# Constrained Generalized Additive Mixed-Effects Model Fitting This routine is an addition to the main routine cgam in this package. A random-intercept component is included in a cgam model. ```r cgamm(formula, nsim = 100, family = gaussian(), cpar = 1.2, data = NULL, weights = NULL, sc_x = FALSE, sc_y = FALSE, bisect = TRUE, reml = TRUE, multicore = getOption("cgam.parallel"), CIC = FALSE, nAGQ = 1L) ``` ## Arguments - `formula`: A formula object which gives a symbolic description of the model to be fitted. It has the form "response ~ predictor + (1|id)", where id is the label for a group effect. For now, only gaussian responses are considered and this routine only includes a random-intercept effect. See `cgam` for more details. - `nsim`: The number of simulations used to get the cic parameter. The default is nsim = 0. - `family`: A parameter indicating the error distribution and link function to be used in the model. For now, the options are family = gaussian() and family = binomial(). - `cpar`: A multiplier to estimate the model variance, which is defined as $\sigma^2 = SSR / (n - cpar * edf)$. SSR is the sum of squared residuals for the full model and edf is the effective degrees of freedom. The default is cpar = 1.2. The user-defined value must be between 1 and 2. See Meyer, M. C. and M. Woodroofe (2000) for more details. - `data`: An optional data frame, list or environment containing the variables in the model. The default is data = NULL. - `weights`: An optional non-negative vector of "replicate weights" which has the same length as the response vector. If weights are not given, all weights are taken to equal 1. The default is weights = NULL. - `sc_x`: Logical flag indicating if or not continuous predictors are normalized. The default is sc_x = FALSE. - `sc_y`: Logical flag indicating if or not the response variable is normalized. The default is sc_y = FALSE. - `bisect`: If bisect = TRUE, a 95 percent confidence interval will be found for the variance ratio parameter by a bisection method. - `reml`: If reml = TRUE, restricted maximum likelihood (REML) method will be used to find estimates instead of maximum likelihood estimation (MLE). - `multicore`: A parameter retrieving the current global option for "csurvey.multicore" and assigns its value to the multicore variable, allowing the function to respect a user-defined setting for parallel processing behavior across the package. - `CIC`: Logical flag indicating if or not cic is computed. - `nAGQ`: Integer scalar - the number of points per axis for evaluating the adaptive Gauss-Hermite approximation to the log-likelihood. Defaults to 1, corresponding to the Laplace approximation. Values greater than 1 produce greater accuracy in the evaluation of the log-likelihood at the expense of speed. ## Returns - **muhat**: The fitted fixed-effect term. - **ahat**: A vector of estimated random-effect terms. - **sig2hat**: Estimate of the variance ($\sigma^2$) of between-cluster error terms. - **siga2hat**: Estimate of the variance ($\sigma_a^2$) of within-cluster error terms. - **thhat**: Estimate of the ratio ($\theta$) of two variances. - **pv.siga2**: $p$-value of the test $H_0: \sigma_a^2=0$ - **ci.siga2**: 95 percent confidence interval for the variance of within-cluster error terms. - **ci.th**: 95 percent confidence interval for ratio of two variances. - **ci.rho**: 95 percent confidence interval for intraclass correlation coefficient. - **ci.sig2**: 95 percent confidence interval for the variance of between-cluster error terms. - **call**: The matched call. ## Examples ```r # Example 1 (family = gaussian). # simulate a balanced data set with 30 clusters # each cluster has 30 data points n <- 30 m <- 30 # the standard deviation of between cluster error terms is 1 # the standard deviation of within cluster error terms is 2 sige <- 1 siga <- 2 # generate a continuous predictor x <- 1:(m*n) for(i in 1:m) { x[(n*(i-1)+1):(n*i)] <- round(runif(n), 3) } # generate a group factor group <- trunc(0:((m*n)-1)/n)+1 # generate the fixed-effect term mu <- 10*exp(10*x-5)/(1+exp(10*x-5)) # generate the random-intercept term asscosiated with each group avals <- rnorm(m, 0, siga) # generate the response y <- 1:(m*n) for(i in 1:m){ y[group == i] <- mu[group == i] + avals[i] + rnorm(n, 0, sige) } # use REML method to fit the model ans <- cgamm(y ~ s.incr(x) + (1|group), reml=TRUE) summary(ans) anova(ans) muhat <- ans$muhat plot(x, y, col = group, cex = .6) lines(sort(x), mu[order(x)], lwd = 2) lines(sort(x), muhat[order(x)], col = 2, lty = 2, lwd = 2) legend("topleft", bty = "n", c("true fixed-effect term", "cgamm fit"), col = c(1, 2), lty = c(1, 2), lwd = c(2, 2)) # Example 2 (family = binomial). # simulate a balanced data set with 20 clusters # each cluster has 20 data points n <- 20 m <- 20# N <- n*m # siga is the sd for the random intercept siga <- 1 # generate a group factor group <- trunc(0:((m*n)-1)/n)+1 group <- factor(group) # generate the random-intercept term asscosiated with each group avals <- rnorm(m,0,siga) # generate the fixed-effect mean term: mu, systematic term: eta and the response: y x <- runif(m*n) mu <- 1:(m*n) y <- 1:(m*n) eta <- 2 * (1 + tanh(7 * (x - .8))) - 2 eta0 <- eta for(i in 1:m){eta[group == i] <- eta[group == i] + avals[i]} for(i in 1:m){mu[group == i] <- 1 - 1 / (1 + exp(eta[group == i]))} for(i in 1:m){y[group == i] <- rbinom(n, size = 1, prob = mu[group == i])} dat <- data.frame(x = x, y = y, group = group) ansc <- cgamm(y ~ s.incr.conv(x) + (1|group), family = binomial(link = "logit"), reml = FALSE, data = dat) summary(ansc) anova(ansc) ``` ## Author(s) Xiyue Liao

cgamm function