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smooth.construct.cb.smooth.spec() and Predict.matrix.cb.smooth() now defined as method functions and registered as such in namespace.
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Changes in crosspred() to fix issues with penalized version
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Documentation amended accordingly.
- Fixes for CRAN checks.
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Allowed incremental cumulative predictions for any lag interval.
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Small fixes in exphist(), getcoef(), and getvcov().
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Documentation amended.
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Fixed bug in exphist() with negative lags.
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Added colnames in object returned by exphist().
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Documentation amended.
- Fixed bug in if/stop statements with && and !!.
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Changes in the function exphist() to allow negative times and lags. This has required a complete recoding of the internal steps which has also made the code simpler and the function faster.
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Minor correction to documentation.
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Some changes in crosspred(), where now model.link can be set directly independently from the model class, making the use of the function more flexible and general. This is implemented with a minor change in getlink(). In addition, the inclusion of the coxme objects (see below) has been removed.
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Minor correction to documentation.
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Fixed a bug in getlink(), now with correct link extraction for coxph objects. In addition, added coxme objects. Thanks to Chau-Ren Jung.
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Minor correction to documentation.
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Replaced spline.des() with splineDesign() in ps(), and changed namespace.
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Fixed a bug in crosspred() and crossreduce() when extracting vcov without accounting for the fact that missing parameters were excluded.
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Minor correction to documentation.
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Extension to penalized DLMs and DLNMs implemented with the inclusion of new functions and modification of existing ones.
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Revision of the package vignettes, with improved overview of the various developments, and addition of the new vignette dlnmPenalized.
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The package has now a development webpage in GitHub (https://github.com/gasparrini/dlnm).
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Addition of a NEWS file that replaces the changeLog, also with HTML version included in the new GitHub page.
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Extension and improvements of Examples section of help files, in particular for main functions.
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Argument 'fill=0' added to exphist() to allow exposure histories with undefined values to be padded with different values that 0 (the default), in particuar NA.
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Former internal function exphistint() now included within exphist().
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mkcen() now centers at only approximately the mid-value, and return a message with info on the centering value if this is not defined.
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Improved Description file, with links to GitHub page.
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Fixed links, in particular to article in www.ag-myresearch.com.
- Bug fixed in crossreduce when ncol of cb is 1.
- The order of transformation in the tensor for cross-basis transformation is changed and now consistent with tensor.prod.model.matrix() in mgcv. This change affects crossbasis(), mkXpred() and crossreduce(), where the order between var-lag has been reversed. The development only concerns internal code and no change should be seen in the usage of dlnm.
- Revised centering procedure to fix minor issues with centering selection with function 'strata', 'thr', 'integer'. Fixed in checkonebasis() and mkcen().
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Centering procedure moved from onebasis() to crosspred()-crossreduce(). This change simplifies the steps of obtaining predictions with different references, as it avoids refitting the model. At the moment the inclusion of 'ce' in onebasis()-crossbasis() generates a warning, but the info is kept internally and the old code should still work.
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Consistently withe the change above, crosspred()-crossreduce() now have a 'cen' argument to specify the reference value.
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Major changes in crosspred()-crossreduce(), with several auxiliary functions build to simplify the internal code. Specifically: mkat(), mkcen(), mklag(), mkXpred(). See the related help page.
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New import of the function tensor.prod.model.matrix() from mgcv, to simplify the computation of the tensor product in crosspred().
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Published code has been updated accordingly, and included in the related web pages at http://www.ag-myresearch.com/. The function attrdl() (not included in the package but used in published code) has been changed as well.
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Changed default for colour (now black) and frame (now bty=”l”) in plotting functions.
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Namespace changed accordingly, with imports from mgcv.
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Lag2() removed, back to Lag() imported from package tsModel.
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Documentation changed accordingly, references updated.
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Changes in function strata(), now with possibility of setting 'ref=0', thus obtaining a different dummy parameterization.
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Changes in summary.crossbasis() to print only a subset of long arguments
- Bug fixed in plot()-points()-lines() methods when model.link was not provided.
- Bug fixed in function integer() when int=FALSE for lag-response.
- Negative lag can now be specified in crossbasis(), although presumably rarely needed.
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Added attribute 'df' in crossbasis objects, with df for each dimension.
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Adjustment to the example on seasonal analysis.
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References corrected.
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Function strata() now accepts an additional argument 'ref' to select the reference category. Also, the intercept is now defined as a vector of 1's.
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Old functions crossplot(), mkbasis() and mklagbasis() removed.
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Functions now defined with unquoted names (problem with RStudio).
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Internal functions now defined with names without initial dots.
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checkgroup modified: now number of obs in each groups can also be less than df in argvar. Required in previous versions, not anymore.
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Documentation changed accordingly, references updated.
