============================================================================== Changes in dlnm 1.5.2 (05 Jan 2011) =================================== See also: file.show(system.file("Changesince151",package="dlnm")) Major changes ------------- o New function 'onebasis' to create the 1-dimensional basis matrices. The function is made available and documented. This replace 'mkbasis' and 'mklagbasis', which are kept only for compatibility. The functions returns a matrix with attributes. o The usage of 'crossbasis' has been extensively revised. Now the function has 2 arguments var and lag with a list of arguments for each space. Also, maxlag has been replaced by lag, defining the lag range (min and max). Old usage has been kept (with a warning) for compatibility reasons. o New function 'crossreduce' to reduce the fit to one of the 2 dimensions. Methods functions (summary, plot, points, lines) are also included. o 'crosspred' changed accordingly: now prediction also from simple basis, and computation based on faster new method in 'crossreduce'. o Argument cenvalue eliminated from 'basis'-crossbasis': centering now entirily determined by cen, which can be logical or numeric. Minor changes ------------- o Bug fixed in 'onebasis' (previously 'mkbasis') for type hthr-lthr. o Internal functions included: '.onAttach' and '.fci'. o coef and vcov methods for 'crosspred' and 'crossreduce'. o In 'onebasis'-'crossbasis': bound and cen argument now with no default. degree=3 returned now for type='ns', similarly to the original function. o In plot functions: changed default of ptype, added default titles. o In plots and documentation: effects changed to outcome-association. o Documentation and examples changed accondingly with changed above. ============================================================================== Changes in dlnm 1.4.2 ======================= Minor changes ------------- o Partial matching fixed in mkbasis() and plot.crosspred(). ============================================================================== Changes in dlnm 1.4.1 ======================= Minor changes ------------- o Reference added in vignette, citation and help pages. ============================================================================== Changes in dlnm 1.4.0 ======================= Major changes ------------- o Argument 'ci.arg' added to plotting functions. Now it is possible to (almost) completely specify the confidence intervals display. o onAttach function added, to display a message when the package is attached. o Dependencies revised: splines excluded from Depends, and accordingly library(splines) included in examples and vignette. Also excluded graphics and stats, already imported. Minor changes ------------- o Documentation and examples changed accondingly. ============================================================================== Changes in dlnm 1.3.2 ======================= Minor changes ------------- o Argument 'group' of crossbasis() forced to define consecutive series. Documentation changed accordingly. ============================================================================== Changes in dlnm 1.3.1 ======================= Major changes ------------- o Function crossplot() replaced by method functions plot(), lines() and points() for class ‘crosspred’. The user can now flexibly choose all the arguments through '...' to modify axes, colours, labels etc. o Arguments 'coef', 'vcov' and 'model.link' added to crosspred(), to provide the user a way to manually include the parameters for models without methods for coef() and vcov(). o Improved routine for automatic selection of rounded values used for prediction in crosspred() with 'at'-'from'-'to'-'by'. Minor changes ------------- o Included 'ci.level' in crosspred() and plot() method and 'ci="n"' in plot() method for no confidence intervals. o Improved model parameters extraction method in crosspred() through regular expressions. o Added class "matrix" to crossbasis objects. o Included summary.crosspred(). o Added lazyData to description file. o Improved coherence checks in functions and centering in mkbasis(). o A detailed description of the functions added in the vignette. o Help pages, vignette and citation changes accordingly. ============================================================================== Changes in dlnm 1.2.4 ======================= Major changes ------------- o mkbasis substantially revised: now 'int' unrelated to df, then relation 'type'-'df'-'int' more logical. ============================================================================== Changes in dlnm 1.2.3 ======================= Minor changes ------------- o Updated reference. ============================================================================== Changes in dlnm 1.2.2 ======================= Minor changes ------------- o Bug in crosspred() for vcov-coef: fixed. ============================================================================== Changes in dlnm 1.2.1 ======================= Minor changes ------------- o Bug in crosspred() with cumul=T: fixed. o Error in regression commands for crosspred(): fixed. o Help pages and citation changed accordingly. ============================================================================== Changes in dlnm 1.2.0 ======================= Major changes ------------- o New argument 'group' in crossbasis() to generate functions for each sub-group defined by the factor. o crosspred() now works also with lm, gam (mgcv), gee (geepack), clogit and coxph (survival). o change in mkbasis: now knots