# 9.2 - Modeling Count Data

9.2 - Modeling Count Data

## Example: Horseshoe Crabs and Satellites This problem refers to data from a study of nesting horseshoe crabs (J. Brockmann, Ethology 1996). Each female horseshoe crab in the study had a male crab attached to her in her nest. The study investigated factors that affect whether the female crab had any other males, called satellites, residing near her. Explanatory variables that are thought to affect this included the female crab's color, spine condition, and carapace width, and weight. The response outcome for each female crab is the number of satellites. There are 173 females in this study.

Let's first see if the carapace width can explain the number of satellites attached. We will start by fitting a Poisson regression model with carapace width as the only predictor.

proc genmod data=crab;
model Sa=w / dist=poi link=log obstats;
run;

Model Sa=w specifies the response (Sa) and predictor width (W). Also, note that specifications of Poisson distribution are dist=pois and link=log. The obstats option as before will give us a table of observed and predicted values and residuals. We can use any additional options in GENMOD, e.g., TYPE3, etc.

Here is the output that we should get from running just this part:

#### Model Information

What do we learn from the "Model Information" section? How is this different from when we fitted logistic regression models? This section gives information on the GLM that's fitted. More specifically, we see that the response is distributed via Poisson, the link function is log, and the dependent variable is Sa. The number of observations in the data set used is 173.

The SAS System

The GENMOD Procedure

Model Information
Data Set WORK.CRAB
Distribution Poisson
Dependent Variable Sa
 Number of Observations Read 173 173

Does the model fit well? What does the Value/DF tell us? Given the value of deviance statistic of 567.879 with 171 df, the p-value is zero and the Value/DF is much bigger than 1, so the model does not fit well. The lack of fit may be due to missing data, predictors, or overdispersion. It should also be noted that the deviance and Pearson tests for lack of fit rely on reasonably large expected Poisson counts, which are mostly below five, in this case, so the test results are not entirely reliable. Still, we'd like to see a better-fitting model if possible.

Criteria For Assessing Goodness Of Fit
Criterion DF Value Value/DF
Deviance 171 567.8786 3.3209
Scaled Deviance 171 567.8786 3.3209
Pearson Chi-Square 171 544.1570 3.1822
Scaled Pearson X2 171 544.1570 3.1822
Log Likelihood   68.4463
Full Log Likelihood   -461.5881
AIC (smaller is better)   927.1762
AICC (smaller is better)   927.2468
BIC (smaller is better)   933.4828
 Algorithm converged.

Is width a significant predictor? From the "Analysis of Parameter Estimates" table, with Chi-Square stats of 67.51 (1df), the p-value is 0.0001 and this is significant evidence to reject the null hypothesis that $$\beta_W=0$$. We can conclude that the carapace width is a significant predictor of the number of satellites.

Analysis Of Maximum Likelihood Parameter Estimates
Parameter DF Estimate Standard
Error
Wald 95% Confidence Limits Wald Chi-Square Pr > ChiSq
Intercept 1 -3.3048 0.5422 -4.3675 -2.2420 37.14 <.0001
W 1 0.1640 0.0200 0.1249 0.2032 67.51 <.0001
Scale 0 1.0000 0.0000 1.0000 1.0000

Note:The scale parameter was held fixed.

The estimated model is: $$\log (\mu_i) = -3.3048 + 0.164W_i$$

The standard error of the estimated slope is 0.020, which is small, and the slope is statistically significant.

