2009-11-12 kingaa * [r175] R/nlf.R, tests/ou2-nlf.R, tests/ou2-nlf.Rout.save: - bug fix in NLF code (for eval.only=TRUE) 2009-10-12 kingaa * [r174] tests/ou2-mif.Rout.save: - update ou2-mif.Rout.save * [r173] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: - version 0.25-6 * [r172] DESCRIPTION, R/mif.R, tests/ou2-mif.R: - add error trap to prevent non-finite parameters from being estimated 2009-10-07 kingaa * [r171] DESCRIPTION, NAMESPACE, inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: - version 0.25-5 * [r170] R/slice.R, man/slice.Rd, man/sobol.Rd: - add a new function: profile.design, to aid in construction of likelihood profiles 2009-09-30 kingaa * [r169] DESCRIPTION: - fix Carles' name 2009-09-21 kingaa * [r163] inst/ChangeLog: * [r162] DESCRIPTION, NAMESPACE, inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: - version 0.25-4 * [r161] src/euler.c: - fix bug that crops up when dt=0 * [r160] R/slice.R, man/slice.Rd: - add a new function "slice.design" for help with sliced likelihoods * [r159] R/aaa.R, R/pomp-methods.R, man/pomp-methods.Rd, tests/rw2.R, tests/rw2.Rout.save, tests/sir.R, tests/sir.Rout.save: - add a new "time<-" method for manipulating/subsetting time series 2009-07-08 kingaa * [r158] man/trajmatch.Rd: make the documentation a bit more explicit 2009-07-07 kingaa * [r157] data/verhulst.rda, man/verhulst.Rd: add stochastic Verhulst-Pearl (logistic) model to the set of examples * [r156] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: * [r155] DESCRIPTION, NAMESPACE, R/trajmatch.R, data/euler.sir.rda, data/ou2.rda, data/rw2.rda, man/trajmatch.Rd, tests/ou2-mif.Rout.save, tests/ou2-trajmatch.R, tests/ou2-trajmatch.Rout.save: add trajectory-matching method 2009-06-24 kingaa * [r154] tests/rw2.R, tests/rw2.Rout.save: fix tests of 'rw2' * [r153] DESCRIPTION, R/mif.R, R/pomp-methods.R, inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf, man/mif.Rd, tests/logistic.Rout.save, tests/ou2-kalman.Rout.save, tests/ou2-mif.R, tests/ou2-mif.Rout.save, tests/ou2-nlf.R, tests/ou2-nlf.Rout.save, tests/ou2-simulate.Rout.save, tests/rw2.R, tests/rw2.Rout.save, tests/sir.R, tests/sir.Rout.save: better testing some more error checking in 'mif' 2009-06-23 kingaa * [r152] DESCRIPTION, R/mif.R, data/euler.sir.rda, data/ou2.rda, data/rw2.rda, inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf, man/mif.Rd, tests/ou2-mif.R, tests/ou2-mif.Rout.save: alg.pars has been removed as an argument to 'mif' 2009-06-19 kingaa * [r151] DESCRIPTION, inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: version 0.24-7 * [r150] src/initstate.c: check for duplication of names between states and parameters manage the pointer protection stack more sensibly 2009-06-17 kingaa * [r149] src/lookup_table.c: minor changes to C code (remove unused variable) * [r148] DESCRIPTION, NAMESPACE, R/mvnorm.R, R/nlf-guts.R: make use of mvtnorm::dmvnorm now instead of our own version * [r147] R/nlf-guts.R: duplicate codes removed * [r146] R/mvnorm.R: updated 2009-06-03 kingaa * [r145] DESCRIPTION, inst/ChangeLog: version 0.24-5 * [r144] data/euler.sir.rda, inst/doc/advanced_topics_in_pomp.Rnw, inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: improvements to vignettes 2009-06-02 kingaa * [r143] inst/ChangeLog: version 0.24-4 * [r142] data/euler.sir.rda, data/ou2.rda, inst/doc/Makefile, inst/doc/advanced_topics_in_pomp.Rnw, inst/doc/advanced_topics_in_pomp.pdf, inst/doc/compiled_code_in_pomp.Rnw, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: more changes to documentation reconfigure vignettes somewhat * [r141] DESCRIPTION: * [r140] man/init.state-pomp.Rd, man/pomp.Rd, man/simulate-pomp.Rd, man/trajectory-pomp.Rd: add some nice examples * [r139] R/nlf.R: * [r138] man/bsplines.Rd, man/dmeasure-pomp.Rd, man/dprocess-pomp.Rd, man/euler.Rd, man/euler.sir.Rd, man/eulermultinom.Rd, man/init.state-pomp.Rd, man/mif-class.Rd, man/mif-methods.Rd, man/mif.Rd, man/nlf.Rd, man/ou2.Rd, man/particles-mif.Rd, man/pfilter.Rd, man/pomp-class.Rd, man/pomp-methods.Rd, man/pomp-package.Rd, man/pomp.Rd, man/rmeasure-pomp.Rd, man/rprocess-pomp.Rd, man/simulate-pomp.Rd, man/skeleton-pomp.Rd, man/sobol.Rd, man/trajectory-pomp.Rd: further improvements to documentation 2009-06-01 kingaa * [r137] man/euler.Rd, man/pomp.Rd: further clarify documentation 2009-05-28 kingaa * [r136] inst/ChangeLog, inst/doc/compiled_code_in_pomp.Rnw, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: remove prompt and continue characters from vignette documents * [r135] data/euler.sir.rda, data/ou2.rda, data/rw2.rda, inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: version 0.24-3 * [r134] DESCRIPTION, R/bsplines.R, man/bsplines.Rd, src/bspline.c: fix up the bspline.basis function 2009-05-26 kingaa * [r133] DESCRIPTION, man/pomp-package.Rd, man/pomp.Rd: clarify some documentation 2009-05-21 kingaa * [r132] man/pomp-package.Rd, man/pomp.Rd: clarify the documentation on pomp object construction 2009-05-14 kingaa * [r131] inst/include/pomp.h: fix documentation * [r130] man/nlf.Rd: fix documentation * [r129] src/pomp.h: fix documentation * [r128] src/euler.c: clean up the C codes in 'euler.c' 2009-05-13 kingaa * [r127] inst/ChangeLog, inst/doc/compiled_code_in_pomp.Rnw, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: version 0.24-1 * [r126] inst/ChangeLog: * [r125] DESCRIPTION, R/simulate-pomp.R, data/euler.sir.rda, data/ou2.rda, data/rw2.rda, inst/examples/logistic.R, man/simulate-pomp.Rd, tests/logistic.R, tests/logistic.Rout.save, tests/ou2-nlf.R, tests/ou2-nlf.Rout.save, tests/ou2-simulate.R, tests/ou2-simulate.Rout.save: now when 'simulate' is called with nsim=1 (the default), a single 'pomp' object is returned rather than (per the old behavior) a list containing one 'pomp' object. 2009-05-12 kingaa * [r124] DESCRIPTION: fix bug in documentation * [r123] man/pfilter.Rd: fix bug in documentation 2009-05-07 kingaa * [r122] DESCRIPTION, inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: version 0.23-6 * [r121] inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf, inst/include/pomp.h, src/eulermultinom.c, src/pomp.h, tests/sir.R, tests/sir.Rout.save: streamline "reulermultinom" by moving GetRNGstate() and PutRNGstate() outside of a level of looping. If you want to use 'reulermultinom' at the C level, you must take care that it is wrapped inside of the RNGstate functions. An approx. 10-fold increase in speed for the euler.simulate function is realized by this simple change. 2009-05-05 kingaa * [r120] inst/include/pomp.h: fix the pomp.h header comments 2009-05-01 kingaa * [r119] R/init.state-pomp.R: when params is missing, use params <- coef(object) 2009-04-29 kingaa * [r118] src/pomp.h: fix comments * [r117] inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: * [r116] DESCRIPTION, inst/include/pomp.h, man/euler.Rd, src/euler.c, src/lookup_table.c, src/pomp.h, src/pomp_internal.h: rearrange the headers rename the prototypes for native routines used in Euler and onestep plugins * [r115] src/bspline.c, src/dsobol.c: 2009-04-28 kingaa * [r114] inst/ChangeLog: version 0.23-4 * [r113] data/rw2.rda, man/rw2.Rd, tests/rw2.R, tests/rw2.Rout.save: add a new data()-accessible pomp object, coding a very simple 2D random walk * [r112] DESCRIPTION, NAMESPACE, R/euler.R, data/euler.sir.rda, data/ou2.rda, inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf, inst/examples/euler_sir.R, inst/examples/logistic.R, inst/examples/rw2.R, man/euler.Rd, src/euler.c, tests/logistic.R, tests/logistic.Rout.save, tests/sir.R, tests/sir.Rout.save: