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ChangeLog
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ChangeLog
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Changes in version 1.1-11
2021/10/06 Ignacio Lopez de Ullibarri <ilu@udc.es>
* DESCRIPTION: 'Description' field now includes a references and its doi; some minor changes in other fields.
* inst/CITATION: 'doi' field used instead of 'url'.
* man: All the files have been revised, reformatting them, adding doi's of the references (with \doi{} instead of \url{}), and correcting some typos.
* src/presmestim.c: Fixed error in left-boundary effect correction when 'estimand' is "h" (final denominator is '*nt - j + counter'; before, 'counter' was summed out of the division). Fixed similar error when correcting both boundary effects: 'counter' was missing in '(*nt - j + counter)'.
Changes in version 1.1-10
2017/09/06 Ignacio Lopez de Ullibarri <ilu@udc.es>
* inst/CITATION: citation file modified for use with utils::bibentry().
* src: 'init.c' file added for routine registration.
* NAMESPACE: the '.registration = TRUE' option is used in the call to 'useDynLib()'.
* DESCRIPTION: 'Author' field rewritten; 'NeedsCompilation' field added.
* man/presmooth.Rd (examples): typo corrected.
Changes in version 1.1-9
2016/03/09 Ignacio Lopez de Ullibarri <ilu@udc.es>
* NAMESPACE: 'importFrom("utils", "head")' added.
* R/presmooth.R (control.presmooth): 'k' argument from version 1.1-2 recovered.
* R/presmooth.R (presmooth): new 'range.t' added in line 248 (plugin bandwidth without presmoothing for f); 'control$k' reintroduced, multiplying all the appearances of 'range.t' (including line 333, which was not multiplied in version 1.1-2: note that this change modifies all the elements of the default grid); the approach of version 1.1-6 is recovered: in plug-in bandwidth computation for S and H, when p=0 and p.nw=0 the bandwidth is set to the maximum possible value, as it was for p=1 and p.nw=1 (the if-else making the distinction has been removed); the text of the corresponding warning is modified.
* man/control.presmooth.Rd (usage, arguments, examples): the 'k' argument is reintroduced.
Changes in version 1.1-8
2013/08/30 Ignacio Lopez de Ullibarri <ilu@udc.es>
* inst/CITATION: new directory and file with the citation details.
Changes in version 1.1-7
2013/08/26 Ignacio Lopez de Ullibarri <ilu@udc.es>
* R/presmooth.R (presmooth): in line 56 'presmoothing == FALSE' replaced with '!presmoothing'; new check: when 'bw.selec' is "fixed", 'presmoothing' is FALSE and 'estimand' is "f" or "h", the presmoothing bandwidth ('fixed.bw[1]') is forced to be 0 or an error is produced if 'fixed.bw' is NULL or his length is not 2; new if-else added in plug-in bandwidth computation for S and H: when p=0 the bandwidth is set to 0, when p=1, the bandwidth is set to the maximum possible value; the same thing is done when p.nw=0 or p.nw=1; the text of the warnings is modified accordingly.
* src/funplugin.c: in the auxfunplugin function, the default of the switch now includes the statement 'return 0' (to avoid warnings with clang).
* src/isevect.c: 'if(*presmoothing == 0)' condition deleted (it is always TRUE).
* src/kernelder.c: the default of every switch now includes a 'return 0' statement (to avoid warnings with clang).
Changes in version 1.1-6
2013/03/11 Ignacio Lopez de Ullibarri <ilu@udc.es>
* ChangeLog: the item 'Changes in version 1.1-5' was missing; by error these changes, done on 2013/01/09, were placed under the item 'Changes in version 1.1-4'
Changes in version 1.1-5
2013/01/09 Ignacio Lopez de Ullibarri <ilu@udc.es>
* R/zzz.R (.Last.lib): the function has been deleted and substituted by .onUnload().
* R/zzz.R (.First.lib): the function has been deleted.
* man/control.presmooth.Rd (arguments): in 'length.grid.ise', Simpson's rule is used instead of trapezium's rule.
Changes in version 1.1-4
2012/11/20 Ignacio Lopez de Ullibarri <ilu@udc.es>
* R/presmooth.R (control.presmooth): the 'trim' argument has been deleted.
* R/presmooth.R (presmooth): in the calls to 'isevect.c', the 'ise' component now is defined as either 'numeric(if(forh) le.bw.1*le.bw.2 else le.bw.1)' (with 'presmoothing= TRUE') or 'numeric(le.bw.1)' (with 'presmoothing = FALSE'); the previous result, after being divided by 'n.boot', is saved in 'mise'; 'trim' component deleted from the returned list; the 'ise.array' object has been deleted.
