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Jun 20, 2017 1:17 PM
(898 views)

I am using the Simple Probit Analysis script add-in to determine LD50, LD90, and LD95.

Is this script capable of correcting with Abbott's, or how do you set this up? Currently, I corrected the data myself by applying the Abbott's correction to the raw data to adjust for mortalities.

After running the Probit Add-In, how do I determine goodness of fit? There are no Chi Squared results. Is there another way I can run this analysis to get my LD values, as well as getting the Chi Square?

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Jun 21, 2017 2:08 PM
(1185 views)

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Please see my reply with a complete analysis that ends with the question, "So we agree now, no?" It shows you how to set up your data in a JMP data table. It also shows you how to assign the data columns to the analysis roles in the Fit Model launch dialog and change the other settings for a proper Probit analysis. I did not apply any transformation to the dose levels - it is unnecessary.

Learn it once, use it forever!

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Jun 22, 2017 12:16 PM
(1072 views)

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Excluding the high responses is * not *acceptable from a modeling or statistics point of view. You are suggesting that you

Excluding the high dose samples might be acceptable in your situation but I could not justify it. The fact that you (possibly) obtain a 'better' model this way is not validation. You simply cannot determine the LD50 from this sample of dose-response data except to say that LD50 occurs between 0 and 1.64.

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Jun 20, 2017 3:29 PM
(888 views)

Did you contact the author of the add-in or read the description and instructions first?

JMP has several built-in platforms that can estimate such quantities and provide goodness of fit statistics. These leads should get you started.

**Fit Curve**can fit common non-linear functions.**Nonlinear**is more general and it can fit custom models.**Generalized Linear Models**can perform a probit analysis.

Did you search *probit* yet in **Help** or **Help** > **Books** > **Fitting Linear Models**?

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Jun 21, 2017 7:20 AM
(873 views)

I have not.

I have been attempting to run the model in the Generalized Linear with Probit, however, my LD values do not match up with what the Probit Add-In is giving me, so I'm not sure what is going on. I've read through the Fitting Linear models, but what I am trying to run analysis on is nonlinear, which I honestly don't have any experience with in JMP.

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Jun 21, 2017 7:36 AM
(871 views)

This example is from our training course, JMP Software: Analyzing Discrete Responses.

We are testing seals for failures at increasing pressure levels. Here is the data table with the preferred layout:

Note that we do * not *enter the failure rate (Failed / Tested) for the response.

Select **Analyze** > **Fit Model**. Select **Pressure** and click **Add**. Select **Failed** and click **Y**. Select **Total** and click **Y**. (Note that (1) you must enter a column with the count of targets and another column with the count of opportunities and (2) the must be entered exactly in that order.) Click **Standard Least Squares** and select **Generalized Linear Model**. Select **Binomial** for the Distribution model. Select **Probit** for the Link function. Your launch dialog should look like:

Click **Run**.

You can see the non-linear response and the regression diagnostics below:

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Jun 21, 2017 7:38 AM
(870 views)

Okay,

It seems if I include my 0s (Control for Mortality) into the model, both the general linear probit model and the probit add-in match up the LD recommendations. If I use Abbott corrected data, then they have discrepancy between the two.

Should I run the model with the 0s and the raw data (no Abbott's adjustment), or is it more correct to adjust the raw data with Abbott's prior to inputing into the probit and disclude the 0s?

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Jun 21, 2017 7:54 AM
(867 views)

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Jun 21, 2017 8:09 AM
(863 views)

I attached the wrong Linear models with raw data. Here are the correct:

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Jun 21, 2017 8:32 AM
(859 views)

Abbott's correction is applied to *mortality rates* (i.e., proportions) to account for the *natural mortality* in the absence of the agent be tested. GLM is modeling a binomial distribution with a linear predictor. The GLM model has an intercept for that purpose (baseline mortality). So it is not necessary to apply this correction and doing so will, in fact, change the output. So don't do it if you are using GLM for your analysis.

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Jun 21, 2017 8:38 AM
(856 views)

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Jun 21, 2017 9:04 AM
(847 views)

I am confused as much as you are.

You should have *two* counts for your response for *each* level of the predictor: one count is the number that died and the other count is the number that might have died. You should have *one* predictor. It is usually concentration or log concentration. Is that true? Or is it time? Are you trying to estimate the time for LD50 at a fixed concentration?

Please use the data format exhibited in the example that I shared and * not *rates or proportions. Counts are necessary for the inference. A rate of 0.1 might result from a case of 1/10 or a case of 100/1000. The rate is the same in both cases but the sample size is very different.

Once again, if you enter the data as I showed and set up the GLM as I showed, you can forget about Abbott's correction for rates. You should enter both counts for time=0.

Learn it once, use it forever!