Description
mice/ H5N1,DKGX/35 strain model data [4]
Dose Dead Survived Total
10 1 4 5
100 3 2 5
1000 5 0 5
1E+04 5 0 5
1E+05 5 0 5
1E+06 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 0.498 0.0917 5 3.84 
0.762 		11.1 
0.992
Beta Poisson 0.406 4 9.49 
0.982
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 1.09E-02 3.14E-03 3.29E-03 4.56E-03 2.78E-02 3.48E-02 5.42E-02
ID50/LD50/ETC* 6.38E+01 1.28E+01 1.99E+01 2.49E+01 1.52E+02 2.11E+02 2.21E+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
6.00
Μodel
exponential
LD50/ID50
6.38E+01
Dose Units
EID50
Response
death
Exposure Route
intranasal
Contains Preferred Model
k
1.09E-02
Agent Strain
H5N1, DKGX/35 strain
Experiment ID
259
Host type
mice
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
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
Humans/ type 4 Strain model data 
Dose Infected Non-infected Total
3 0 6 6
10 0 2 2
14 1 1 2
79 2 1 3
400 3 0 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 2.14 -0.00118 4 3.84 
1 		9.49 
0.71
Beta Poisson 2.14 3 7.81 
0.544
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 1.51E-02 4.00E-03 5.88E-03 6.35E-03 4.56E-02 4.56E-02 4.56E-02
ID50/LD50/ETC* 4.59E+01 1.52E+01 1.52E+01 1.52E+01 1.09E+02 1.18E+02 1.73E+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
5.00
Μodel
exponential
LD50/ID50
4.59E+01
Dose Units
TCID50
Response
infection
Exposure Route
intranasal
Contains Preferred Model
k
1.51E-02
Agent Strain
type 4
Experiment ID
255
Host type
human
Description
Mice/Naegleria fowleri LEE strain data 
Dose Dead Survived Total
1E+06 4 16 20
2.5E+06 12 8 20
5E+06 14 6 20
1E+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 3.47 -0.000862 3 3.84 
1 		7.81 
0.325
Beta Poisson 3.47 2 5.99 
0.177
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 3.07E-07 2.11E-07 2.31E-07 2.41E-07 3.98E-07 4.21E-07 4.68E-07
ID50/LD50/ETC* 2.26E+06 1.48E+06 1.65E+06 1.74E+06 2.88E+06 3.01E+06 3.28E+06
*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
2.26E+06
Dose Units
no of trophozoites
Response
death
Exposure Route
intravenous
Contains Preferred Model
k
3.07E-07
Agent Strain
LEE strain
Experiment ID
254
Host type
mice
Description
mice/ Naegleria fowleri LEE strain model data 
Dose Dead Survived Total
1E+06 4 16 20
2.5E+06 4 6 10
2.5E+06 12 8 20
5E+06 19 1 20
5E+06 14 6 20
1E+07 10 0 10
1E+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 8.85 -0.000501 6 3.84 
1 		12.6 
0.182
Beta Poisson 8.85 5 11.1 
0.115
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 3.42E-07 2.57E-07 2.75E-07 2.84E-07 4.15E-07 4.34E-07 4.67E-07
ID50/LD50/ETC* 2.03E+06 1.48E+06 1.60E+06 1.67E+06 2.44E+06 2.52E+06 2.70E+06
*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
7.00
Μodel
exponential
LD50/ID50
2.03E+06
Dose Units
no of trophozoites
Response
death
Exposure Route
intravenous
Contains Preferred Model
k
3.42E-07
Agent Strain
LEE strain
Experiment ID
253, 254
Host type
mice
Description
mice/Naegleria fowleri LEE strain data 
Dose Dead Survived Total
2.5E+06 4 6 10
5E+06 19 1 20
1E+07 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 4.11 -9.67 2 3.84 
1 		5.99 
0.128
Beta Poisson 13.8 1 3.84 
0.000206
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 4.21E-07 2.77E-07 3.04E-07 3.25E-07 5.95E-07 6.79E-07 8.02E-07
ID50/LD50/ETC* 1.64E+06 8.65E+05 1.02E+06 1.16E+06 2.13E+06 2.28E+06 2.50E+06
*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
1.64E+06
Dose Units
no of trophozoites
Response
death
Exposure Route
intravenous
Contains Preferred Model
k
4.21E-07
Agent Strain
LEE strain
Experiment ID
253
Host type
mice
Description
mice/BSE agent model data 
Dose Infected Non-infected Total
0.0186 0 13 13
0.186 4 12 16
1.86 9 5 14
18.6 13 0 13

 

Goodness of fit and model selection
Model Deviance Δ Degrees 
of freedom		 χ20.95,1 
p-value 		χ20.95,m-k 
p-value
Exponential 2.78 0.763 3 3.84 
0.382 		7.81 
0.427
Beta Poisson 2.01 2 5.99 
0.365
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-01 3.03E-01 3.69E-01 4.16E-01 1.14E+00 1.32E+00 1.70E+00
ID50/LD50/ETC* 1E+00 4.08E-01 5.27E-01 6.08E-01 1.67E+00 1.88E+00 2.29E+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
Dose Units
ID50 unit
Response
infection
Exposure Route
unknown type of injection
Contains Preferred Model
k
6.93E-01
Agent Strain
BSE agent
Experiment ID
252
Host type
mice
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