* R/presmooth.R (print.survPresmooth): the 'trim' component has been deleted.
* man/control.presmooth.Rd (usage, arguments, value): the 'trim' argument and all the references to it have been deleted.
* man/presmooth.Rd (value, examples): the 'trim' item has been deleted; an example has been corrected and slightly changed; a new example has been added.
* man/print.survPresmooth.Rd (arguments): "trim" deleted from the text in the 'more' argument.
* src/isevect.c: 'isev' now accumulates the sum of all the '*isecomp' (previously, all the values were saved).
2012/11/07 Ignacio Lopez de Ullibarri <ilu@udc.es>
* R/presmooth.R (presmooth): 'bw.selec' is now 'c("fixed", "plugin", "bootstrap")' instead of 'c("plugin", "bootstrap", "fixed")'; the previous change also induces changes in the management of 'n.bw.selec' (key for the conversion oldvalue -> new value: 1 -> 2, 2 -> 3, 3 -> 1); when 'presmoothing == FALSE' and 'n.estimand %in% 1:2', 'fixed.bw' is set to 0.
* man/presmooth.Rd (usage, arguments): Changes in 'bw.selec' (see above).
2012/11/02 Ignacio Lopez de Ullibarri <ilu@udc.es>
* DESCRIPTION: typing of the name of the first author and maintainer changed to 'Lopez de Ullibarri' (without hyphens).
* R/presmooth.R (presmooth): due to a programming error, 'pilot.bw1' was not computed when 'bw.selec = "bootstrap"' and 'presmoothing = FALSE': the condition '((n.bw.selec == 1) & forh) | (n.bw.selec == 2 & presmoothing)' is replaced with '((n.bw.selec == 1) & forh) | (n.bw.selec == 2)'; the correction of the inputted values of 'grid.bw' and 'grid.bw.pil' are checked; in bootstrap bandwidth selection the computation of 'grid.bw.1' and 'grid.bw.2' when 'presmoothing = FALSE' is changed, and the arguments 'grid.bw.2' and 'le.bw.2' in the call to 'isevect' are replaced by 'grid.bw.1' and 'le.bw.1', resp.; the computation of'ise.array' is modified; for the bootstrap bandwidth, when computing 'bw' for f or h and 'presmoothing=FALSE', 'grid.bw.2' is replaced with 'grid.bw.1'; in 'ps', the component 'problem.pi' has been deleted from 'ps', and the components 'grid.pil' and 'grid.bw' have been modified; a logical variable, 'allcens', added for controlling the warnings printed when all data are censored.
* R/presmooth.R (print.survPresmooth): 'problem.pi' removed from the 'comps' vector.
* man/control.presmooth.Rd (author): typing of the name of the first author changed to 'Lopez de Ullibarri'.
* man/presmooth.Rd (arguments, value, author): the description of the 'grid.bw.pil' and 'grid.bw' arguments have been rewritten; the 'problem.pi' component of the output has been deleted; typing of the name of the first author changed to 'Lopez de Ullibarri'.
* man/print.survPresmooth.Rd (arguments, author): 'call' and 'bw.selec' removed from the set of valid names for the 'more' argument; typing of the name of the first author changed to 'Lopez de Ullibarri'.
* man/pscheck.Rd (author): typing of the name of the first author changed to 'Lopez de Ullibarri'.
Changes in version 1.1-3
2012/10/15 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* R/presmooth.R (control.presmooth): the 'k' argument has been removed.
* R/presmooth.R (print.survPresmooth): the call is printed by default; new argument 'long' added; the printed text now distinguishes between presmoothed and non-presmoothed estimates; for f or h estimation, the value of 'bound' is printed; components 'call', 'bw.selec', 'bandwidth', 'x.est', 'estimand' removed from 'ext.names'; the components printed by default cannot be printed twice; some other little modifications and minor bugs corrected.
* R/presmooth.R (presmooth): 'k' (more precisely, 'control$k') has been removed; in the computation of 'bw' for the plug-in bandwidth of h, 'pilot.bw[-3]' is replaced with 'pilot.bw' in the call to 'constrOptim'; when computing the bootstrap bandwidth for f and h, an if-else is added in the computations for the 2nd pilot: the else arm gives Muller pilot as an alternative when all data are censored within the interval taken; the program stops if 'bw.selec' does not (partially) match with one of 'plug-in', 'bootstrap' or 'fixed'; when partial matching is present, the correct values of 'kernel', 'bound' and 'bw.selec' are calculated; now the value of 'bound' is also returned.
* man/control.presmooth.Rd (usage, arguments, examples): 'k' has been removed; some retyping for improving the PDF manual.
* man/print.survPresmooth.Rd (arguments, examples): more details on the argument 'more' are given; some retyping for improving the PDF manual.