model = glm(Sa ~ W, family=poisson(link=log), data=hcrabs)
summary(model)
model$fitted.values rstandard(model) Just as with logistic regression, the glm function specifies the response (Sa) and predictor width (W) separated by the "~" character. Also, note the specification of the Poisson distribution and link function. The fitted (predicted) values are the estimated Poisson counts, and rstandard reports the standardized deviance residuals. Here is the output that we should get from the summary command: > summary(model) Call: glm(formula = Sa ~ W, family = poisson(link = log), data = hcrabs) Deviance Residuals: Min 1Q Median 3Q Max -2.8526 -1.9884 -0.4933 1.0970 4.9221 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -3.30476 0.54224 -6.095 1.1e-09 *** W 0.16405 0.01997 8.216 < 2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Dispersion parameter for poisson family taken to be 1) Null deviance: 632.79 on 172 degrees of freedom Residual deviance: 567.88 on 171 degrees of freedom AIC: 927.18 Number of Fisher Scoring iterations: 6 Does the model fit well? Given the value of deviance statistic of 567.879 with 171 df, the p-value is zero and the Value/DF is much bigger than 1, so the model does not fit well. The lack of fit may be due to missing data, predictors, or overdispersion. It should also be noted that the deviance and Pearson tests for lack of fit rely on reasonably large expected Poisson counts, which are mostly below five, in this case, so the test results are not entirely reliable. Still, we'd like to see a better-fitting model if possible. Is width a significant predictor? From the "Coefficients" table, with Chi-Square stat of $$8.216^2=67.50$$ (1df), the p-value is 0.0001, and this is significant evidence to reject the null hypothesis that $$\beta_W=0$$. We can conclude that the carapace width is a significant predictor of the number of satellites. The estimated model is: $$\log (\mu_i) = -3.3048 + 0.164W_i$$ The standard error of the estimated slope is 0.020, which is small, and the slope is statistically significant. #### Interpretation Since the estimate of $$\beta > 0$$, the wider the carapace is, the greater the number of male satellites (on average). Specifically, for each 1-cm increase in carapace width, the expected number of satellites is multiplied by $$\exp(0.1640) = 1.18$$. Looking at the standardized residuals, we may suspect some outliers (e.g., the 15th observation has a standardized deviance residual of almost 5!), but these seem less obvious in the scatterplot, given the overall variability. Also, with a sample size of 173, such extreme values are more likely to occur just by chance. Still, this is something we can address by adding additional predictors or with an adjustment for overdispersion. From the observations statistics, we can also see the predicted values (estimated mean counts) and the values of the linear predictor, which are the log of the expected counts. For example, for the first observation, the predicted value is $$\hat{\mu}_1=3.810$$, and the linear predictor is $$\log(3.810)=1.3377$$. From the above output, we see that width is a significant predictor, but the model does not fit well. We can further assess the lack of fit by plotting residuals or influential points, but let us assume for now that we do not have any other covariates and try to adjust for overdispersion to see if we can improve the model fit. #### Strategies to Improve the Fit ## Adjusting for Overdispersion In the above model, we detect a potential problem with overdispersion since the scale factor, e.g., Value/DF, is greater than 1. What does overdispersion mean for Poisson Regression? What does it tell us about the relationship between the mean and the variance of the Poisson distribution for the number of satellites? Recall that one of the reasons for overdispersion is heterogeneity, where subjects within each predictor combination differ greatly (i.e., even crabs with similar width have a different number of satellites). If that's the case, which assumption of the Poisson model is violated? As we saw in logistic regression, if we want to test and adjust for overdispersion we can add a scale parameter by changing scale=none to scale=pearson; see the third part of the SAS program crab.sas labeled 'Adjust for overdispersion by "scale=pearson" '. (As stated earlier we can also fit a negative binomial regression instead) proc genmod data=crab; model Sa=w / dist=poi link=log scale=pearson; output out=data2 p=pred; run; proc print; run; Below is the output when using "scale=pearson". How does this compare to the output above from the earlier stage of the code? Do we have a better fit now? Consider the "Scaled Deviance" and "Scaled Pearson chi-square" statistics. The overall model seems to fit better when we account for possible overdispersion. The SAS System The GENMOD Procedure Model Information Data Set WORK.CRAB Distribution Poisson Link Function Log Dependent Variable Sa  Number of Observations Read 173 173 Criteria For Assessing Goodness Of Fit Criterion DF Value Value/DF Deviance 171 567.8786 3.3209 Scaled Deviance 171 178.4544 1.0436 Pearson Chi-Square 171 544.1570 3.1822 Scaled Pearson X2 171 171.0000 1.0000 Log Likelihood 21.5091 Full Log Likelihood -461.5881 AIC (smaller is better) 927.1762 AICC (smaller is better) 927.2468 BIC (smaller is better) 933.4828  Algorithm converged. Analysis Of Maximum Likelihood Parameter Estimates Parameter DF Estimate Standard Error Wald 95% Confidence Limits Wald Chi-Square Pr > ChiSq Intercept 1 -3.3048 0.9673 -5.2006 -1.4089 11.67 0.0006 W 1 0.1640 0.0356 0.0942 0.2339 21.22 <.0001 Scale 0 1.7839 0.0000 1.7839 1.7839 Note:The scale parameter was estimated by the square root of Pearson's Chi-Square/DOF. The SAS System Obs Obs C S W Sa Wt pred 1 1 3 3 28.3 8 3.050 3.81034 2 2 4 3 22.5 0 1.550 1.47146 3 3 2 1 26.0 9 2.300 2.61278 4 4 4 3 24.8 0 2.100 2.14590 5 5 4 3 26.0 4 2.600 2.61278 6 6 3 3 23.8 0 2.100 1.82124 7 7 2 1 26.5 0 2.350 2.83612 8 8 4 2 24.7 0 1.900 2.11099 ... ... ... ... ... ... ... ... 170 170 4 3 29.0 4 3.275 4.27400 171 171 2 1 28.0 0 2.625 3.62736 172 172 5 3 27.0 0 2.625 3.07855 173 173 3 2 24.5 0 2.000 2.04285 As we saw in logistic regression, if we want to test and adjust for overdispersion we can add a scale parameter with the family=quasipoisson option. The estimated scale parameter will be labeled as "Overdispersion parameter" in the output. (As stated earlier we can also fit a negative binomial regression instead) model.disp = glm(Sa ~ W, family=quasipoisson(link=log), data=hcrabs) summary.glm(model.disp) summary.glm(model.disp)$dispersion