also outside range, but for types "strata" and "-thr" there's the chance to generate collinear variables: included a warning in help for crossbasis(). o Vignette 'dlnmOverview" rearranged with new examples, one of them on seasonal analysis. Reference to new paper Gasparrini 2010 Stat Med. Minor changes ------------- o Help pages and citation changed accordingly. ============================================================================== Changes in dlnm 1.1.1 ======================= Minor changes ------------- o Bug in mkbasis() with 'type="strata"': fixed. ============================================================================== Changes in dlnm 1.1.0 ======================= Major changes ------------- o The estimate of the cumulative effects along lags has been included in crosspred() and can be plotted with crossplot() setting 'cumul=T'. o The confidence intervals for 'type' equal to "slices" or "overall" can be now represented both by "area" (default), "bars" or "lines", by the argument 'ci' in crossplot(). Minor changes ------------- o Help pages, examples and vignette changed accordingly. ============================================================================== Changes in dlnm 1.0.2 ======================= Minor changes ------------- o Some html links giving warnings have been fixed. ============================================================================== Changes in dlnm 1.0.1 ======================= Major changes ------------- o The dataset chicagoNMMAPS has been added, relaxing the dependence on the package NMMAPSlite. Now the examples can be run using these data and without an internet connection. o The function crosspred() has been improved: now there is no constraint on the range of the predicted values. Moreover, the values 'model.class' and 'model.link' have been added. The command now works also when the estimation is carried out by 'clogit()'. Minor changes ------------- o The section 'Functions' in the vignette 'dlnmOverview' has been reduced: a reference to the functions help pages has been added. o Help pages, examples and vignette changed accordingly. ============================================================================== Changes in dlnm 0.4.1 ======================= Major changes ------------- o The argument 'degree' included in mkbasis()-crossbasis(), defining the degree of the unconstrained B-spline ('type' equal to 'bs') or the maximum power of the polynomial ('type' equal to 'poly'). o Linear piecewise function above a threshold included for type='hthr'/'lthr'; added an example in help pages and vignette. Improvements ------------ o Automatic knot selection also for thr-type functions o New example related to the changes above in the help pages and in the vignette o Improved error messages in mkbasis() and mklagbasis() Fixed bugs ---------- o Choices and error messages in mkbasis() and mklagbasis() Minor changes ------------- o Double threshold type changed from 'thr' to 'dthr'; added an error message in mkbasis() to explain the change. o For type='dthr', knots choice when more than 2 changed from first two to first and last ones. o Basis choices changed in example3 in order to show a quadratic spline. o Examples for mkbasis()-mklagbasis() expanded in help pages and vignette. o Help pages, examples and vignette changed accordingly. ============================================================================== Changes in dlnm 0.3.0 ======================= Major changes ------------- o A contour/level plot has been added to crossplot(). o The option 'bs' has been added to the argument 'type' of mkbasis()-crossbasis(), to specify a cubic spline without natural constraints. Improvements ------------ o Argument 'ylim' added for 'type="3d"'. Minor changes ------------- o Minor bugs fixed in mkbasis() and mklagbasis(). o Typing errors fixed in vignette 'dlnmOverview'. o Help pages, examples and vignette changed accordingly. Corrections ----------- o Original series of pollutants in NNMAPS data given by *tmean and *mtrend, not *mean and *trend. Corrected ============================================================================== Changes in dlnm 0.2.1 ======================= Fixed bugs ---------- o par options in crossplot() o titles for 'slices' in crossplot() ============================================================================== Changes in dlnm 0.2.0 ======================= Major changes ------------- o The package vignette 'dlnmOverview' has been added. Improvements ------------ o Intercept added to type equal to 'thr', 'hthr', 'lhr', and 'lin' o The vector 'predvar' of predictor values for which the prediction must be performed, included in crosspred(), is now automatically ordered and made unique. Fixed bugs ---------- o Two links to mkbasis() and mklagbasis() added to the help of crossbasis() in order to let the internal functions help page available o par(par.old) included in 'type="slices"' for crossplot() in order to redifine a single plot after the command o Error messages added to mkbasis() if argument types are wrong Minor changes ------------- o Default value for argument 'lagbound' of crossbasis() changed from c(-1,maxlag) to c(0,maxlag). o Help pages changed accordingly with the new features. o The example 2 (in crosspred()) the threshold has been set to 40.3, in order to show the ordering functionality. ============================================================================== First version in R CRAN dlnm 0.1.0 ==============================================================================