* man/presmooth.Rd (usage, examples): corrected a bug repeated several times in the examples ('seq' instead of 'by' as an argument to seq); 'grid.bw' changed when computing the 'hboot' object; '\ldots' replaced with '...'; the 'dboot2' object is not computed; the last plot is redone; some retyping for improving the PDF manual.
2012/10/09 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* R/presmooth.R (presmooth): when computing the plug-in bandwidth for S or H, if 'Q' and 'A' are 0 'bw' is set to 0; when all the times are censored a warning is printed and NA returned for both the selected bandwidth and the estimate; the maximum value for all the pilots is set to control$k*range.t; the definition of 'grid.bw.pil' is changed; since 'grid.bw.pil' is not needed for bootstrap bandwidth selection when 'presmoothing' is FALSE, the new condition for computing or returning this grid is 'if(((n.bw.selec == 1) & forh) | (n.bw.selec == 2 & presmoothing))'.
* man/control.presmooth.Rd (arguments, details): the length of 'pilot.par.ini' is 8 instead 6 and an explanation of the meaning of each component is included.
2012/10/07 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* src/termsmisenopresmooth.c: new function similar to 'termsmise.c' for the case without presmoothing.
* src/isevect.c: numerical integration is done with Simpson's rule, instead of trapezium rule. Some pointers (pnull, pnull2) are initialized, or the memory allocated to them freed, within the arm of the switch where they are used. A new if-else is added, the if arm for the old code, and the else arm for the case with presmoothing = FALSE.
* src/simpson.c: the argument 'step' is deleted (the multiplication by step is now done outside the function). Also, the numerical constants are written with a decimal point (although this has no effect on the results).
* R/presmooth.R (presmooth): new argument 'presmoothing' added, whose value is returned by the function; the 'mise' component of the output is redefined; when computing the plug-in and bootstrap bandwidths of f and h, an if-else controlled by the value of the argument 'presmoothing' is added; in the final computation of 'p', if 'bw[1]' is 0 'p' is set to 'as.numeric(dfr$d)'; for estimating S and H with either a plug-in or bootstrap bandwidth, if presmoothing is FALSE the case is treated as 'bw.selec = "fixed"' and 'fixed.bw = 0', and a warning is printed; in the computation of 'C1', 'C2', 'D1', 'D2' and 'A', the multiplication by 'step.plugin' is done outside the call to 'simpson.c'(for the changes in 'simpson.c', see below).
* man/presmooth.Rd (usage, arguments, details): new argument 'presmoothing' added and its use is explained in the 'details' section; typo corrected in details: the upper bound for the selected bandwidths is equal to the range of observed times.
2012/09/06 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* R/presmooth.R (presmooth): The NULL value of arguments 5, 6, 7 and, sometimes, 9 in the call to 'presmestim.c' is set to an arbitrary value of the type specified by the function declaration; also, in the call to 'isevect.c', the NULL for arguments 9 and 10 is substituted for 0. The warning 'passing an object of type NULL to .C is deprecated', appearing with versions >2.15.0, is thus avoided.
Changes in version 1.1-2
2011/10/17 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* ChangeLog: file added.
* DESCRIPTION: 'LazyLoad: no' deleted; 'LazyData: yes' added.
* NAMESPACE: file added.
* man/presmooth.Rd (examples): 'data(pscheck)' deleted.
* man/print.survPresmooth.Rd (examples): 'data(pscheck)' deleted.
Changes in version 1.1-1
2011/03/09 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* R/presmooth.R (control.presmooth): default value of 'k' is 1.
* man/control.presmooth.Rd (usage, arguments): default value of 'k' is 1.
2011/02/04 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* R/presmooth.R (control.presmooth): new argument 'k' added.
* man/control.presmooth.Rd (usage, arguments): new argument 'k' added.
2011/01/13 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* src/isevect.c: R_FlushConsole(); R_ProcessEvents() added in each of the main loops for S, H, f and h.
* man/control.presmooth.Rd (details): the recommended 'nboot' is 10000.
* man/presmooth.Rd (arguments): the explanation about 'bound' is changed.
(details): the upper bound for the selected bandwidth and the meaning of 'q.weight' are explained.
2011/01/07 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* R/presmooth.R (presmooth): for the bootstrap bandwidth, the 2nd pilot for h is computed with the same formula as for f.
2011/01/04 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* DESCRIPTION: description changed.
* man/survPresmooth-package.Rd: file deleted.
* man/presmooth.Rd (value): heading changed.
2011/01/02 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* R/presmooth.R (print.survPresmooth): some minor modifications.
2010/12/28 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* DESCRIPTION: LazyLoad: no.
