Very minor cosmetic update.
This combines the changes in GitHub releases 3.11.7 and 3.11.6.
This release is focused on moving the MARSS User Guide and derivation files into a inst/userguide and inst/derivations along with Makefiles to build. This will facilitate updating MARSS and converting the User Guide to an eBook.
pkgdown folder.Suggests: that were associated with the User Guide and tests and not used in examples.Quick_Start.Rnw to Rmd so it works better with pkgdown and renders to html for CRAN.Additional_repositories: https://atsa-es.r-universe.devpredict_marssMLE(), the newdata model.tsp was not being set.plot.marssMLE(), the CIs for the state residuals did not plot correctly because there is always a NA at the end.vignettes/Learning_MARSS.RmdMARSS.dfa() to the manual built by CRAN by removing keyword internal.inst/DEVELOPER_NOTES.mdEMDerivation.Rnw in slant font as they are random variables.all.equal.vector to vector.all.equal() so it is not interpreted as a method of all.equal().This release is focused on improving the plotting functions for marssMLE, marssResiduals and marssPredict objects. The website links also needed to be updated to the new GitHub organization home for MARSS (and the other ATSA material): atsa-es.
autoplot.marssMLE and plot.marssMLE: all types of residuals with all possible standardizations versus time, plus ACF and QQPlots for the same, and all possible fitted y and x plots. Cleaned-up the plots in various ways (e.g. missing CIs). Added notes (that can be turned off) to the bottom of the autoplot plots to explain what the plot is and guide the user to the more standard plots.autoplot.marssMLE() and plot.marssMLE() to allow a full range of residuals plots but to only show a subset for a specific set of residuals diagnostics plots by default.autoplot.marssResiduals() and plot.marssResiduals() for marssResiduals objects. Simplifies standard residuals plots. This needs to be separate from plot.marssMLE() (i.e. cannot be called from plot.marssMLE) since it is designed to plot whatever happens to be in the marssResiduals object passed to plot.marssResiduals(). plot.marssMLE() runs residuals() to create a specific set of residuals diagnostics plots.autoplot.marssPredict() with better titles and notes below the plots. Removed pi.int as an argument for autoplot.marssPredict() and plot.marssPredict() as this was extraneous. The PI/CI info is pulled in from the marssPredict object.match.arg.exact() which does exact argument matching. The base R match.arg() uses pmatch() and does partial matching. This is a problem for many functions where "xtt1" is different than "xtt". This function implements exact matching.coef.marssMLE() when type="matrix".MARSSresiduals() to explain variance and correlation for standardized residuals.var.ytt1 and var.Eytt1 to the output from MARSShatyt() when only.kem=FALSE. This is for convenience for the plot functions.str_to_sentence utility function for the notes in autoplot.marssMLE() plots.interval.type to the marssPredict objects otherwise the type of interval in the object (prediction or confidence) cannot be known.plot.predictMARSS() was not showing the forecasts and the state predictions when h=0 was garbling the CIs and PIs when a short newdata was passed in (short = shorter than original data).autoplot.marssPredict() was not using the time info from ts object, so x-axis was showing 1, 2, 3 etc instead of the years, for example.MARSS.dfa() used if form="dfa" allowed Z to be passed in. This form is a helper function that forms a default DFA model with a user specified number of trends (m). If the user needs a custom Z, they should not use form="dfa" but use the default MARSS() (form="marxss"). MARSS.dfa() was changed to not allow Z to be passed into the model argument.coef.marssMLE() was not properly showing a time-varying A or U when type="matrix", form="marss" and D or C estimated.plot.marssMLE() was not resetting par() when done thus affecting users plot environment.residuals.marssMLE() value column for states was wrong when there were more than one state because c($.x[2:TT], NA) was used. Changed to not offsetting either .x or .fitted columns and instead added clarification to the documentation for residuals.marssMLE(). The value column was used for examples in help file for residuals.marssMLE() and for the coefficient of determination reported by glance.marssMLE().MARSS() was not setting convergence to an error code when Kalman filter function throws and error before model is fit.MARSSsettings(). This was replaced with pkg_globals in the package environment via .onLoad().\eqn{} when R, Q etc refer to the matrices in the MARSS equation versus code.residuals_marssMLE.Rd had a few typos. Main one was that name column was called .type column.Residuals.Rnw. LaTeX definition for Vtt1 was not working. Also fixed a couple misspellings in EMDerivation.Rnw.This is an update based on version 3.11.2 (GitHub release). It is mainly focused on providing graceful exiting for models that report errors due to ill-conditioned variance matrices and for models with fixed parameters. The testing and output (plot, residuals, tsSmooth, fitted) was made less reliant on MARSSkfss(), which involves an inversion of Vtt1 and which can become ill-conditioned and report an error. The update also fixes a bug in the log-likelihood calculation due to not specifying the tol=0 in SSModel() call. This bug would come up only for variance matrices with extremely high condition numbers fit with method=BFGS. Data and covariates can now be a ts object and the time information will be used for plotting.