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Included function equalknots() to place knots at equally-spaced values.
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Changes in .get-() functions to allow changes in lme4 objects.
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Error fixed in examples of vignette dlnmExtended.
See also: file.show(system.file("Changesince200",package="dlnm"))
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The usage of functions crossbasis() and onebasis() has been extensively revised, as detailed below. The old usage is maintained with a warning for compatibility reasons. However, the old usage can return now different results if compared to previous versions. See the file Changesince200 using the link above.
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The functions in dlnm can now be used also for data other than time series. The only difference is the inclusion of a matrix of lagged occurrences as the 'x' argument of crossbasis, instead than the usual vector of time series data. The extension is detailed in the article Gasparrini Stat Med 2013 and in the new vignette 'dlnmExtended'.
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The functions onebasis() now calls existing functions for generating the basis matrix. The functions poly(), strata(), thr(), integer() and lin() have been added, although not exported in the namespace. User-defined functions with attributes reporting the arguments exactly defining the transformation can be added as well.
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Given the change above, the arguments of onebasis() and the list of arguments composing the arguments 'argvar' and 'arglag' in crossbasis() are now those of the called functions. In particular, the old usage is not guaranteed to work any more, and if it does a warning is reported.
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The default knots placements for ns and bs functions for the lag dimension in crossbasis() is not at equally-spaced log-values as before, but at equally-spaced percentiles, consistently with the predictor space. The old default can be reproduced with the new function logknots().
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Two new data sets included in the package, 'nested' and 'drug'. They are composed of simulated data on nested case-control and randomized controlled trial designs respectively.
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The new function exphist() can be used to build matrices of exposure histories to be used in crosspred() to obtain specific predictions given an exposure profile.
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The documentation of the package has beed extensively revised. The vignette 'dlnmOverview now provides a general introduction to the methodology and functions, while the two new vignettes 'dlnmTS' and 'dlnmExtended' describes specific applications in time series design and in other study designs, respectively.
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Basis matrices now keep names from original vector/matrix.
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Argument 'lag' in crossbasis() now given default value depending on the format of the argument 'x'.
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Summary method functions have been changed accordingly.
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Internal functions .getcoef(), .getvcov() and .getlink() added within crosspred(0 tro extract coef, vcov and model link.
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Internal functions .checkgroup(), .oldonebasis and .oldcrossbasis() for checks in onebasis() and crossbasis().
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Print of summary.crossreduce() fixed.
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Resolved the dependency with package NMMAPSlite, now archived.
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Bug fixed in crosspred() when specifying the 'lag' argument (thanks to Joseph Ogutu).
- Import from tsModel removed. An internal function .Lag has been created, using the code from the same function in tsModel written by Roger Peng.
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URL link added in Description file. Copyright statement added in each function.
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Updated citations.
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Documentation changed accordingly.
- Bug fixed in Description file.
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Argument 'lag' included in crosspred() and crossreduce(), to define sub-periods of lag on which predict. Useful for computing overall cumulative effects on different portions of the lag period.
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Second example in vignette about seasonal analysis has been corrected. Now the model includes also a term for trend, forgotten so far.
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Terminology in documentation largely revised.
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In onebasis(), now strata defined by 'bound', not range, and reported.
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Bug fixed in names assignment to objects in crossreduce().
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Bug fixed in crosspred() for argument 'bylag'.
- Bug fixed in onebasis() regarding the argument 'cen'. Now cen=0 and cen=FALSE do not return the same value, and in the former the centering is acknowledged by summary(). Thanks to Yasushi Honda.
- Documentation changed accordingly.
- Argument 'bylag' included in crosspred() and crossreduce() to define the sequence of lag values used for prediction. It does not apply to cumulative effects.
- Documentation changed accordingly.
- crossbasis() and crosspred() now accept as 'x' argument also a matrix of exposure histories. The package now works also with non-time series data, for example cohort or case-control data. The documentation will be changed accordingly as soon as the methodological paper will be published.
- onebasis() now accepts vectors/matrices for less than df+int observations. crosspred() and crossreduce() changed accordingly.
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Added as.vector(x) to constraint the type of first argument in onebasis().
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Change in colnames(crossbasis).
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Fixed bug in lines.crosspred() and points.crosspred()
See also: file.show(system.file("Changesince151",package="dlnm"))
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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.
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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.
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New function crossreduce() to reduce the fit to one of the 2 dimensions. Methods functions (summary, plot, points, lines) are also included.
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crosspred() changed accordingly: now prediction also from simple basis, and computation based on faster new method in crossreduce().
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Argument cenvalue eliminated from basis()-crossbasis(): centering now entirily determined by cen, which can be logical or numeric.
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Bug fixed in onebasis() (previously mkbasis()) for type hthr-lthr.
