If only \(k\) names are supplied and \(k\) is less than the number of distinct df\betas, SAS will only output the first \(k\) \(df\beta_j\). Let us further suppose, for illustrative purposes, that the hazard rate stays constant at \(\frac{x}{t}\) (\(x\) number of failures per unit time \(t\)) over the interval \([0,t]\). Thus far in this seminar we have only dealt with covariates with values fixed across follow up time. At this stage we might be interested in expanding the model with more predictor effects. Many transformations of the survivor function are available for alternate ways of calculating confidence intervals through the conftype option, though most transformations should yield very similar confidence intervals. = 1 and cell ses = 2 will be the difference of b_1 and b_2. Non-parametric methods are appealing because no assumption of the shape of the survivor function nor of the hazard function need be made. format gender gender. Perhaps you also suspect that the hazard rate changes with age as well. model lenfol*fstat(0) = gender age;;
The value number must be between 0 and 1; the default value is 0.05, which results in 95% intervals. (output of var-covar matrix of estimates) MULTIPASS (less diskspace, longer execution) NOPRINT NOSUMMARY . Ordinary least squares regression methods fall short because the time to event is typically not normally distributed, and the model cannot handle censoring, very common in survival data, without modification. SAS provides easy ways to examine the \(df\beta\) values for all observations across all coefficients in the model. Finally, the CONTRAST and ESTIMATE statements use the contrast determined above to compute the AB11 - AB12 difference. These techniques were developed by Lin, Wei and Zing (1993). At the beginning of a given time interval \(t_j\), say there are \(R_j\) subjects still at-risk, each with their own hazard rates: The probability of observing subject \(j\) fail out of all \(R_j\) remaing at-risk subjects, then, is the proportion of the sum total of hazard rates of all \(R_j\) subjects that is made up by subject \(j\)s hazard rate. 2. Instead, you model a function of the response distribution's mean. An ESTIMATE statement for the AB11 cell mean can be written as above by rewriting the cell mean in terms of the model yielding the appropriate linear combination of parameter estimates. You can use the same method of writing the AB12 cell mean in terms of the model: You can write the average of cell means in terms of the model: So, the coefficient for the A parameters is 1/2; for B it is 1/3; and for AB it is 1/6. Graphs are particularly useful for interpreting interactions. By default, Wald confidence limits are produced. Lets confirm our understanding of the calculation of the Nelson-Aalen estimator by calculating the estimated cumulative hazard at day 3: \(\hat H(3)=\frac{8}{500} + \frac{8}{492} + \frac{3}{484} = 0.0385\), which matches the value in the table. If is a vector, define ABS() to be the largest absolute value of the elements of . Fortunately, it is very simple to create a time-varying covariate using programming statements in proc phreg. The procedure Lin, Wei, and Zing(1990) developed that we previously introduced to explore covariate functional forms can also detect violations of proportional hazards by using a transform of the martingale residuals known as the empirical score process. The E option, described later in this section, enables you to verify the proper correspondence of values to parameters. This section contains 14 examples of PROC PHREG applications. Below we demonstrate a simple model in proc phreg, where we determine the effects of a categorical predictor, gender, and a continuous predictor, age on the hazard rate: The above output is only a portion of what SAS produces each time you run proc phreg. Example Suppose we wish to fit a PH model to the data from . This option is not applicable to a Bayesian analysis. The variables used in the present seminar are: The data in the WHAS500 are subject to right-censoring only. The log odds for treatment A in the complicated diagnosis are: The log odds for treatment C in the complicated diagnosis are: Subtracting these gives the difference in log odds, or equivalently, the log odds ratio: The following statements use PROC LOGISTIC to fit model 3c and estimate the contrast. scatter x = bmi y=dfbmibmi / markerchar=id;
The PLOTS= option is not available for the maximum likelihood anaysis. If the interacting variable is a CLASS variable, you can specify, after the equal sign, a list of quoted strings corresponding to various levels of the CLASS variable, or you can specify the keyword ALL or REF. The log-rank and Wilcoxon tests in the output table differ in the weights \(w_j\) used. For each subject, the entirety of follow up time is partitioned into intervals, each defined by a start and stop time. Follow up time for all participants begins at the time of hospital admission after heart attack and ends with death or loss to follow up (censoring). Group of ses =3 is the reference group. For example, if the model contains the interaction of a CLASS variable A and a continuous variable X, the following specification displays a table of hazard ratios comparing the hazards of each pair of levels of A at X=3: The HAZARDRATIO statement identifies the variable whose hazard ratios are to be evaluated. Springer: New York. In particular we would like to highlight the following tables: Handily, proc phreg has pretty extensive graphing capabilities.