MARSSkfss() calls when trace=-1. MARSSkfss() is used for error checks (because it has verbose information to indicate model problems) but because it uses matrix inversions, it will stop models from being fit just because they cannot be run through MARSSkfss() even if they run fine with MARSSkfas(), which doesn't use these matrix inversions.t column in fitted, residuals and tsSmooth output.xtt and Vtt to MARSSkfas() to avoid MARSSkfss() calls when unnecessary.MARSS() was run with fit=FALSE.MARSSparamCIs() when model is fixed and thus no parameters estimated.VtT which sometimes happens for MARSSkfas(). Give user helpful suggestions for switching the Kalman filter/smoother function.KFS(), a tolerance correction affected the log-likelihood value when R was below square root of machine tolerance or condition number was very high (if R non-diagonal). This created a large (incorrect) jump in the log-likelihood. This would be reported with a warning that the log-likelihood dropped if using the EM algorithm. Solution was to set the tolerance to 0 in the KFAS model in MARSSkfas(). Note this did not happen for all cases of small R and a warning would have been generated alerting the user to a problem.MARSSkfas() did not recognize if H was time-varying.MARSS() call was a marssMLE or marssMODEL object, the tinitx and diffuse elements were not being passed in, only the parameter matrices.plot.marssMLE() and autoplot.marssMLE().marssMLE$fun.kf was not always being passed to MARSShatyt() so it didn't necessarily use the function requested by the user.coef.marssMLE() did not change what to, say, par.se if type passed in so coef(fit, what="par.lowCI", type="Z") returned coef(fit, type="Z").print.marssMLE() and coef.marssMLE() would fail ungracefully if all the parameters were fixed or MARSS() was run with fit=FALSE.xtt and xtt1 etc.Residuals.Rnw.kem.plank.4.tinitx=1, then Vtt1T[,,1] does not exist. Replaced Vtt1T[,,1] with NA instead of 0 in this case. Note Vtt1T[,,1] would never be used in this case as V10T is used instead however a value of 0 is not correct. The value is does not exist so NA is the correct value.This is an update is focused on graceful exiting for models that report errors due to ill-conditioned variance matrices or for models with fixed parameters. The testing and output (plots, residuals, tsSmooth, fitted) was made less reliant on MARSSkfss(), which involves an inversion of Vtt1 and which can become ill-conditioned and report an error. The update also fixes a bug in the log-likelihood calculation due to not specifying the tol=0 in SSModel() call. This bug would come up only for variance matrices with extremely high condition numbers fit with method=BFGS. Data and covariates can now be a ts object and the time information will be used for plotting.
See notes above for version 3.11.3 (CRAN release).
skip_on_cran() as they are for internal testing. This directory is not part of the CRAN package but is on the GitHub site.Version 3.11.1 is focused on addition of the predict, forecast, fitted and residuals functions along with plotting functions for the output. Documentation for these functions along with background literature and the derivation of the residuals algorithms have been updated. Residuals in state-space models are complex as there are two processes (observation and state), three types of conditioning (data to t-1, t or T), and four types of standardization used in the literature (none, marginal, Cholesky on the full variance matrix, and Cholesky on only model or state residual variance). The MARSS package computes all the variants of residuals. Many of the predict changes are listed below for 3.10.13 release on GitHub. New chapters illustrating structural equation models using MARSS versus StructTS and the KFAS package were added. The KFAS chapter compares the KFAS residuals functions to the MARSS residuals functions. The two packages use different algorithms and different semantics to compute the same residuals.