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Internal functions included: .onAttach() and .fci().
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coef and vcov methods for crosspred() and crossreduce().
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In onebasis()-crossbasis(): bound and cen argument now with no default. degree=3 returned now for type='ns', similarly to the original function.
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In plot functions: changed default of ptype, added default titles.
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In plots and documentation: effects changed to outcome-association.
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Documentation and examples changed accondingly with changes above.
- Partial matching fixed in mkbasis() and plot.crosspred().
- Reference added in vignette, citation and help pages.
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Argument 'ci.arg' added to plotting functions. Now it is possible to (almost) completely specify the confidence intervals display.
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onAttach function added, to display a message when the package is attached.
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Dependencies revised: splines excluded from Depends, and accordingly library(splines) included in examples and vignette. Also excluded graphics and stats, already imported.
- Documentation and examples changed accondingly.
- Argument 'group' of crossbasis() forced to define consecutive series. Documentation changed accordingly.
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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.
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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().
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Improved routine for automatic selection of rounded values used for prediction in crosspred() with 'at'-'from'-'to'-'by'.
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Included 'ci.level' in crosspred() and plot() method and 'ci="n"' in plot() method for no confidence intervals.
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Improved model parameters extraction method in crosspred() through regular expressions.
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Added class "matrix" to crossbasis objects.
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Included summary.crosspred().
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Added lazyData to description file.
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Improved coherence checks in functions and centering in mkbasis().
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A detailed description of the functions added in the vignette.
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Help pages, vignette and citation changes accordingly.
- mkbasis substantially revised: now 'int' unrelated to df, then relation 'type'-'df'-'int' more logical.
- Updated reference.
- Bug in crosspred() for vcov-coef: fixed.
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Bug in crosspred() with cumul=T: fixed.
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Error in regression commands for crosspred(): fixed.
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Help pages and citation changed accordingly.
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New argument 'group' in crossbasis() to generate functions for each sub-group defined by the factor.
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crosspred() now works also with lm, gam (mgcv), gee (geepack), clogit and coxph (survival).
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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().
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Vignette 'dlnmOverview" rearranged with new examples, one of them on seasonal analysis. Reference to new paper Gasparrini 2010 Stat Med.
- Help pages and citation changed accordingly.
- Bug in mkbasis() with 'type="strata"': fixed.
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The estimate of the cumulative effects along lags has been included in crosspred() and can be plotted with crossplot() setting 'cumul=T'.
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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().
- Help pages, examples and vignette changed accordingly.
- Some html links giving warnings have been fixed.
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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.
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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()'.
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The section 'Functions' in the vignette 'dlnmOverview' has been reduced: a reference to the functions help pages has been added.
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Help pages, examples and vignette changed accordingly.
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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').
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Linear piecewise function above a threshold included for type='hthr'/'lthr'; added an example in help pages and vignette.
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Automatic knot selection also for thr-type functions
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New example related to the changes above in the help pages and in the vignette
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Improved error messages in mkbasis() and mklagbasis()
- Choices and error messages in mkbasis() and mklagbasis()
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Double threshold type changed from 'thr' to 'dthr'; added an error message in mkbasis() to explain the change.
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For type='dthr', knots choice when more than 2 changed from first two to first and last ones.
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Basis choices changed in example3 in order to show a quadratic spline.
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Examples for mkbasis()-mklagbasis() expanded in help pages and vignette.
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Help pages, examples and vignette changed accordingly.
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A contour/level plot has been added to crossplot().
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The option 'bs' has been added to the argument 'type' of mkbasis()-crossbasis(), to specify a cubic spline without natural constraints.
- Argument 'ylim' added for 'type="3d"'.
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Minor bugs fixed in mkbasis() and mklagbasis().
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Typing errors fixed in vignette 'dlnmOverview'.
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Help pages, examples and vignette changed accordingly.
- Original series of pollutants in NNMAPS data given by tmean and mtrend, not mean and trend. Corrected
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par options in crossplot()
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titles for 'slices' in crossplot()
- The package vignette 'dlnmOverview' has been added.
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Intercept added to type equal to 'thr', 'hthr', 'lhr', and 'lin'
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The vector 'predvar' of predictor values for which the prediction must be performed, included in crosspred(), is now automatically ordered and made unique.
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Two links to mkbasis() and mklagbasis() added to the help of crossbasis() in order to let the internal functions help page available
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par(par.old) included in 'type="slices"' for crossplot() in order to redifine a single plot after the command
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Error messages added to mkbasis() if argument types are wrong
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Default value for argument 'lagbound' of crossbasis() changed from c(-1,maxlag) to c(0,maxlag).
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Help pages changed accordingly with the new features.
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The example 2 (in crosspred()) the threshold has been set to 40.3, in order to show the ordering functionality.