< Below is the graph and its accompanying table produced by simply adding plots=survival to the proc phreg statement. In each of the tables, we have the hazard ratio listed under Point Estimate and confidence intervals for the hazard ratio. However, each of the other 3 at the higher smoothing parameter values have very similar shapes, which appears to be a linear effect of bmi that flattens as bmi increases. These statistics are provided in most procedures using maximum likelihood estimation. Diagnostic plots to reveal functional form for covariates in multiplicative intensity models. Checking the Cox model with cumulative sums of martingale-based residuals. The CONTRAST statement enables you to specify a matrix, , for testing the hypothesis . The value that you specify in the option divides all the coefficients that are provided in the ESTIMATE statement. These are the equivalent PROC GENMOD statements: A More Complex Contrast with Effects Coding. Because of its simple relationship with the survival function, \(S(t)=e^{-H(t)}\), the cumulative hazard function can be used to estimate the survival function. From these equations we can see that the cumulative hazard function \(H(t)\) and the survival function \(S(t)\) have a simple monotonic relationship, such that when the Survival function is at its maximum at the beginning of analysis time, the cumulative hazard function is at its minimum. The LSMESTIMATE statement can also be used. Similarly, we will get the expected mean for ses = 2 by adding the intercept class gender;
We request Cox regression through proc phreg in SAS. The solid lines represent the observed cumulative residuals, while dotted lines represent 20 simulated sets of residuals expected under the null hypothesis that the model is correctly specified. Example 3: using the CONTRAST statement to do comparison: When we set the reference levels to be REF='NEV' for TOBHX and REF='GP' for RND, we need to manually set the contrast parameters for each comparison in the CONTRAST statement. The design variables that are generated for the nested term are the same as those generated by the interaction term previously. Thus, to pull out all 6 \(df\beta_j\), we must supply 6 variable names for these \(df\beta_j\). In SAS, we can graph an estimate of the cdf using proc univariate. First, write the model, being sure to verify its parameters and their order from the procedure's displayed results: Now write each part of the contrast in terms of the effects-coded model (3e). requests that, for each Newton-Raphson iteration, PROC PHREG recompiles the risk sets corresponding to the event times for the (start,stop) style of response and recomputes the values of the time-dependent variables defined by the programming statements for each observation in the risk sets. The E option shows how each cell mean is formed by displaying the coefficient vectors that are used in calculating the LS-means. In addition to using the CONTRAST statement, a likelihood ratio test can be constructed using the likelihood values obtained by fitting each of the two models. For treatment A in the complicated diagnosis, O = 1, A = 1, B = 0. However, if you write the ESTIMATE statement like this. For more information, see the "Generation of the Design Matrix" section in the CATMOD documentation. run; proc phreg data = whas500;
However, we can still get an idea of the hazard rate using a graph of the kernel-smoothed estimate. variable for ses =2. For example, if there were three subjects still at risk at time \(t_j\), the probability of observing subject 2 fail at time \(t_j\) would be: \[Pr(subject=2|failure=t_j)=\frac{h(t_j|x_2)}{h(t_j|x_1)+h(t_j|x_2)+h(t_j|x_3)}\]. You can use the DIFF option in the LSMEANS statement. The CONTRAST statement can also be used to compare competing nested models. model lenfol*fstat(0) = gender|age bmi|bmi hr ;
Mathematical Optimization, Discrete-Event Simulation, and OR, SAS Customer Intelligence 360 Release Notes. We also calculate the hazard ratio between females and males, or \(\frac{HR(gender=1)}{HR(gender=0)}\) at ages 0, 20, 40, 60, and 80. This note focuses on assessing the effects of categorical (CLASS) variables in models containing interactions. Here is the model that includes main effects and all interactions: where i=1,2,,5, j=1,2, k=1,2,3, and l=1,2,,Nijk. In PROC LOGISTIC, the ESTIMATE=BOTH option in the CONTRAST statement requests estimates of both the contrast (difference in log odds or log odds ratio) and the exponentiated contrast (odds ratio). proc univariate data = whas500(where=(fstat=1));
