R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0

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> ### * <HEADER>
> ###
> attach(NULL, name = "CheckExEnv")
> assign(".CheckExEnv", as.environment(2), pos = length(search())) # base
> ## add some hooks to label plot pages for base and grid graphics
> setHook("plot.new", ".newplot.hook")
> setHook("persp", ".newplot.hook")
> setHook("grid.newpage", ".gridplot.hook")
> 
> assign("cleanEx",
+        function(env = .GlobalEnv) {
+ 	   rm(list = ls(envir = env, all.names = TRUE), envir = env)
+            RNGkind("default", "default")
+ 	   set.seed(1)
+    	   options(warn = 1)
+ 	   delayedAssign("T", stop("T used instead of TRUE"),
+ 		  assign.env = .CheckExEnv)
+ 	   delayedAssign("F", stop("F used instead of FALSE"),
+ 		  assign.env = .CheckExEnv)
+ 	   sch <- search()
+ 	   newitems <- sch[! sch %in% .oldSearch]
+ 	   for(item in rev(newitems))
+                eval(substitute(detach(item), list(item=item)))
+ 	   missitems <- .oldSearch[! .oldSearch %in% sch]
+ 	   if(length(missitems))
+ 	       warning("items ", paste(missitems, collapse=", "),
+ 		       " have been removed from the search path")
+        },
+        env = .CheckExEnv)
> assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now
> assign("ptime", proc.time(), env = .CheckExEnv)
> grDevices::postscript("pgam-Examples.ps")
> assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv)
> options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))
> options(warn = 1)    
> library('pgam')
This is pgam library version 0.4.3 
> 
> assign(".oldSearch", search(), env = .CheckExEnv)
> assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
> cleanEx(); ..nameEx <- "AIC.pgam"
> 
> ### * AIC.pgam
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: AIC.pgam
> ### Title: AIC extraction
> ### Aliases: AIC.pgam
> ### Keywords: ts smooth regression
> 
> ### ** Examples
> 
> library(pgam)
> data(aihrio)
> attach(aihrio)
> form <- ITRESP5~f(WEEK)+HOLIDAYS+rain+PM+g(tmpmax,7)+g(wet,3)
> m <- pgam(form,aihrio,omega=.8,beta=.01,maxit=1e2,eps=1e-4,optim.method="BFGS")
iter: 1  |  norm: Inf 
iter: 2  |  norm: 0.0020767 
iter: 3  |  norm: 3.82e-05 

Semiparametric model estimation algorithm has converged.

Final run: Getting estimated parameters, functions and numerical hessian matrix...
Counts (fn | gr): 37 2

Estimation process took 00:00:02 (hh:mm:ss)
> 
> AIC(m)
[1] 1.313397
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "coef.pgam"
> 
> ### * coef.pgam
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: coef.pgam
> ### Title: Coefficients extraction
> ### Aliases: coef.pgam
> ### Keywords: ts smooth regression
> 
> ### ** Examples
> 
> library(pgam)
> data(aihrio)
> attach(aihrio)
> form <- ITRESP5~f(WEEK)+HOLIDAYS+rain+PM+g(tmpmax,7)+g(wet,3)
> m <- pgam(form,aihrio,omega=.8,beta=.01,maxit=1e2,eps=1e-4,optim.method="BFGS")
iter: 1  |  norm: Inf 
iter: 2  |  norm: 0.0020767 
iter: 3  |  norm: 3.82e-05 

Semiparametric model estimation algorithm has converged.

Final run: Getting estimated parameters, functions and numerical hessian matrix...
Counts (fn | gr): 37 2

Estimation process took 00:00:02 (hh:mm:ss)
> 
> coef(m)
   (Discount)        WEEK.1        WEEK.2        WEEK.3        WEEK.4 
 0.8608709184 -0.4747100583  0.2453708909  0.1651389660  0.1873044777 
       WEEK.5        WEEK.6        WEEK.7      HOLIDAYS          rain 
 0.1104593126  0.1465003289 -0.3800639177 -0.3101366665 -0.0035355425 
           PM 
 0.0009979136 
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "deviance.pgam"
> 
> ### * deviance.pgam
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: deviance.pgam
> ### Title: Deviance extraction
> ### Aliases: deviance.pgam
> ### Keywords: ts smooth regression
> 
> ### ** Examples
> 
> library(pgam)
> data(aihrio)
> attach(aihrio)
> form <- ITRESP5~f(WEEK)+HOLIDAYS+rain+PM+g(tmpmax,7)+g(wet,3)
> m <- pgam(form,aihrio,omega=.8,beta=.01,maxit=1e2,eps=1e-4,optim.method="BFGS")
iter: 1  |  norm: Inf 
iter: 2  |  norm: 0.0020767 
iter: 3  |  norm: 3.82e-05 

Semiparametric model estimation algorithm has converged.