add onestep plugin to facilitate the construction of models for which explicit formulae are available for one-step transitions. * [r111] inst/CITATION: fix citation info * [r110] src/dprocess.c, src/rprocess.c: explicitly cast 'times' to double to avoid potential problems when R casts a sequence to integer storage type * [r109] man/pomp-package.Rd: 2009-04-27 kingaa * [r108] inst/ChangeLog, inst/doc/Makefile, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: 2009-04-26 kingaa * [r107] DESCRIPTION, inst/ChangeLog: version 0.23-3 * [r106] data/euler.sir.rda, data/ou2.rda: use R-2.8.1 to generate the data/*.rda files * [r105] data/euler.sir.R, data/euler.sir.rda, data/ou2.R, data/ou2.rda: It turns out not to work to use R files in the 'data' directory if these involve actual computations. It appears that, during the package check process, the shared-object library is loaded *after* the data files are read. Consequently, the simulations used to generate the pomp objects in 'ou2.R' and 'euler.sir.R' will not work. As a temporary fix, I have replaced these with binary files containing the objects. I do not yet have a satisfactory way of including the code used to generate these into the package yet. 2009-04-24 kingaa * [r104] R/trajectory-pomp.R, data/euler.sir.R, man/euler.sir.Rd, tests/sir.R, tests/sir.Rout.save: put 'euler.sir' in as an example pomp object obtainable via 'data(euler.sir)' make 'trajectory' a bit more user-friendly * [r103] man/euler.Rd: remove the examples in the 'euler' and 'SSA.simulate' man pages: refer the user to the 'examples' directory instead * [r102] DESCRIPTION, data/ou2.R, data/ou2.rda, inst/doc/compiled_code_in_pomp.Rnw, tests/ou2-kalman.Rout.save, tests/ou2-mif.Rout.save: replace the binary data 'ou2.rda' with R code in 'ou2.R' 2009-04-21 kingaa * [r101] R/pomp.R: better error handling * [r100] R/pomp.R: time variable is not needed in the covar table 2009-04-17 kingaa * [r99] inst/ChangeLog: * [r98] DESCRIPTION, data/ou2.rda, inst/ChangeLog, inst/doc/compiled_code_in_pomp.Rnw, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf, inst/examples/euler_sir.R, inst/examples/euler_sir.c, inst/include/pomp.h, man/euler.Rd, src/euler.c, src/euler_sir.c, src/ou2.c, src/pomp.h, src/rmeasure.c, tests/sir.R, tests/sir.Rout.save: The 'euler' and 'rmeasure' evaluation codes now call GetRNGstate() and PutRNGstate() when the user-supplied function they will evaluate is a native routine. This means that potentially many fewer calls to these expensive functions can be made in, e.g., particle filtering or simulation of a large number of replicates and consequently significant performance gains. 2009-04-16 kingaa * [r97] R/mif-methods.R, R/mif.R: use rowMeans and colMeans in place of apply where appropriate * [r96] man/mif-class.Rd, man/mif-methods.Rd, man/mif.Rd: update references for 'mif' * [r95] man/mif.Rd: fix order of arguments in documentation for 'mif' 2009-04-14 kingaa * [r94] inst/ChangeLog: * [r93] DESCRIPTION, R/mif.R, data/ou2.rda, inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf, man/mif.Rd, tests/ou2-mif.R, tests/ou2-mif.Rout.save, tests/sir.Rout.save: The parameter 'alg.pars' is now deprecated. The four algorithm parameters Np, ic.lag, var.factor, cooling.factor are now specified directly as required arguments to pomp. The 'alg.pars' argument will be removed in a future release. Use of this argument now results in a warning message. 