Description
TITLE 
Dose INFECTION NOT

INFECTION || Total
0.05 0 4 4
0.15 1 4 5
0.5 0 4 4
0.5 3 14 17
1.5 2 3 5
1.5 4 10 14
5 1 4 5
5 4 11 15
15 4 3 7
50 28 14 42
150 13 8 21
300 5 2 7

"

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 78.6 72.3 11 3.84 
{{{pbPbetter}}} 		19.7 
2.8e-12
Beta Poisson 6.22 10 18.3 
0.796
{{{interpretation}}}

"

Optimized parameters for the beta-Poisson model, from 10000 bootstrapiterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
α 1.82E-01 1.04E-03 1.03E-01 1.14E-01 3.04E-01 3.38E-01 4.09E-01
N50 1.38E+01 2.98E+00 5.64E+00 6.67E+00 3.77E+01 4.98E+01 1.32E+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
12.00
Μodel
beta-Poisson
N50
1.38E+01
LD50/ID50
1.38E+01
Dose Units
TCID50
Response
infection
Exposure Route
intranasal
Contains Preferred Model
a
1.82E-01
Agent Strain
type 14
Experiment ID
312, 313
Host type
human
Description
TITLE 
Dose INFECTION NOT

INFECTION || Total
0.5 0 4 4
1.5 2 3 5
5 1 4 5
15 4 3 7
150 13 8 21
300 5 2 7
Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 24.3 21.5 5 3.84 
{{{pbPbetter}}} 		11.1 
0.000194
Beta Poisson 2.77 4 9.49 
0

selection
Beta-Poisson fits better than exponential; cannot reject good fit for beta-Poisson.
Optimized parameters for the beta-Poisson model, from 10000 bootstrapiterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
α 1.81E-01 3.92E-02 7.30E-02 9.02E-02 4.00E-01 4.79E-01 7.28E-01
N50 2.22E+01 3.12E+00 5.01E+00 6.38E+00 1.22E+02 2.06E+02 1.26E+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
2.22E+01
LD50/ID50
2.22E+01
Dose Units
TCID50
Response
infection
Exposure Route
intranasal
Contains Preferred Model
a
1.81E-01
Agent Strain
type 14
Experiment ID
312
Host type
human
Description

Optimization Output for experiment 311

TITLE 
Dose INFECTION NOT

INFECTION || Total
0.05 0 2 2
0.15 1 3 4
0.5 5 2 7
1.5 18 1 19
5 1 0 1
50 19 1 20
Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 61.7 56.8 5 3.84 
{{{pbPbetter}}} 		11.1 
5.32e-12
Beta Poisson 4.95 4 9.49 
0

selection
Beta-Poisson fits better than exponential; cannot reject good fit for beta-Poisson.
Optimized parameters for the beta-Poisson model, from 10000 bootstrapiterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
α 7.01E-01 2.29E-01 3.14E-01 3.63E-01 1.81E+06 3.82E+06 1.41E+07
N50 1.9E-01 2.27E-02 5.85E-02 7.93E-02 4.20E-01 4.52E-01 5.56E-01

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
1.9E-01
LD50/ID50
1.9E-01
Dose Units
TCID50
Response
infection
Exposure Route
intranasal
Contains Preferred Model
a
7.01E-01
Agent Strain
type 39
Experiment ID
311
Host type
human
Description
TITLE 
Dose INFECTION NOT

INFECTION || Total
0.5 1 4 5
1.5 2 3 5
5 3 2 5
15 2 1 3
150 14 5 19
300 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 29.7 27.3 5 3.84 
{{{pbPbetter}}} 		11.1 
1.71e-05
Beta Poisson 2.42 4 9.49 
0

selection
Beta-Poisson fits better than exponential; cannot reject good fit for beta-Poisson.
Optimized parameters for the beta-Poisson model, from 10000 bootstrapiterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
α 2.52E-01 9.79E-04 9.14E-02 1.16E-01 5.50E-01 6.41E-01 1.06E+00
N50 3.83E+00 9.08E-03 3.23E-01 6.41E-01 1.48E+01 2.04E+01 8.86E+01

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
3.83E+00
LD50/ID50
3.83E+00
Dose Units
TCID50
Response
infection
Exposure Route
intranasal
Contains Preferred Model
a
2.52E-01
Agent Strain
type 14
Experiment ID
310
Host type
human
Description
Humans/ type 4 Strain model data 
Dose Infected Non-infected Total
1 1 2 3
5 3 0 3
11 3 0 3
1000 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 0.487 -0.000723 3 3.84 
1 		7.81 
0.922
Beta Poisson 0.488 2 5.99 
0.784
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 6.07E-01 3.87E-01 3.87E-01 3.87E-01 1.13E+00 1.13E+00 1.13E+00
ID50/LD50/ETC* 1.14E+00 6.11E-01 6.11E-01 6.11E-01 1.79E+00 1.79E+00 1.79E+00
*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
4.00
Μodel
exponential
LD50/ID50
1.14E+00
Dose Units
TCID50
Response
infection
Exposure Route
inhalation
Contains Preferred Model
k
6.07E-01
Agent Strain
type 4
Experiment ID
31
Host type
human
Description
Human data( Rickettsia rickettsii) 
Dose CLINICAL SIGNS NOT CLINICAL SIGNS Total
13 2 4 6
126 6 1 7
1260 17 1 18