Final run: Getting estimated parameters, functions and numerical hessian matrix...
Counts (fn | gr): 37 2

Estimation process took 00:00:02 (hh:mm:ss)
> 
> deviance(m)
[1] 426.3603
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "fitted.pgam"
> 
> ### * fitted.pgam
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: fitted.pgam
> ### Title: Fitted values extraction
> ### Aliases: fitted.pgam
> ### Keywords: ts smooth regression
> 
> ### ** Examples
> 
> library(pgam)
> data(aihrio)
> attach(aihrio)
> form <- ITRESP5~f(WEEK)+HOLIDAYS+rain+PM+g(tmpmax,7)+g(wet,3)
> m <- pgam(form,aihrio,omega=.8,beta=.01,maxit=1e2,eps=1e-4,optim.method="BFGS")
iter: 1  |  norm: Inf 
iter: 2  |  norm: 0.0020767 
iter: 3  |  norm: 3.82e-05 

Semiparametric model estimation algorithm has converged.

Final run: Getting estimated parameters, functions and numerical hessian matrix...
Counts (fn | gr): 37 2

Estimation process took 00:00:02 (hh:mm:ss)
> 
> f <- fitted(m)
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "logLik.pgam"
> 
> ### * logLik.pgam
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: logLik.pgam
> ### Title: Loglik extraction
> ### Aliases: logLik.pgam
> ### Keywords: ts smooth regression
> 
> ### ** Examples
> 
> library(pgam)
> data(aihrio)
> attach(aihrio)
> form <- ITRESP5~f(WEEK)+HOLIDAYS+rain+PM+g(tmpmax,7)+g(wet,3)
> m <- pgam(form,aihrio,omega=.8,beta=.01,maxit=1e2,eps=1e-4,optim.method="BFGS")
iter: 1  |  norm: Inf 
iter: 2  |  norm: 0.0020767 
iter: 3  |  norm: 3.82e-05 

Semiparametric model estimation algorithm has converged.

Final run: Getting estimated parameters, functions and numerical hessian matrix...
Counts (fn | gr): 37 2

Estimation process took 00:00:02 (hh:mm:ss)
> 
> logLik(m)
[1] 1075.727
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "pgam"
> 
> ### * pgam
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: pgam
> ### Title: Poisson-Gamma Additive Models
> ### Aliases: pgam
> ### Keywords: ts smooth regression
> 
> ### ** Examples
> 
> library(pgam)
> data(aihrio)
> attach(aihrio)
> form <- ITRESP5~f(WEEK)+HOLIDAYS+rain+PM+g(tmpmax,7)+g(wet,3)
> m <- pgam(form,aihrio,omega=.8,beta=.01,maxit=1e2,eps=1e-4,optim.method="BFGS")
iter: 1  |  norm: Inf 
iter: 2  |  norm: 0.0020767 
iter: 3  |  norm: 3.82e-05 

Semiparametric model estimation algorithm has converged.

Final run: Getting estimated parameters, functions and numerical hessian matrix...
Counts (fn | gr): 37 2

Estimation process took 00:00:02 (hh:mm:ss)
> 
> summary(m)
Function call:
pgam(formula = form, dataset = aihrio, omega = 0.8, beta = 0.01, 
    maxit = 100, eps = 1e-04, optim.method = "BFGS")

Model formula:
ITRESP5 ~ f(WEEK) + HOLIDAYS + rain + PM + g(tmpmax, 7) + g(wet, 
    3)

Parametric coefficients:
                 Estimate     std. err.     t ratio      Pr(>|t|)
  (Discount)     0.8608709    0.04614704      18.65495    < 2.22e-16
      WEEK.1    -0.4747101    0.03915625     -12.12348    < 2.22e-16
      WEEK.2     0.2453709    0.02868606      8.553664    4.4409e-16
      WEEK.3      0.165139    0.02965303      5.569042    5.1698e-08
      WEEK.4     0.1873045    0.02936112      6.379337    5.7401e-10
      WEEK.5     0.1104593    0.03039694      3.633895    0.00032176
      WEEK.6     0.1465003    0.03040014      4.819068    2.1674e-06
      WEEK.7    -0.3800639      0.102413     -3.711091    0.00024059
    HOLIDAYS    -0.3101367    0.07786684      -3.98291    8.3108e-05
        rain  -0.003535543   0.002024043     -1.746772    0.08157
          PM  0.0009979136  0.0007971613      1.251834    0.21148

Approximate significance of smooth terms:
                   edf       chi.sq     p-value
  tmpmax             6              NA     NA
     wet             2              NA     NA

Log-likelihood value is 1075.727 after BFGS has converged.