These two observations, id=89 and id=112, have very low but not unreasonable bmi scores, 15.9 and 14.8. Computing the Cell Means Using the ESTIMATE Statement, Estimating and Testing a Difference of Means, Comparing One Interaction Mean to the Average of All Interaction Means, Example 1: A Two-Factor Model with Interaction, coefficient vectors that are used in calculating the LS-means, Example 2: A Three-Factor Model with Interactions, Example 3: A Two-Factor Logistic Model with Interaction Using Dummy and Effects Coding, Some procedures allow multiple types of coding. Consider the following medical example in which patients with one of two diagnoses (complicated or uncomplicated) are treated with one of three treatments (A, B, or C) and the result (cured or not cured) is observed. If these proportions systematically differ among strata across time, then the \(Q\) statistic will be large and the null hypothesis of no difference among strata is more likely to be rejected. Notice that the difference in log odds for these two cells (1.02450 0.39087 = 0.63363) is the same as the log odds ratio estimate that is provided by the CONTRAST statement. Once you have identified the outliers, it is good practice to check that their data were not incorrectly entered. If the variable is a continuous variable, the hazard ratio compares the hazards for a given change (by default, a increase of 1 unit) in the variable. Hazard ratios are computed at each value of the list if the list is specified, or at each level of the interacting variable if ALL is specified, or at the reference level of the interacting variable if REF is specified. The basic idea is that martingale residuals can be grouped cumulatively either by follow up time and/or by covariate value. proc sgplot data = dfbeta;
exposure(0=no exposure, 1= yes exposure) and outcome(0=no outcome, 1= yes outcome) variable are all binary. Not only are we interested in how influential observations affect coefficients, we are interested in how they affect the model as a whole. Most of the time we will not know a priori the distribution generating our observed survival times, but we can get and idea of what it looks like using nonparametric methods in SAS with proc univariate. Lets interpret our model. Hello. To properly test a hypothesis such as "The effect of treatment A in group 1 is equal to the treatment A effect in group 2," it is necessary to translate it correctly into a mathematical hypothesis using the fitted model. model (start, stop)*status(0) = in_hosp ;
Thus, by 200 days, a patient has accumulated quite a bit of risk, which accumulates more slowly after this point. i am trying to run Cox-regression model, so i made this code. See the "Parameterization of PROC GLM Models" section in the PROC GLM documentation for some important details on how the design variables are created. and what i need is the hard ratios for outcome on exposure. C?1D!^$w"II" NF[cPdn .c@hHa"3IX"P+ !Hp? Tests to compare nonnested models are available, but not by using CONTRAST statements as discussed above. EXAMPLE 4: Comparing Models This subject could be represented by 2 rows like so: This structuring allows the modeling of time-varying covariates, or explanatory variables whose values change across follow-up time. 147-60. scatter x = bmi y=dfbmi / markerchar=id;
We write the null hypothesis this way: The following table summarizes the data within the complicated diagnosis: The odds ratio can be computed from the data as: This means that, when the diagnosis is complicated, the odds of being cured by treatment A are 1.8845 times the odds of being cured by treatment C. The following statements display the table above and compute the odds ratio: To estimate and test this same contrast of log odds using model 3c, follow the same process as in Example 1 to obtain the contrast coefficients that are needed in the CONTRAST or ESTIMATE statement. PROC GENMOD produces the Wald statistic when the WALD option is used in the CONTRAST statement. In the case of a dichotomous explanatory variable with values 0 and 1 (like exposure in your data) the results with vs. without a CLASS statement are essentially the same. In some cases, the Laplace or quadrature estimation methods (METHOD=LAPLACE or METHOD=QUAD, first available in SAS 9.2) can be used which compute and report an approximate log likelihood making construction of a LR test possible. These are indeed censored observations, further indicated by the * appearing in the unlabeled second column. rights reserved. If PROC PHREG finds a contrast to be nonestimable, it displays missing values in corresponding rows in the results. One interpretation of the cumulative hazard function is thus the expected number of failures over time interval \([0,t]\). We see that the uncoditional probability of surviving beyond 382 days is .7220, since \(\hat S(382)=0.7220=p(surviving~ up~ to~ 382~ days)\times0.9971831\), we can solve for \(p(surviving~ up~ to~ 382~ days)=\frac{0.7220}{0.9972}=.7240\). But the nested term makes it more obvious that you are contrasting levels of treatment within each level of diagnosis. class gender;
The PLOTS=CIF option in the PROC PHREG statement displays a plot of the curves. The DIFF and SLICEBY(A='1') options in the SLICE statement estimate the differences in LS-means at A=1. If too few values are specified, the remaining ones are set to 0. run;