Below is the output when using the quasi-Poisson model. How does this compare to the output above from the earlier stage of the code? Do we have a better fit now?

> summary.glm(model.disp)

Call:
glm(formula = Sa ~ W, family = quasipoisson(link = log), data = hcrabs)

Deviance Residuals:
Min       1Q   Median       3Q      Max
-2.8526  -1.9884  -0.4933   1.0970   4.9221

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -3.30476    0.96729  -3.417 0.000793 ***
W            0.16405    0.03562   4.606 7.99e-06 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for quasipoisson family taken to be 3.182205)

Null deviance: 632.79  on 172  degrees of freedom
Residual deviance: 567.88  on 171  degrees of freedom


With this model, the random component does not technically have a Poisson distribution any more (hence the term "quasi" Poisson) because that would require that the response has the same mean and variance. From the estimate given (Pearson $$X^2/171 = 3.1822$$), the variance of the number of satellites is roughly three times the size of the mean.

The new standard errors (in comparison to the model without the overdispersion parameter), are larger, (e.g., $$0.0356 = 1.7839( 0.02)$$ which comes from the scaled SE ($$\sqrt{3.1822}=1.7839$$); the adjusted standard errors are multiplied by the square root of the estimated scale parameter. Thus, the Wald statistics will be smaller and less significant.

What could be another reason for poor fit besides overdispersion? Can we improve the fit by adding other variables?