2009-04-13 kingaa * [r92] DESCRIPTION, data/ou2.rda, inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf, tests/ou2-mif.Rout.save: * [r91] inst/ChangeLog: * [r90] R/mif.R, man/mif.Rd, tests/ou2-mif.R: rewrite mif methods to use 'mif.internal'. this obviates the need for a user-visible '.ndone' argument. add some reporting when verbose=TRUE. the 'particles' function can now be altered after the mif object is created. some new tests have been added to tests/ou2-mif.R * [r89] R/pfilter.R: a bit less reporting when verbose=TRUE 2009-04-11 kingaa * [r88] tests/ou2-mif.R, tests/ou2-mif.Rout.save: tests added for 'mif' and 'pfilter' * [r87] R/mif.R: modified in accordance with changes made in revision 86. * [r86] R/pfilter-mif.R, R/pfilter.R, man/pfilter.Rd: put the guts of the particle filter into 'pfilter.internal'. this can be used by 'mif' directly and by methods for 'pfilter'. this obviates the need for the argument .rw.sd in the user-visible methods. 2009-04-10 kingaa * [r85] inst/ChangeLog: * [r84] DESCRIPTION: * [r83] DESCRIPTION, R/mif.R, R/pfilter.R, man/mif.Rd, man/pfilter.Rd: The handling of the argument 'pars' and 'ivps' in mif has been changed to eliminate redundancy and a possible source of errors. Now 'pars' and 'ivps' are checked to make sure that all names are in 'names(start)' and 'names(rw.sd)' and that they are mutually disjoint. Further, all the entries in 'rw.sd[pars]' and 'rw.sd[ivps]' must be positive or an error is generated. If 'rw.sd' has positive values in slots not in the union of 'ivps' and 'pars', these are ignored and a warning is generated. The 'random.walk.sd' slot of the resulting 'mif' object contains only nonzero entries corresponding to the union of 'pars' and 'ivps'. If 'pars' is not specified in the arguments, then it is taken to be 'names(rw.sd)[!(names(rw.sd)%in%ivps)]' Thus it is no longer necessary to specify 'pars' explicitly, provided one takes care that all and only nonzero entries in 'rw.sd' correspond to parameters that one wishes to estimate. One can be a bit more careless with 'rw.sd' if one uses 'pars'. In any case, entries in 'rw.sd' that are zero are ignored. The computation of prediction means and variances and filtering means in 'pfilter' is handled differently. When used as a toplevel function (i.e., when the .rw.sd parameter used internally by 'mif' is unset), then the prediction means and variances and the filtering means are only computed for the state variables. This eliminates an annoying and unnecessary behavior that arose when parameters were set to nonfinite values. When .rw.sd is set (as when 'mif' calls 'pfilter'), the prediction means and variances are computed only for all state variables, but for only those parameters which are undergoing the MIF random walk. Filtering means are computed for all state variables and parameters, since they are needed for the fixed-lag smoothing on the initial-value parameters. * [r82] man/mif-class.Rd, man/mif-methods.Rd: fix some documentation infelicities and bugs 2009-03-16 kingaa * [r81] inst/CITATION: fix Carles accent 2009-03-13 kingaa * [r80] man/pomp-methods.Rd: improve documentation for coef<- method for pomp object 2009-03-11 kingaa * [r79] DESCRIPTION, inst/ChangeLog: * [r78] man/eulermultinom.Rd, src/eulermultinom.c: replace "euler infelicity" Rprintf statements with warnings * [r77] inst/CITATION: add CITATION file 2009-02-03 kingaa * [r76] inst/ChangeLog: * [r75] DESCRIPTION, R/mif.R, man/mif.Rd, man/pomp-methods.Rd, man/trajectory-pomp.Rd, src/euler_sir.c, src/sir.c: changes to documentation and default arguments so as to bring these into agreement. (discrepancies revealed by Kurt Hornik's extensive codoc testing). 