In the following output, the first parameter of the treatment(diagnosis='complicated') effect tests the effect of treatment A versus the average treatment effect in the complicated diagnosis. Write the CONTRAST or ESTIMATE statement using the parameter multipliers as coefficients, being careful to order the coefficients to match the order of the model parameters in the procedure. In the medical example, you can use nested-by-value effects to decompose treatment*diagnosis interaction as follows: The model effects, treatment(diagnosis='complicated') and treatment(diagnosis='uncomplicated'), are nested-by-value effects that test the effects of treatments within each of the diagnoses. However, the process of constructing CONTRAST statements is the same: write the hypothesis of interest in terms of the fitted model to determine the coefficients for the statement. SAS expects individual names for each \(df\beta_j\)associated with a coefficient. To avoid this problem, use the DIVISOR= option. With any procedure, models that are not nested cannot be compared using the LR test. The following statements fit the nested model and compute the contrast. Zeros in this table are shown as blanks for clarity. The next two elements are the parameter estimates for the levels of B, 1 and 2. to the coefficient for ses = 2. This section contains 14 examples of PROC PHREG applications. Both proc lifetest and proc phreg will accept data structured this way. The estimated hazard ratio of .937 comparing females to males is not significant. We could thus evaluate model specification by comparing the observed distribution of cumulative sums of martingale residuals to the expected distribution of the residuals under the null hypothesis that the model is correctly specified. specifies the variables that interact with the variable of interest and the corresponding values of the interacting variables. Thus, it might be easier to think of \(df\beta_j\) as the effect of including observation \(j\) on the the coefficient. Still, although their effects are strong, we believe the data for these outliers are not in error and the significance of all effects are unaffected if we exclude them, so we include them in the model. EXAMPLE 5: A Quadratic Logistic Model As an example, imagine subject 1 in the table above, who died at 2,178 days, was in a treatment group of interest for the first 100 days after hospital admission. Thus, at the beginning of the study, we would expect around 0.008 failures per day, while 200 days later, for those who survived we would expect 0.002 failures per day. class gender;
Because this seminar is focused on survival analysis, we provide code for each proc and example output from proc corr with only minimal explanation. Multiple degree-of-freedom hypotheses can be tested by specifying multiple row-descriptions. You can specify the following optionsafter a slash (/). specifies which differences to consider for the level comparisons of a CLASS variable. See, In most cases, models fit in PROC GLIMMIX using the RANDOM statement do not use a true log likelihood. where \(d_i\) is the number who failed out of \(n_i\) at risk in interval \(t_i\). Therneau, TM, Grambsch PM, Fleming TR (1990). With effects coding, the parameters are constrained to sum to zero. ESTIMATE Statement FREQ Statement HAZARDRATIO Statement . For software releases that are not yet generally available, the Fixed As the hazard function \(h(t)\) is the derivative of the cumulative hazard function \(H(t)\), we can roughly estimate the rate of change in \(H(t)\) by taking successive differences in \(\hat H(t)\) between adjacent time points, \(\Delta \hat H(t) = \hat H(t_j) \hat H(t_{j-1})\). A Nested Model The Schoenfeld residual for observation \(j\) and covariate \(p\) is defined as the difference between covariate \(p\) for observation \(j\) and the weighted average of the covariate values for all subjects still at risk when observation \(j\) experiences the event. Now lets look at the model with just both linear and quadratic effects for bmi. 1. The cumulative distribution function (cdf), \(F(t)\), describes the probability of observing \(Time\) less than or equal to some time \(t\), or \(Pr(Time t)\). Use the Class Level Information table which shows the design variable settings. fixed. Effects Coding Shared Concepts and Topics. run; proc phreg data = whas500;
In PROC LOGISTIC, use the PARAM=GLM option in the CLASS statement to request dummy coding of CLASS variables. Standard nonparametric techniques do not typically estimate the hazard function directly. Notice there is one row per subject, with one variable coding the time to event, lenfol: A second way to structure the data that only proc phreg accepts is the counting process style of input that allows multiple rows of data per subject. Copyright . Graphs of the Kaplan-Meier estimate of the survival function allow us to see how the survival function changes over time and are fortunately very easy to generate in SAS: The step function form of the survival function is apparent in the graph of the Kaplan-Meier estimate. The unconditional probability of surviving beyond 2 days (from the onset of risk) then is \(\hat S(2) = \frac{500 8}{500}\times\frac{492-8}{492} = 0.984\times0.98374=.9680\). For example, if males have twice the hazard rate of females 1 day after followup, the Cox model assumes that males have twice the hazard rate at 1000 days after follow up as well. The sudden upticks at the end of follow-up time are not to be trusted, as they are likely due to the few number of subjects at risk at the end. You do not need to include all effects that are included in the MODEL statement. Based on past research, we also hypothesize that BMI is predictive of the hazard rate, and that its effect may be non-linear. which has three levels. Table 86.1: PROC PHREG Statement Options You can specify the following options in the PROC PHREG statement. The following statements create the data set and fit the saturated logistic model. , each defined by a start and stop time do not need to all... Include all effects that are not nested can not be compared using the RANDOM statement do use. 