Since we did not use the \$sign in the input statement to specify that the variable "C" was categorical, we can now do it by using class c as seen below. The following change is reflected in the next section of the crab.sas program labeled 'Add one more variable as a predictor, "color" '. proc genmod data=crab; class c; model Sa=w c / dist=poi link=log scale=pearson type3; run; Note the "Class level information" on color indicates that this variable has four levels, and thus are we are introducing three indicator variables into the model. From the "Analysis of Parameter Estimates" output below we see that the reference level is level 5. We continue to adjust for overdispersion with scale=pearson , although we could relax this if adding additional predictor(s) produced an insignificant lack of fit. The SAS System The GENMOD Procedure Model Information Data Set WORK.CRAB Distribution Poisson Link Function Log Dependent Variable Sa  Number of Observations Read 173 173 Class Level Information Class Levels Values C 4 2 3 4 5 Criteria For Assessing Goodness Of Fit Criterion DF Value Value/DF Deviance 168 559.3448 3.3294 Scaled Deviance 168 172.9776 1.0296 Pearson Chi-Square 168 543.2490 3.2336 Scaled Pearson X2 168 168.0000 1.0000 Log Likelihood 22.4866 Full Log Likelihood -457.3212 AIC (smaller is better) 924.6425 AICC (smaller is better) 925.0017 BIC (smaller is better) 940.4089  Algorithm converged. Analysis Of Maximum Likelihood Parameter Estimates Parameter DF Estimate Standard Error Wald 95% Confidence Limits Wald Chi-Square Pr > ChiSq Intercept 1 -3.0974 1.0026 -5.0625 -1.1323 9.54 0.0020 W 1 0.1493 0.0375 0.0759 0.2228 15.88 <.0001 C 2 1 0.4474 0.3760 -0.2897 1.1844 1.42 0.2342 C 3 1 0.2477 0.2934 -0.3274 0.8227 0.71 0.3986 C 4 1 0.0110 0.3244 -0.6249 0.6468 0.00 0.9730 C 5 0 0.0000 0.0000 0.0000 0.0000 . . Scale 0 1.7982 0.0000 1.7982 1.7982 Note:The scale parameter was estimated by the square root of Pearson's Chi-Square/DOF. The estimated model is: $$\log{\hat{\mu_i}}= -3.0974 + 0.1493W_i + 0.4474C_{2i} + 0.2477C_{3i} + 0.0110C_{4i}$$, using indicator variables for the first three colors. There does not seem to be a difference in the number of satellites between any color class and the reference level 5 according to the chi-squared statistics for each row in the table above. Furthermore, by the Type 3 Analysis output below we see that color overall is not statistically significant after we consider the width. LR Statistics For Type 3 Analysis Source Num DF Den DF F Value Pr > F Chi-Square Pr > ChiSq W 1 168 15.40 0.0001 15.40 <.0001 C 3 168 0.88 0.4529 2.64 0.4507   To add the horseshoe crab color as a categorical predictor (in addition to width), we can use the following code. The change of baseline to the 5th color is arbitrary. hcrabs$C = factor(hcrabs$C, levels=c('5','2','3','4')) model = glm(Sa ~ W+C, family=quasipoisson(link=log), data=hcrabs) summary(model) anova(model, test='Chisq') Note in the output that there are three separate parameters estimated for color, corresponding to the three indicators included for colors 2, 3, and 4 (5 as the baseline). We continue to adjust for overdispersion withfamily=quasipoisson, although we could relax this if adding additional predictor(s) produced an insignificant lack of fit. > summary(model) Call: glm(formula = Sa ~ W + C, family = quasipoisson(link = log), data = hcrabs) Deviance Residuals: Min 1Q Median 3Q Max -3.0415 -1.9581 -0.5575 0.9830 4.7523 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -3.09740 1.00260 -3.089 0.00235 ** W 0.14934 0.03748 3.985 0.00010 *** C2 0.44736 0.37604 1.190 0.23586 C3 0.24767 0.29339 0.844 0.39978 C4 0.01100 0.32442 0.034 0.97300 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Dispersion parameter for quasipoisson family taken to be 3.233628) Null deviance: 632.79 on 172 degrees of freedom Residual deviance: 559.34 on 168 degrees of freedom The estimated model is: $$\log{\hat{\mu_i}}= -3.0974 + 0.1493W_i + 0.4474C_{2i}+ 0.2477C_{3i}+ 0.0110C_{4i}$$, using indicator variables for the first three colors. There does not seem to be a difference in the number of satellites between any color class and the reference level 5 according to the chi-squared statistics for each row in the table above. Furthermore, by the ANOVA output below we see that color overall is not statistically significant after we consider the width. > anova(model, test='Chisq') Analysis of Deviance Table Model: quasipoisson, link: log Response: Sa Terms added sequentially (first to last) Df Deviance Resid. Df Resid. Dev Pr(>Chi) NULL 172 632.79 W 1 64.913 171 567.88 7.449e-06 *** C 3 8.534 168 559.34 0.4507 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Is this model preferred to the one without color? ## Including Color as a Numerical Predictor As it turns out, the color variable was actually recorded as ordinal with values 2 through 5 representing increasing darkness and may be quantified as such. So, we next consider treating color as a quantitative variable, which has the advantage of allowing a single slope parameter (instead of multiple indicator slopes) to represent the relationship with the number of satellites. We will run another part of the crab.sas program that does not include color as a categorical by removing the class statement for C: proc genmod data=crab; model Sa=w c / dist=poi link=log scale=pearson; run; Compare these partial parts of the output with the output above where we used color as a categorical predictor. We are doing this to keep in mind that different coding of the same variable will give us different fits and estimates. The SAS System The GENMOD Procedure Model Information Data Set WORK.CRAB Distribution Poisson Link Function Log Dependent Variable Sa  Number of Observations Read 173 173 Criteria For Assessing Goodness Of Fit Criterion DF Value Value/DF Deviance 170 560.2013 3.2953 Scaled Deviance 170 173.5034 1.0206 Pearson Chi-Square 170 548.8898 3.2288 Scaled Pearson X2 170 170.0000 1.0000 Log Likelihood 22.3878 Full Log Likelihood -457.7495 AIC (smaller is better) 921.4990 AICC (smaller is better) 921.6410 BIC (smaller is better) 930.9589  Algorithm converged. Analysis Of Maximum Likelihood Parameter Estimates Parameter DF Estimate Standard Error Wald 95% Confidence Limits Wald Chi-Square Pr > ChiSq Intercept 1 -2.3506 1.1516 -4.6076 -0.0936 4.17 0.0412 W 1 0.1496 0.0372 0.0767 0.2224 16.20 <.0001 C 1 -0.1694 0.1111 -0.3872 0.0484 2.32 0.1274 Scale 0 1.7969 0.0000 1.7969 1.7969 Note:The scale parameter was estimated by the square root of Pearson's Chi-Square/DOF. To add color as a quantitative predictor, we first define it as a numeric variable. Although the original values were 2, 3, 4, and 5, R will by default use 1 through 4 when converting from factor levels to numeric values. So, we add 1 after the conversion. data(hcrabs) colnames(hcrabs) = c("C","S","W","Sa","Wt") hcrabs$C = as.numeric(hcrabs$C)+1 model = glm(Sa ~ W+C, family=quasipoisson(link=log), data=hcrabs) summary(model) anova(model, test='Chisq') Compare these partial parts of the output with the output above where we used color as a categorical predictor. We are doing this to keep in mind that different coding of the same variable will give us different fits and estimates. > summary(model) Call: glm(formula = Sa ~ W + C, family = quasipoisson(link = log), data = hcrabs) Deviance Residuals: Min 1Q Median 3Q Max -2.9919 -1.9539 -0.5526 0.9836 4.7596 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -2.35058 1.15156 -2.041 0.0428 * W 0.14957 0.03716 4.025 8.55e-05 *** C -0.16940 0.11112 -1.524 0.1292 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Dispersion parameter for quasipoisson family taken to be 3.228764) Null deviance: 632.79 on 172 degrees of freedom Residual deviance: 560.20 on 170 degrees of freedom AIC: NA Number of Fisher Scoring iterations: 6 > anova(model, test='Chisq') Analysis