ldiag() convenience function added to make list diagonal matrices. This replaces having to do code like a <- matrix(list(0),2,2); diag(a) <- list(2,"a"). Now you can call ldiag(list(2,"a")).accurancy.marssMLE() and accuracy.marssPredict() which returns accuracy metrics sensu the forecast package.is.unitcircle() utility function and added tol so that it does not fail if abs(eigenvalue) is above 1 by machine tolerance.plot.marssMLE() and autoplot.marssMLE().residuals.marssMLE(). Got rid of augment.marssMLE() and renamed it residuals.marssMLE(). The old residuals.marssMLE() became MARSSresiduals(). There was too much duplication between residuals.marssMLE() and augment.marssMLE() and between augment.marssMLE() and fitted.marssMLE(). Also I want to minimize dependency on other packages and augment is a class in the broom package. This required changes to the glance.marssMLE(), plot.marssMLE() and autoplot.marssMLE() code.tidy.marssMLE. tsSmooth.marssMLE now returns the estimates from the Kalman filter or smoother which tidy.marssMLE had returned. tidy.marssMLE only returns a data frame for the parameter estimates.solve(t(Vtt1[,,1]), B%*%V00) which should be faster and seems to have lower numerical error.predict.marssMLE updated to return ytt1, ytt, ytt1.MARSSresiduals.tt1 and MARSSresiduals.tt but not returned by residuals.marssMLE() (unless clean=FALSE). Only returned by MARSSresiduals().residuals() in cases where R=0. In v 3.10.12, I introduced a bug into MARSSkfss() for cases where R has 0s on diagonal. History: To limit propagation of numerical errors when R=0, the row/col of Vtt for the fully determined x need to be set to 0. In v 3.10.11 and earlier, my algorithm for finding these x was not robust and zero-d out Vtt row/cols when it should not have if Z was under-determined. This bug (in < 3.10.12) only affected underdetermined models (such as models with a stochastic trend and AR-1 errors). To fix I added a utility function fully.spec.x(). This returns the x that are fully determined by the data. There was a bug in these corrections which made MARSSkfss()$xtT wrong whenever there were 0s on diagonal of R. This would show up in residuals() since that was using MARSSkfss() (in order to get some output that MARSSkfas() doesn't provide.) The problem was fully.spec.x(). It did not recognize when Z.R0 (the Z for the R=0) was all 0 for an x and thus was not (could not be) fully specified by the data. Fix was simple check that colSums of Z.R0 was not all 0.MARSSresiduals.tt1() was reporting the smoothations instead of innovations residuals so reporting same model residuals as MARSSresiduals.tT().base::chol() returns the upper triangle. Thus the lines in MARSSresiduals.tT() and MARSSresiduals.tt1() that applied the standardization need t(chol()).trace=1 would fail because MARSSapplynames() did not recognize that kf$xtt and kf$Innov were a message instead of a matrix. I had changed the MARSSkfas() behavior to not return these due to some questions about the values returned by the KFAS function.is.validvarcov() used eigenvalues >= 0 as passing positive-definite test. Should be strictly positive so > 0.MARSSkfas() had bug on the line where V0T was computed when tinitx=0. It was using * instead of %*% for the last J0 multiplication. It would affect models with a non-zero V0 under certain B matrices, such as structural models fit by StructTS().MARSSresiduals.tT() and MARSSresiduals.tt1() but was in the old residuals.marssMLE() also. If MLE object had the kf element, kf was not assigned in code since there was no kf <- MLEobj$kf line for that case. Normally MLE objects do not have the kf element, but it could be added or is added for some settings of control$trace. This caused residuals() to fail if trace=2.MARSS_dfa.RdStructTS() to MARSS() output.augment() from documentation and manuals. Replaced with residuals().predict.marssMLE.Rd (help page) had bug in the examples. remove Q=Q from the model list in the first example.predict() and predict.marssMLE().fitted.marssMLE to have column with .x which is conceptually the same as the y column for observations. It is the left-side of the x equation (with error term) while fitted is the right-side without the error term.predict.marssMLE() when no data passed in.predict.marssMLE() so that user can specify x0 if needed.residuals.marssMLE(). The data frames are still in tibble form. Removed all reference to tibbles in the documentation.trace = -1 some tests were still being done. I added a test for trace = -1 to a few more test lines in MARSS.R and MARSS_marxss.R.residuals.marssMLE() to return innovations instead of smoothations.fitted.marssMLE, residuals.marssMLE, and tsSmooth.marssMLE have a leading ".".Version 3.7 update was required due to new version of KFAS that changed its API.
allow.degen() bug that would set elements to zero, leading to non positive definite matrices. Test if Q and R are diagonal. If not, don't allow 0s to be set on diagonal since that is likely to lead to non-positive definite matrices. I could test if the row/col covariance are 0s but that would be costly.loglog.conv.test() bug that returned NAs when logLik > 720 due to exp(LL) call. Changed to exp(LL-mean(LL))Version 3.6 update is mainly concerned with speeding up MARSS() for problems with large number of time series (n > 100) and where many R elements are being estimated (e.g. R="diagonal and unequal"). This comes up in dynamic factor analyses often. The changes also improve speed for small R problems by about 25%, but speed increase is 10 fold for problems with R matrices that are 100x100 with 100 estimated R elements.