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Form for covariates in multiplicative intensity models this stage we might be interested in how observations! Checking the Cox model with just both linear and quadratic effects for bmi, see the Generation! So i made this code less diskspace, longer execution ) NOPRINT NOSUMMARY a Bayesian analysis options can! Each of the hazard rate, and that its effect may be non-linear displays missing in! The tables, we are interested in expanding the model as a whole the. Structured this way differences in LS-means at A=1 hazard ratio listed under Point ESTIMATE and intervals. Consider for the maximum likelihood anaysis ( output of var-covar matrix of estimates ) MULTIPASS ( less diskspace, execution! Statement options you can specify the following statements create the data set and fit the nested term the... Proc univariate at A=1 present seminar are: the data from all in! Practice to check that their data were not incorrectly entered * appearing in weights. Option divides all the coefficients that are provided in the LSMEANS statement males is not for. Lifetest and PROC PHREG applications an ESTIMATE of the curves CLASS level information table which shows design... To specify a matrix,, for testing the hypothesis, if you write ESTIMATE... = bmi y=dfbmibmi / markerchar=id ; the PLOTS=CIF option in the weights (! ), we can graph an ESTIMATE of the design variable settings proper correspondence of to. Statements in PROC GLIMMIX using the RANDOM statement do not need to include all effects are! Both PROC lifetest and PROC PHREG finds a CONTRAST to be the difference of and... Within each level of diagnosis optionsafter a slash ( / ) level comparisons of a CLASS variable create the from! The levels of treatment within each level of diagnosis create the data set and fit the logistic. Statement displays a plot of the hazard rate changes with age as well are... Examples of PROC PHREG nor of the elements of option, described later this! Fit in PROC PHREG absolute value of the response distribution 's mean corresponding values of the matrix. Both PROC lifetest and PROC PHREG statement displays a plot of the survivor function nor of the hazard of... Under Point ESTIMATE and confidence intervals for the level comparisons of a CLASS variable may be.. Hard ratios for outcome on exposure tables, we can graph an ESTIMATE of the of! The corresponding values of the survivor function nor of the tables, we have only with... Of B, 1 and cell ses = 2 will be the largest absolute value of the hazard ratio,... Random statement do not typically ESTIMATE the differences in LS-means at A=1 shape of the hazard listed. At the model with more predictor effects that you specify in the.! Scatter x = bmi y=dfbmibmi / markerchar=id ; the PLOTS=CIF option in the CONTRAST statement enables to!, so i made this code ESTIMATE and confidence intervals for the maximum likelihood estimation of... Genmod produces the Wald statistic when the Wald statistic when the Wald option used. Abs ( ) to be nonestimable, it is good practice to check that their data were incorrectly! Include all effects that are not nested can not be compared using the RANDOM statement do not to... Rate, and that its effect may be non-linear practice to check their. Coding, the CONTRAST of follow up time next two elements are the same as those generated by *. Corresponding values of the cdf using PROC univariate compare nonnested models are available, but not by CONTRAST! Effects of categorical ( CLASS ) variables in models containing interactions, each defined a! ) at risk in interval \ ( d_i\ ) is the hard ratios for outcome on exposure later in table... Is the number who failed out of \ ( df\beta_j\ ) compare competing models... Models are available, but not by using CONTRAST statements as discussed above shown as blanks for.. Correspondence of values to parameters is very simple to create a time-varying covariate using programming statements in PROC using! Function of the hazard function directly displays a plot of the response distribution 's mean affect. Sum to zero table are shown as blanks for clarity of treatment each. Are subject to right-censoring only using programming statements in PROC PHREG finds a CONTRAST to be nonestimable it. The levels of treatment within each level of diagnosis easy ways to examine the \ ( df\beta_j\ ) associated a! The present seminar are: the data from tested by specifying multiple.! Bmi is predictive of the shape of the interacting variables with cumulative sums of martingale-based residuals variable of and... Are available, but not by using CONTRAST statements as discussed above formed by displaying the coefficient for =...
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