of Deviance Table Model: quasipoisson, link: log Response: Sa Terms added sequentially (first to last) Df Deviance Resid. Df Resid. Dev Pr(>Chi) NULL 172 632.79 W 1 64.913 171 567.88 7.332e-06 *** C 1 7.677 170 560.20 0.1231 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 The estimated model is now $$\log{\hat{\mu_i}}= -2.3506 + 0.1496W_i - 0.1694C_i$$ And the interpretation of the single slope parameter for color is as follows: for each 1-unit increase in the color (darkness level), the expected number of satellites is multiplied by $$\exp(-.1694)=.8442$$. In terms of the fit, adding the numerical color predictor doesn't seem to help; the overdispersion seems to be due to heterogeneity. Is there something else we can do with this data? We can either (1) consider additional variables (if available), (2) collapse over levels of explanatory variables, or (3) transform the variables. Let's consider grouping the data by the widths and then fitting a Poisson regression model that models the rate of satellites per crab. ## Collapsing over Explanatory Variable Width In this approach, we create 8 width groups and use the average width for the crabs in that group as the single representative value. While width is still treated as quantitative, this approach simplifies the model and allows all crabs with widths in a given group to be combined. The disadvantage is that differences in widths within a group are ignored, which provides less information overall. However, another advantage of using the grouped widths is that the saturated model would have 8 parameters, and the goodness of fit tests, based on $$8-2$$ degrees of freedom, are more reliable. To account for the fact that width groups will include different numbers of crabs, we will model the mean rate $$\mu/t$$ of satellites per crab, where $$t$$ is the number of crabs for a particular width group. This variable is treated much like another predictor in the data set. The difference is that this value is part of the response being modeled and not assigned a slope parameter of its own. We will see more details on the Poisson rate regression model in the next section. The data, after being grouped into 8 intervals, is shown in the table below. Two columns to note in particular are "Cases", the number of crabs with carapace widths in that interval, and "Width", which now represents the average width for the crabs in that interval.  Interval Cases Width AvgSa SDSa VarSa =23.25 14 22.693 1.0000 1.6641 2.7692 23.25-24.25 14 23.843 1.4286 2.9798 8.8792 24.25-25.25 28 24.775 2.3929 2.5581 6.5439 25.25-26.25 39 25.838 2.6923 3.3729 11.3765 26.26-27.25 22 26.791 2.8636 2.6240 6.8854 27.25-28.25 24 27.738 3.8750 2.9681 8.8096 28.25-29.25 18 28.667 3.9444 4.1084 16.8790 >29.25 14 30.407 5.1429 2.8785 8.2858 In this approach, each observation within a group is treated as if it has the same width. In SAS, the Cases variable is input with the OFFSET option in the Model statement. We also create a variable LCASES=log(CASES) which takes the log of the number of cases within each grouping. This is our adjustment value $$t$$ in the model that represents (abstractly) the measurement window, which in this case is the group of crabs with a similar width. So, $$t$$ is effectively the number of crabs in the group, and we are fitting a model for the rate of satellites per crab, given carapace width. data crabgrp; input width cases SaTotal AvgSa; lcases=log(cases); cards; 22.69 14 14 1.00 23.84 14 20 1.428571 24.77 28 67 2.392857 25.84 39 105 2.692308 26.79 22 63 2.863636 27.74 24 93 3.875 28.67 18 71 3.944444 30.41 14 72 5.142857 ; proc genmod data=crabgrp order=data; model SaTotal = width / dist=poisson link=log offset=lcases obstats residuals; output out=data3 p=pred; run; Here is the output. Note "Offset variable" under the "Model Information". The SAS System The GENMOD Procedure Model Information Data Set WORK.CRABGRP Distribution Poisson Link