* R/presmooth.R (presmooth): definition of 'grid.bw' changed; the role of 'median(dfr$t)' is changed by 'range.t'.
* man/control.presmooth.Rd: 'Rdversion' deleted.
* man/presmooth.Rd: 'Rdversion' deleted; '...' changed by \dots or \ldots.
* man/print.survPresmooth.Rd: 'Rdversion' deleted; ; '...' changed by \dots or \ldots.
* man/pscheck.Rd: 'Rdversion' deleted; '\docType{data}' added.
Changes in version 1.1-0
2010/09/17 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* src/misevect.c: deleted.
* src/isevect.c: new funtion replacing 'misevect.c'
* R/presmooth.R (control.presmooth): new argument 'trim' added.
* R/presmooth.R (presmooth): call to 'misevect' replaced with call to 'isevect' when computing the bootstrap bandwidths; the list returned includes component 'trim'; component 'mise' computed without dividing by 'n.boot'.
* R/presmooth.R (print.survPresmooth): component 'trim' added to 'ext.names'.
* man/control.presmooth.Rd: new argument 'trim' added.
* man/presmooth.Rd: 'bw.selec' was duplicated; the position of 'mise' and 'q.weight' was incorrect; 'trim' component added.
2010/08/29 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* src/presmestim.c: changes for H made on 2010/08/28 applied to h.
* src/misevect.c: for h, the value of 'dup' is passed to the argument 'dup' of presmtwfast.c.
* src/presmtwfast.c: same changes made to presmestim.c on 2010/08/28.
* R/presmooth.R (control.presmooth): default value of 'n.boot' is c(5000, 1000).
* R/presmooth.R (presmooth): calls to presmtwfast.c include the value of the argument 'dup'; 'n.boot' redefined.
* man/control.presmooth.Rd (arguments): explanation about 'n.boot' changed.
* man/print.survPresmooth.Rd (examples): not run.
* man/presmooth.Rd (examples): search grid for the bandwidth for 'Hboot2' changed.
2010/08/28 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* src/presmestim.c: new argument 'dup' added; new variable 'counter' defined; if-else added in the computation of H:.
* src/termsmise.c: in the call to presmestim.c, a 'dummy', pnull, is passed as the value for 'dup'.
* src/misevect.c: new argument 'dup' added; in the calls to presmestim.c, a 'dummy', pnull, (for S) or dup (for H) is passed as the value for 'dup'.
* R/presmooth.R (presmooth): 'dup' defined; calls to presmestim.c include 'dup'.
* man/presmooth.Rd (examples): error in the definition of hpi2 corrected.
2010/07/18 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* data/pscheck.rda: format changed to 'rda'.
2010/07/11 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* R/presmooth.R (presmooth): the if-else added on 2010/07/07 is slightly modified; the procedure implemented on 2010/07/01 for detecting p=1 is extended to deal with the case p=0; the warning message and the value of 'problem' are changed.
2010/07/07 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* R/presmooth.R (presmooth): 'problem' defined and its value returned in the result; 'coef.logis' defined; 'ind.p1' deleted; if-else added implementing a procedure for detecting overflow when computing C1; the 'lower' argument of integrate() when computing 'C1integrand1' and 'C1integrand2' is changed.
2010/07/06 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* R/presmooth.R (presmooth): when computing the 2nd pilot for the bootstrap bandwidth for f and h, 'if(estparboot[5] < 0.1)' replaced with 'if( estparboot[5] < 0.1 | estparboot[5] > 0.9)'; when computing the bootstrap bandwidth, 'pos.min.mise <- which(mise == min.mise)' replaced with 'pos.min.mise <- max(which(mise == min.mise))'.
2010/07/01 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* R/presmooth.R (presmooth): when computing the pilot and plug-in bandwidths for S and H estimation, an if-else is added, implementing a procedure to use in case p is estimated as equal to 1; new variable 'ind.p1' defined and its value returned in the result; 'p', the Nadaraya-Watson estimate of p, renamed as 'p.nw'.
2010/06/26 Ignacio Lopez-de-Ullibarri <ilu@udc.es>
* R/presmooth.R (presmooth): when computing the 2nd pilot for the plug-in bandwidth for f, 'if(estparplug[5] < 0.1)' replaced with 'if( estparplug[5] < 0.1 | estparplug[5] > 0.9)'; when computing the 3rd pilot for the plug-in bandwidth for f, 'if(estparplug2[5] < 0.1)' replaced with 'if( estparplug2[5] < 0.1 | estparplug2[5] > 0.9)'; when computing the 2nd pilot for the plug-¡n bandwidth for h, 'if(estparplug[5] < 0.1)' replaced with 'if( estparplug[5] < 0.1 | estparplug[5] > 0.9)'.