Estimation process of semiparametric model stopped after 3 iterations at 3.82e-05.

Residual deviance is 426.3603 on 344 estimated degrees of freedom.

Approximate dispersion parameter equals 1.231335 based on generalized Pearson statistics 423.5793.

Diffuse initialization wasted the 1 first observation(s). Besides, 0 observation(s) was(were) lost due to missing data.
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "plot.pgam"
> 
> ### * plot.pgam
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: plot.pgam
> ### Title: Plot of estimated curves
> ### Aliases: plot.pgam
> ### Keywords: ts smooth regression
> 
> ### ** Examples
> 
> library(pgam)
> data(aihrio)
> attach(aihrio)
> form <- ITRESP5~f(WEEK)+HOLIDAYS+rain+PM+g(tmpmax,7)+g(wet,3)
> m <- pgam(form,aihrio,omega=.8,beta=.01,maxit=1e2,eps=1e-4,optim.method="BFGS")
iter: 1  |  norm: Inf 
iter: 2  |  norm: 0.0020767 
iter: 3  |  norm: 3.82e-05 

Semiparametric model estimation algorithm has converged.

Final run: Getting estimated parameters, functions and numerical hessian matrix...
Counts (fn | gr): 37 2

Estimation process took 00:00:02 (hh:mm:ss)
> 
> plot(m,at.once=TRUE)
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "predict.pgam"
> 
> ### * predict.pgam
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: predict.pgam
> ### Title: Prediction
> ### Aliases: predict.pgam
> ### Keywords: ts smooth regression
> 
> ### ** Examples
> 
> library(pgam)
> data(aihrio)
> attach(aihrio)
> form <- ITRESP5~f(WEEK)+HOLIDAYS+rain+PM+g(tmpmax,7)+g(wet,3)
> m <- pgam(form,aihrio,omega=.8,beta=.01,maxit=1e2,eps=1e-4,optim.method="BFGS")
iter: 1  |  norm: Inf 
iter: 2  |  norm: 0.0020767 
iter: 3  |  norm: 3.82e-05 

Semiparametric model estimation algorithm has converged.

Final run: Getting estimated parameters, functions and numerical hessian matrix...
Counts (fn | gr): 37 2

Estimation process took 00:00:02 (hh:mm:ss)
> 
> p <- predict(m)$yhat
> plot(ITRESP5)
> lines(p)
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "residuals.pgam"
> 
> ### * residuals.pgam
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: residuals.pgam
> ### Title: Residuals extraction
> ### Aliases: residuals.pgam
> ### Keywords: ts smooth regression
> 
> ### ** Examples
> 
> library(pgam)
> data(aihrio)
> attach(aihrio)
> form <- ITRESP5~f(WEEK)+HOLIDAYS+rain+PM+g(tmpmax,7)+g(wet,3)
> m <- pgam(form,aihrio,omega=.8,beta=.01,maxit=1e2,eps=1e-4,optim.method="BFGS")
iter: 1  |  norm: Inf 
iter: 2  |  norm: 0.0020767 
iter: 3  |  norm: 3.82e-05 

Semiparametric model estimation algorithm has converged.

Final run: Getting estimated parameters, functions and numerical hessian matrix...
Counts (fn | gr): 37 2

Estimation process took 00:00:02 (hh:mm:ss)
> 
> r <- resid(m,"pearson")
> plot(r)
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "summary.pgam"
> 
> ### * summary.pgam
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: summary.pgam
> ### Title: Summary output
> ### Aliases: summary.pgam
> ### Keywords: ts smooth regression
> 
> ### ** Examples
> 
> library(pgam)
> data(aihrio)
> attach(aihrio)
> form <- ITRESP5~f(WEEK)+HOLIDAYS+rain+PM+g(tmpmax,7)+g(wet,3)
> m <- pgam(form,aihrio,omega=.8,beta=.01,maxit=1e2,eps=1e-4,optim.method="BFGS")
iter: 1  |  norm: Inf 
iter: 2  |  norm: 0.0020767 
iter: 3  |  norm: 3.82e-05 

Semiparametric model estimation algorithm has converged.