Function Log Dependent Variable SaTotal Offset Variable lcases  Number of Observations Read 8 8 Parameter Information Parameter Effect Prm1 Intercept Prm2 width Criteria For Assessing Goodness Of Fit Criterion DF Value Value/DF Deviance 6 6.5168 1.0861 Scaled Deviance 6 6.5168 1.0861 Pearson Chi-Square 6 6.2470 1.0412 Scaled Pearson X2 6 6.2470 1.0412 Log Likelihood 1652.1028 Full Log Likelihood -26.4809 AIC (smaller is better) 56.9617 AICC (smaller is better) 59.3617 BIC (smaller is better) 57.1206  Algorithm converged. Analysis Of Maximum Likelihood Parameter Estimates Parameter DF Estimate Standard Error Wald 95% Confidence Limits Wald Chi-Square Pr > ChiSq Intercept 1 -3.5355 0.5760 -4.6645 -2.4065 37.67 <.0001 width 1 0.1727 0.0212 0.1311 0.2143 66.18 <.0001 Scale 0 1.0000 0.0000 1.0000 1.0000 Note:The scale parameter was held fixed. Based on the Pearson and deviance goodness of fit statistics, this model clearly fits better than the earlier ones before grouping width. For example, the Value/DF for the deviance statistic now is 1.0861. The estimated model is: $$\log (\hat{\mu}_i/t) = -3.535 + 0.1727\mbox{width}_i$$ For each 1-cm increase in carapace width, the mean number of satellites per crab is multiplied by $$\exp(0.1727)=1.1885$$. Observation Statistics Observation SaTotal lcases width Predicted Value Linear Predictor Standard Error of the Linear Predictor HessWgt Lower Upper Raw Residual Pearson Residual Deviance Residual Std Deviance Residual Std Pearson Residual Likelihood Residual Leverage CookD DFBETA_Intercept DFBETA_width DFBETAS_Intercept DFBETAS_width 1 14 2.6390573 22.69 20.544353 3.0225861 0.1027001 20.544353 16.798637 25.12528 -6.544353 -1.443845 -1.532938 -1.732037 -1.631372 -1.710727 0.2166875 0.3681075 -0.460663 0.0164188 -0.799711 0.7733011 2 20 2.6390573 23.84 25.058503 3.2212132 0.0813848 25.058503 21.363886 29.392059 -5.058503 -1.010519 -1.047745 -1.14727 -1.106509 -1.140606 0.1659747 0.1218267 -0.24937 0.008775 -0.432905 0.4132908 3 67 3.3322045 24.77 58.849849 4.0749893 0.0657446 58.849849 51.734881 66.943322 8.1501507 1.062412 1.039205 1.2034817 1.2303572 1.2103746 0.2543698 0.2582108 0.3254536 -0.011232 0.5649873 -0.528993 4 105 3.6635616 25.84 98.608352 4.591156 0.0513763 98.608352 89.162468 109.05493 6.3916476 0.6436592 0.636887 0.740506 0.74838 0.7425635 0.2602795 0.0985341 0.144533 -0.004711 0.2509092 -0.221869 5 63 3.0910425 26.79 65.543892 4.18272 0.0448389 65.543892 60.029581 71.564747 -2.543892 -0.314219 -0.316285 -0.33944 -0.337223 -0.339149 0.1317776 0.0086301 -0.015069 0.0003426 -0.026159 0.0161352 6 93 3.1780538 27.74 84.252198 4.4338147 0.0468532 84.252198 76.859888 92.355494 8.7478019 0.9530338 0.9372168 1.0381222 1.0556422 1.0413848 0.1849521 0.1264386 -0.069134 0.0033416 -0.120017 0.1573828 7 71 2.8903718 28.67 74.1998 4.3067615 0.0562513 74.1998 66.454059 82.848368 -3.1998 -0.371468 -0.374187 -0.427757 -0.424648 -0.427029 0.2347839 0.0276639 0.0743554 -0.003055 0.129081 -0.143886 8 72 2.6390573 30.41 77.943052 4.3559785 0.0840923 77.943052 66.099465 91.908752 -5.943052 -0.673164 -0.682002 -1.017999 -1.004806 -1.010749 0.5511749 0.6199362 0.5164022 -0.02006 0.8964738 -0.944816 The residuals analysis indicates a good fit as well. From the table above we also see that the predicted values correspond a bit better to the observed counts in the "SaTotal" cells. Let's compare the observed and fitted values in the plot below: In R, the lcases variable is specified with the OFFSET option, which takes the log of the number of cases within each grouping. This is our adjustment value $$t$$ in the model that represents (abstractly) the measurement window, which in this case is the group of crabs with similar width. So, $$t$$ is effectively the number of crabs in the group, and we are fitting a model for the rate of satellites per crab, given carapace width. # creating the 8 width groups width.long = cut(hcrabs$W, breaks=c(0,seq(23.25, 29.25),Inf))