2009-02-01 kingaa * [r74] inst/NEWS, man/nlf.Rd: 2009-01-31 kingaa * [r73] DESCRIPTION: * [r72] inst/ChangeLog: * [r71] man/nlf.Rd: documentation fix 2009-01-28 kingaa * [r70] R/plot-pomp.R: remove default for the (unused) 'y' argument * [r69] man/nlf.Rd: fix typos 2009-01-27 kingaa * [r68] inst/ChangeLog: * [r67] DESCRIPTION, R/trajectory-pomp.R: 'odesolve' has been replaced by 'deSolve' * [r66] inst/examples/euler_sir.R, inst/examples/euler_sir.c, inst/examples/sir.R, inst/examples/sir.c: moved 'sir.*' examples to 'euler_sir.*' * [r65] DESCRIPTION, R/plot-pomp.R, inst/ChangeLog, inst/examples/sir.R, man/pomp-methods.Rd: add package 'subplex' as dependency run examples that compile native code only if Sys.info()['sysname']=='Linux'. This replaces the previous test that .Platform$OS.type=='unix', which resulted in errors under some versions of MacOSX. * [r64] inst/ChangeLog: 2009-01-26 kingaa * [r62] inst/ChangeLog: 2009-01-25 kingaa * [r61] DESCRIPTION: minor documentation corrections * [r60] man/mif-class.Rd, man/mif-methods.Rd, man/mif.Rd: 2009-01-17 kingaa * [r59] inst/ChangeLog: * [r58] tests/ou2-nlf.Rout.save: * [r57] tests/ou2-mif.Rout.save, tests/ou2-nlf.Rout: * [r56] tests/ou2-nlf.R, tests/ou2-nlf.Rout.save: 2009-01-16 kingaa * [r55] DESCRIPTION: add functionality for parameter estimation via nonlinear forecasting, method due to Stephen P. Ellner and Bruce E. Kendall * [r54] NAMESPACE, R/mvnorm.R, R/nlf-funcs.R, R/nlf-guts.R, R/nlf-lql.R, R/nlf-objfun.R, R/nlf.R, data/ou2.rda, inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf, man/nlf.Rd, tests/ou2-nlf.R, tests/ou2-nlf.Rout: add functionality for parameter estimation via nonlinear forecasting, method due to Stephen P. Ellner and Bruce E. Kendall * [r53] R/pfilter.R, man/pfilter.Rd: add 'verbose' option to 'pfilter' 2008-08-25 kingaa * [r52] data/ou2.rda, inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: * [r51] R/mif.R, man/mif.Rd, tests/ou2-mif.Rout.save: error trap in 'mif': 'rw.sd' must have names * [r50] DESCRIPTION, inst/NEWS, man/euler.Rd: better documentation in 'euler.Rd' 2008-08-19 kingaa * [r49] inst/NEWS: 2008-08-15 kingaa * [r48] data/ou2.rda, inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: * [r47] tests/ou2-mif.Rout.save: fix bug in Euler step * [r46] tests/sir.R, tests/sir.Rout.save: improve test of SIR model * [r45] tests/logistic.Rout.save: * [r44] DESCRIPTION, src/euler.c: fix bug in Euler step 2008-08-14 kingaa * [r43] DESCRIPTION: make description more descriptive * [r42] inst/examples/sir.R: put trajectory computation into SIR example 2008-08-13 kingaa * [r41] data/ou2.rda, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: * [r40] inst/ChangeLog: * [r39] inst/examples/sir.c: cosmetic * [r38] DESCRIPTION, NAMESPACE, R/aaa.R, R/pomp.R, R/trajectory-pomp.R, data/ou2.rda, inst/examples/logistic.R, inst/examples/sir.R, inst/examples/sir.c, man/mif-class.Rd, man/pomp-class.Rd, man/pomp.Rd, man/skeleton-pomp.Rd, man/trajectory-pomp.Rd, src/skeleton.c, tests/logistic.R, tests/logistic.Rout.save, tests/sir.R, tests/sir.Rout.save: add support for computing trajectories of the deterministic skeleton the skeleton must now be specified when the pomp is created: if the pomp is a discrete-time system, 'skeleton.map' is used to specify its deterministic skeleton; if it is a continuous-time system, 'skeleton.vectorfield' is used. the new method 'trajectory' will, in the first case, iterate the map to produce an itinerary and in the second case, it will call 'lsoda' from the now-required 'odesolve' package to compute the trajectory. some changes to the basic 'pomp' structure have been made to facilitate all this. specifically, a new slot, 'skeleton-type', distinguishes between discrete-time and continuous-time systems 2008-08-01 kingaa * [r37] inst/ChangeLog: * [r36] inst/ChangeLog: * [r35] inst/examples/logistic.R: make dprocess depend on 'log' 2008-07-31 kingaa * [r34] inst/NEWS: * [r33] DESCRIPTION: * [r32] R/mif.R: improved error handling in mif * [r31] man/pomp.Rd: fix inaccuracy in documentation of rmeasure and dmeasure arguments 2008-07-29 kingaa * [r29] inst/NEWS: * [r28] DESCRIPTION: * [r27] R/mif.R: bug fix in convergence record storage * [r26] R/mif.R: cosmetic 2008-07-26 kingaa * [r25] DESCRIPTION, inst/ChangeLog, inst/NEWS, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf, src/ou2.c: bug fix in "intro_to_pomp.Rnw" 2008-07-25 kingaa * [r24] R/pfilter-mif.R: * [r23] inst/NEWS: * [r22] inst/NEWS: * [r21] data/ou2.rda, inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: * [r20] tests/ou2-mif.Rout.save: no need to set rw.sd for parameters that aren't estimated * [r19] inst/examples/logistic.R, inst/examples/rw2.R, inst/examples/sir.R, tests/examples.R: add a test of the examples in 'inst/examples' to the 'tests' directory modify the sir.R example so that it attempts to build a shared-object library only if .Platform$OS.type=='unix' * [r18] inst/doc/intro_to_pomp.Rnw, tests/ou2-mif.R: no need to include zeros in 'rw.sd' * [r17] man/mif.Rd: improve documentation regarding arguments to mif * [r16] R/aaa.R: remove a whole lot of stuff that somehow got in from pomp.devel * [r15] inst/examples/sir.R: fix up R-function version * [r14] R/aaa.R: improve error handling: fix language and use sQuote, dQuote where appropriate * [r13] DESCRIPTION: * [r12] R/compare.mif.R, R/dmeasure-pomp.R, R/dprocess-pomp.R, R/euler.R, R/init.state-pomp.R, R/mif-methods.R, R/mif.R, R/particles-mif.R, R/pfilter.R, R/plot-pomp.R, R/pomp-methods.R, R/pomp.R, R/rmeasure-pomp.R, R/rprocess-pomp.R, R/simulate-pomp.R, R/skeleton-pomp.R, R/sobol.R: improve error handling: fix language and use sQuote, dQuote where appropriate * [r11] R/mif.R: trap as error parameters (including ivps) which are to be estimated but which have zero rw.sd 2008-07-22 kingaa * [r10] inst/NEWS: * [r9] inst/ChangeLog: * [r8] inst/ChangeLog, inst/O_CHANGES: 2008-07-20 kingaa * [r7] DESCRIPTION, NAMESPACE, R/aaa.R, R/bsplines.R, R/compare.mif.R, R/dmeasure-pomp.R, R/dprocess-pomp.R, R/euler.R, R/eulermultinom.R, R/init.state-pomp.R, R/mif-methods.R, R/mif.R, R/particles-mif.R, R/pfilter-mif.R, R/pfilter.R, R/plot-pomp.R, R/pomp-methods.R, R/pomp.R, R/rmeasure-pomp.R, R/rprocess-pomp.R, R/simulate-pomp.R, R/skeleton-pomp.R, R/sobol.R, inst, inst/ChangeLog, inst/GPL, inst/LICENSE, inst/NEWS, inst/doc, inst/doc/Makefile, inst/doc/compiled_code_in_pomp.Rnw, inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf, inst/examples, inst/examples/logistic.R, inst/examples/rw2.R, inst/examples/sir.R, inst/examples/sir.c, inst/include, inst/include/pomp.h, man/bsplines.Rd, man/dmeasure-pomp.Rd, man/dprocess-pomp.Rd, man/euler.Rd, man/eulermultinom.Rd, man/init.state-pomp.Rd, man/mif-class.Rd, man/mif-methods.Rd, man/mif.Rd, man/ou2.Rd, man/particles-mif.Rd, man/pfilter.Rd, man/pomp-class.Rd, man/pomp-methods.Rd, man/pomp-package.Rd, man/pomp.Rd, man/rmeasure-pomp.Rd, man/rprocess-pomp.Rd, man/simulate-pomp.Rd, man/skeleton-pomp.Rd, man/sobol.Rd, src, src/bspline.c, src/dmeasure.c, src/dprocess.c, src/dsobol.c, src/euler.c, src/eulermultinom.c, src/initstate.c, src/lookup_table.c, src/ou2.c, src/pomp.h, src/pomp_fun.c, src/pomp_internal.h, src/resample.c, src/rmeasure.c, src/rprocess.c, src/sir.c, src/skeleton.c, src/sobol.f, tests, tests/logistic.R, tests/logistic.Rout.save, tests/ou2-kalman.R, tests/ou2-kalman.Rout.save, tests/ou2-mif.R, tests/ou2-mif.Rout.save, tests/ou2-simulate.R, tests/ou2-simulate.Rout.save, tests/rw2.R, tests/rw2.Rout.save, tests/sir.R, tests/sir.Rout.save: initial revision * [r6] data/ou2.rda: * [r5] data: 2007-06-25 stefan7th * [r1] ., R, man: Email in Readme changed