Final run: Getting estimated parameters, functions and numerical hessian matrix...
Counts (fn | gr): 37 2

Estimation process took 00:00:02 (hh:mm:ss)
> 
> summary(m)
Function call:
pgam(formula = form, dataset = aihrio, omega = 0.8, beta = 0.01, 
    maxit = 100, eps = 1e-04, optim.method = "BFGS")

Model formula:
ITRESP5 ~ f(WEEK) + HOLIDAYS + rain + PM + g(tmpmax, 7) + g(wet, 
    3)

Parametric coefficients:
                 Estimate     std. err.     t ratio      Pr(>|t|)
  (Discount)     0.8608709    0.04614704      18.65495    < 2.22e-16
      WEEK.1    -0.4747101    0.03915625     -12.12348    < 2.22e-16
      WEEK.2     0.2453709    0.02868606      8.553664    4.4409e-16
      WEEK.3      0.165139    0.02965303      5.569042    5.1698e-08
      WEEK.4     0.1873045    0.02936112      6.379337    5.7401e-10
      WEEK.5     0.1104593    0.03039694      3.633895    0.00032176
      WEEK.6     0.1465003    0.03040014      4.819068    2.1674e-06
      WEEK.7    -0.3800639      0.102413     -3.711091    0.00024059
    HOLIDAYS    -0.3101367    0.07786684      -3.98291    8.3108e-05
        rain  -0.003535543   0.002024043     -1.746772    0.08157
          PM  0.0009979136  0.0007971613      1.251834    0.21148

Approximate significance of smooth terms:
                   edf       chi.sq     p-value
  tmpmax             6              NA     NA
     wet             2              NA     NA

Log-likelihood value is 1075.727 after BFGS has converged.

Estimation process of semiparametric model stopped after 3 iterations at 3.82e-05.

Residual deviance is 426.3603 on 344 estimated degrees of freedom.

Approximate dispersion parameter equals 1.231335 based on generalized Pearson statistics 423.5793.

Diffuse initialization wasted the 1 first observation(s). Besides, 0 observation(s) was(were) lost due to missing data.
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "tbl2tex"
> 
> ### * tbl2tex
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: tbl2tex
> ### Title: LaTeX table exporter
> ### Aliases: tbl2tex
> ### Keywords: ts smooth regression
> 
> ### ** Examples
> 
> library(pgam)
> data(aihrio)
> m <- aihrio[1:10,4:10]
> tbl2tex(m,label="tbl:r_example",caption="R example of tbl2tex",digits=4)
% File generated in R environment by tbl2tex()
% Creation date: Wed Jul 13 18:04:01 2005
% Suggestions to Washington Junger <wjunger@ims.uerj.br>
\begin{table}
\centering
\caption{R example of tbl2tex}
\label{tbl:r_example}
    \begin{tabular}{|c|c|c|c|c|c|c|c|} \hline
        & ITCIRC65 & ITDPOC65 & ITPNM65 & ITAVC65 & ITIAM65 & ITDIC65 & ITTCA65 \\ \hline
    1 & 21 & 3 & 2 & 2 & 4 & 5 & 0 \\ \hline
    2 & 36 & 6 & 8 & 9 & 1 & 6 & 3 \\ \hline
    3 & 38 & 2 & 10 & 2 & 3 & 6 & 1 \\ \hline
    4 & 43 & 4 & 5 & 4 & 3 & 4 & 5 \\ \hline
    5 & 45 & 4 & 2 & 1 & 4 & 5 & 2 \\ \hline
    6 & 16 & 3 & 1 & 0 & 0 & 0 & 1 \\ \hline
    7 & 23 & 2 & 4 & 3 & 2 & 3 & 3 \\ \hline
    8 & 35 & 5 & 3 & 2 & 5 & 7 & 6 \\ \hline
    9 & 40 & 6 & 4 & 5 & 2 & 5 & 5 \\ \hline
    10 & 33 & 4 & 4 & 6 & 1 & 4 & 4 \\ \hline
    \end{tabular}
\end{table}
% End of tbl2tex() generated file.
> 
> 
> 
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", env = .CheckExEnv),"\n")
Time elapsed:  27.63 0.54 28.25 0 0 
> grDevices::dev.off()
postscript 
         2 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')