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value		 χ20.95,m-k 
p-value
Exponential 13.5 13.2 2 3.84 
0.000277		 5.99 
0.00119
Beta Poisson 0.248 1 3.84 
0.618
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 6.75E-01 1.17E-01 2.44E-01 3.31E-01 1.21E+03 3.74E+03 4.98E+03
N50 2.36E+01 2.56E-02 3.35E+00 7.30E+00 6.41E+01 8.91E+01 1.28E+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
3.00
Μodel
beta-Poisson
N50
2.36E+01
LD50/ID50
2.36E+01
Dose Units
CFU
Response
clinical signs
Exposure Route
intradermal
Contains Preferred Model
a
6.75E-01
Agent Strain
Sheila Smith
Experiment ID
301
Host type
human
Description
Human/Staphylococcus aureus 
Dose Infected Non-infected Total
2430000 4 16 20
6270000 8 12 20
1.27E+07 13 7 20
2.5E+07 14 6 20
3.34E+07 19 1 20
3.91E+07 20 0 20

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 5.52 5.36e-05 5 3.84 
0.994 		11.1 
0.356
Beta Poisson 5.52 4 9.49 
0.238
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 7.64E-08 5.67E-08 6.19E-08 6.41E-08 1.00E-07 1.02E-07 1.35E-06
ID50/LD50/ETC* 9.08E+06 2.70E+06 6.79E+06 6.93E+06 1.08E+07 1.12E+07 1.22E+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
6.00
Μodel
exponential
LD50/ID50
9.08E+06
Dose Units
CFU/cm2
Response
infection
Exposure Route
subcutaneous
Contains Preferred Model
k
7.64E-08
Experiment ID
278
Host type
human
Description
human/H3N2, A/Washington/897/80 attenuated strain model data [3]
Dose Infected Non-infected Total
1E+05 2 10 12
1E+06 8 5 13
1E+07 16 3 19
31622777 16 4 20
1E+08 19 0 19

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 39.1 34.8 4 3.84 
3.66e-09 		9.49 
6.79e-08
Beta Poisson 4.26 3 7.81 
0.235
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 4.29E-01 2.14E-01 2.58E-01 2.83E-01 7.58E-01 8.71E-01 1.20E+00
N50 6.66E+05 1.36E+05 2.19E+05 2.68E+05 1.63E+06 1.87E+06 2.49E+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
beta-Poisson
N50
6.66E+05
LD50/ID50
6.66E+05
Dose Units
TCID50
Response
infection
Exposure Route
intranasal
Contains Preferred Model
a
4.29E-01
Agent Strain
H3N2,A/Washington/897/80 attenuated strain
Experiment ID
258
Host type
human
Description
Pooled dose response data [1]
Dose Infected Non-infected Total
63095.73 0 15 15
1E+05 2 10 12
630957.3 4 7 11
1E+06 8 5 13
6309573 19 3 22
1E+07 16 3 19
31622777 16 4 20
63095734 24 1 25
1E+08 19 0 19

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 64 55.4 8 3.84 
9.68e-14 		15.5 
7.63e-11
Beta Poisson 8.56 7 14.1 
0.285
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 5.81E-01 3.61E-01 3.98E-01 4.24E-01 9.15E-01 1.02E+00 1.36E+00
N50 9.45E+05 4.38E+05 5.28E+05 5.72E+05 1.62E+06 1.79E+06 2.23E+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
9.00
Μodel
beta-Poisson
N50
9.45E+05
LD50/ID50
9.45E+05
Dose Units
TCID50
Response
infection
Exposure Route
intranasal
Contains Preferred Model
a
5.81E-01
Agent Strain
H1N1,A/California/10/78 attenuated strain,H3N2,A/Washington/897/80 attenuated strain
Experiment ID
257, 258
Host type
human
Description
human/H1N1 A/California/10/78 attenuated strain model data [2]
Dose Infected Non-infected Total
63095.73 0 15 15
630957.3 4 7 11
6309573 19 3 22
63095734 24 1 25

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 23.6 21.5 3 3.84 
3.47e-06 		7.81 
3.09e-05
Beta Poisson 2.02 2 5.99 
0.365
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 9.04E-01 4.20E-01 4.91E-01 5.45E-01 1.73E+03 2.57E+04 2.19E+05
N50 1.25E+06 5.27E+05 6.43E+05 7.19E+05 2.39E+06 2.74E+06 3.45E+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
4.00
Μodel
beta-Poisson
N50
1.25E+06
LD50/ID50
1.25E+06
Dose Units
TCID50
Response
infection
Exposure Route
intranasal
Contains Preferred Model
a
9.04E-01
Agent Strain
H1N1,A/California/10/78 attenuated strain
Experiment ID
257
Host type
human
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