# summarizing per group
Cases = aggregate(hcrabs$W, by=list(W=width.long),length)$x
lcases = log(Cases)
Width = aggregate(hcrabs$W, by=list(W=width.long),mean)$x
AvgSa = aggregate(hcrabs$Sa, by=list(W=width.long),mean)$x
SdSa = aggregate(hcrabs$Sa, by=list(W=width.long),sd)$x
VarSa = aggregate(hcrabs$Sa, by=list(W=width.long),var)$x
SaTotal = aggregate(hcrabs$Sa, by=list(W=width.long),sum)$x
cbind(table(width.long), Width, AvgSa, SdSa, VarSa)

hcrabs.grp = data.frame(Width=Width, lcases=lcases, SaTotal=SaTotal)
model.grp = glm(SaTotal ~ Width, offset=lcases, family=poisson, data=hcrabs.grp)
summary(model.grp)

Here is the output. Note the "offset = lcases" under the model expression.

 summary(model.grp)

Call:
glm(formula = SaTotal ~ Width, family = poisson, data = hcrabs.grp,
offset = lcases)

Deviance Residuals:
Min       1Q   Median       3Q      Max
-1.5322  -0.7750  -0.3454   0.7151   1.0347

Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.54018    0.57658  -6.140 8.26e-10 ***
Width        0.17290    0.02125   8.135 4.11e-16 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for poisson family taken to be 1)

Null deviance: 72.3772  on 7  degrees of freedom
Residual deviance:  6.5164  on 6  degrees of freedom

Based on the Pearson and deviance goodness of fit statistics, this model clearly fits better than the earlier ones before grouping width. For example, the Value/DF for the deviance statistic now is 1.0861. The estimated model is:

$$\log (\hat{\mu}_i/t)= -3.54 + 0.1729\mbox{width}_i$$

For each 1-cm increase in carapace width, the mean number of satellites per crab is multiplied by $$\exp(0.1729)=1.1887$$.

> rstandard(model.grp)
1          2          3          4          5          6          7          8
-1.7312682 -1.1474695  1.1980218  0.7447990 -0.3414285  1.0400246 -0.4260710 -1.0213629
> predict.glm(model.grp, type="response", newdata=hcrabs.grp)
1        2        3        4        5        6        7        8
20.54097 25.05952 58.88382 98.57261 65.55897 84.23620 74.18733 77.96057 

The residuals analysis indicates a good fit as well, and the predicted values correspond a bit better to the observed counts in the "SaTotal" cells. Let's compare the observed and fitted values in the plot below:

  Link ↥ Has Tooltip/Popover Toggleable Visibility