6.61E+03 4.01E+03 4.40E+03 4.68E+03 8.84E+03 9.26E+03 1.01E+04
*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
12.00
Μodel
exponential
LD50/ID50
6.61E+03
Dose Units
CFU
Response
death
Exposure Route
injected in eyelids
Contains Preferred Model
k
1.05E-04
Agent Strain
ATCC 19660
Experiment ID
281,282 (pooled)
Host type
Swiss webster mice (5day old)
Description
Swiss webster mice /  Pseudomonas aeruginosa 
Dose Infection (keratitis)

Not Infection (keratitis)

 Total
1E+04 0 8 8
1E+05 1 9 10
1E+06 1 7 8
1E+07 5 5 10
1E+08 10 0 10

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential

3.6

 0.134 4 3.84 
0.715 		9.49 
0.464
Beta Poisson

3.46

 3 7.81 
0.326
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 8.8E-08 3.31E-08 3.89E-08 4.53E-08 1.58E-07 1.94E-07 2.47E-07
ID50/LD50/ETC* 7.88E+06 2.81E+06 3.57E+06 4.38E+06 1.53E+07 1.78E+07 2.09E+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
exponential
LD50/ID50
7.88E+06
Dose Units
CFU
Response
infection (Keratitis)
Exposure Route
contact lens
Contains Preferred Model
k
8.8E-08
Agent Strain
ATCC 19660
Experiment ID
286
Host type
Swiss webster mice
Description
White rabbit /  Pseudomonas aeruginosa 
Dose Severe Stromal Ulceration

Not Corneal Ulceration

 Total
63.2 0 5 5
2220 2 3 5
13200 1 4 5
78000 1 4 5
462000 4 1 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

13.2

 8.73 4 3.84 
0.00313  		9.49 
0.0105
Beta Poisson

4.43

 3 7.81 
0.219
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 1.09E-01 4.05E-02 5.23E-02 5.72E-02 9.05E+06 4.82E+07 2.53E+12
N50 1.52E+05 4.66E+03 1.13E+04 1.55E+04 1.55E+07 6.25E+07 1.96E+09

 

Parameter histogram for exponential model (uncertainty of the parameter)

Exponential model plot, with confidence bounds around optimized model

# of Doses
5.00
Μodel
beta-Poisson
N50
1.52E+05
LD50/ID50
1.52E+05
Dose Units
CFU
Response
Severe stromal ulceration
Exposure Route
contact lens
Contains Preferred Model
a
1.09E-01
Experiment ID
298
Host type
white rabbit
Description
White rabbit /  Pseudomonas aeruginosa 
Dose Corneal Ulceration

Not Corneal Ulceration

 Total
63.2 0 5 5
2220 2 3 5
13200 3 2 5
78000 3 2 5
462000 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

9.41

 7.02 4 3.84 
0.00807  		9.49 
0.0516
Beta Poisson

2.39

 3 7.81 
0.495
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 3.55E-01 1.53E-01 1.76E-01 1.91E-01 4.52E+00 1.73E+07 1.35E+11
N50 6.57E+03 7.71E+02 1.44E+03 1.70E+03 2.55E+04 4.30E+04 8.32E+04

 

Parameter histogram for exponential model (uncertainty of the parameter)

Exponential model plot, with confidence bounds around optimized model

# of Doses
5.00
Μodel
beta-Poisson
N50
6.57E+03
LD50/ID50
6.57E+03
Dose Units
CFU
Response
corneal ulceration
Exposure Route
contact lens
Contains Preferred Model
a
3.55E-01
Experiment ID
297
Host type
white rabbit
Description
Pooled data of White rabbit /  Pseudomonas aeruginosa 
Dose Corneal Ulceration

Not Corneal Ulceration

 Total
63.2 0 5 5
63.2 0 5 5
2220 2 3 5
2220 2 3 5
13200 3 2 5
13200 1 4 5
78000 3 2 5
78000 1 4 5
462000 5 0 5
462000 4 1 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

30.9

 20.8 9 3.84 
5.11e-06  		16.9 
0.000312
Beta Poisson

10.1

 8 15.5 
0.26
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 1.9E-01 9.63E-02 1.15E-01 1.24E-01 3.86E-01 5.51E-01 2.50E+00
N50 1.85E+04 3.18E+03 4.73E+03 6.01E+03 7.05E+04 8.98E+04 1.97E+05

 

Parameter histogram for exponential model (uncertainty of the parameter)

Exponential model plot, with confidence bounds around optimized model

# of Doses
10.00
Μodel
beta-Poisson
N50
1.85E+04
LD50/ID50
1.85E+04
Dose Units
CFU
Response
corneal ulceration
Exposure Route
contact lens
Contains Preferred Model
a
1.9E-01
Experiment ID
297 & 298
Host type
white rabbit
Description
Escherichia coli (EIEC 1624) in the human model data
Dose Positive stool isolation No positive stool isolation Total
1E+04 0 5 5
1E+06 5 4 9
1E+08 3 2 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 28.6 27.2 2 3.84 
1.82e-07 		5.99 
6.18e-07
Beta Poisson 1.38 1 3.84 
0.24
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 1.55E-01 1.26E-03 1.26E-03 2.84E-02 1.84E+01 1.29E+02 1.90E+02
N50 2.11E+06 1.73E+05 2.95E+05 2.95E+05 7.85E+08 9.22E+140 9.22E+140
Parameter scatter plot for beta Poisson model ellipses signify the 0.9, 0.95 and 0.99 confidence of the parameters.
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 mode
beta Poisson model plot, with confidence bounds around optimized mode
# of Doses
3.00
Μodel
beta-Poisson
N50
2.11E+06
LD50/ID50
2.11E+06
Dose Units
CFU
Response
positive stool isolation
Exposure Route
oral (in milk)
Contains Preferred Model
a
1.55E-01
Agent Strain
EIEC 1624
Experiment ID
98
Host type
human
Experiment Dataset
Subscribe to CFU