MARSS.marxss() to speed up conversion of "unconstrained" shortcut to a matrix. Only matters if m or n is big.convert.model.matrix(). Old version was always using slow code to deal with * and + in character matrix. This made formation of the free and fixed matrices very, very slow when the matrix got big (100x100, say).is.design() to not use near equality for test of element==0. This may break MARSS() since R sometimes doesn't maintain "zeroness".MARSSkem() code for working with large matrices. Replaced all crossproducts with crossprod() and tcrossprod() which are significantly faster for large matrices. This increases speed 2-10 fold when working with larger matrices. Largest speed increases are when R is not diagonal and equal.MARSSkfss() instead of using the very slow is.diagonal() function (which is really meant for list matrices)degen.test() function so that it sets a flag to TRUE if any variance-covariance matrix diagonals set to 0. If so, do the updates otherwise skip.parmat() by testing if d and f matrices are not time-varying. In which case, don't subset the array, but rather rest the "dim" attribute. Much, much faster for big d and f matrices.sub3D() to make it a bit faster by using x[,,t] when both nrow and ncol are >1vec() to make it 3x faster by setting dim attr instead of using matrix() when matrix is 2DlakeWAplankton datasets were saved as data.frame. Changed to matrix.MARSS() didn't print out marssMLE object when convergence=12 (maxit set below min for conv test).Minor update to declare S3 objects if user has broom package installed. A few minor changes also made.
is.validvarcov() is expensive. Minimize use in MARSSaic, MARSSboot, MARSSoptim, MARSSparamCIs, MARSSsimulate, MARSS_marxss.is.diagonal() utility functionplot.marssMLE() to autoplot.marssMLE() since it is ggplot2 basedplot.marssMLE() that uses only base R graphicsMARSSkfss() had bug on V0T line. "*" instead of %*%. This code is almost never called.MARSSkfss() had bug. Did not check if G was time-varying. This code is almost never called.Version 3.2 is a minor update to the documentation
MCInit() from working.Minor update. Version 3.10.11 has some edits to speed up the code by minimizing calls to expensive checking functions and fixes a bug in MARSSharveyobsFI() that appeared if a parameter was fixed and time-varying and MARSSparamCIs() was called.
MARSSkfss() had a bug "*" was used in place of %*% with J0. Would never show up unless V0 estimated.MARSSharveyobsFI() which arose if a parameter was fixed and time-varying. This caused MARSSparamCIs() to fail if a parameter was fixed and time-varying.dparmat() did not return values if it was time-varying and fixed. Caused tidy() to return error for dlm models.is.validvarcov() is expensive. minimize calls to it. If called with a diagonal matrix, it should automatically pass so added a check to is.validvarcov() to see if matrix is diagonal.is.marssMLE() is expensive. Replace with a call to class().autoplot.marssMLE() function and updated plot documentation to cover autoplot functions.Version 3.0 is a major update and clean-up. Besides the clean-up, the changes were to allow time-varying parameters and a way for the user to specify linear constraints using an eqn like a+2*b in the parameter matrix.
The changes are extensive but are internal and should be largely invisible to users of MARSS 2.X. The MARSS() 3.0 call is backwards compatible to 2.9 except that kf.x0 changed to tinitx and moved from control list to model list. Use of KFAS remains disabled until I can update to the new version of KFAS. This slows down method="BFGS", but does not affect method="kem".
MARSS() call is retained (for reference).MARSSkf() and MARSShatyt() functions. Takes MLEobj now.parmat() function. This returns a parameter matrix when given a MLEobj.MARSS() looks for a function called MARSS."form", where form is something like "mar1ss" or "dlm". This function takes the MARSS inputs (all of them) and transforms the input into a marssm object ready for the fitting functions as the function writer wishes. All that the function has to do is to return a valid marssm object from the model element of the MARSS() call. This allows me (or anyone else) to use whatever parameter names they want in the model element. This way the user can use familiar names for parameters can set some parameters to specific values (like 0). Or the user could do something totally different with the model element and just have it be a text string like model="my.ts.model.1" or model="my.ts.model.2". The only constraint is that the function output a proper marssm object and that the control, inits, and MCbounds arguments for MARSS are properly specified.checkMARSSInputs() and checkModelList(). These replaced the functionality of popWrap.r and checkPopWrap.rMARSS.marxss(). This is the first MARSS.form() function. This is a standardized format for so that I can add other forms easily.MARSSkf() so that K (Kalman gain) is 0 when tinitx=1 and V0=0. Changed MARSSkf() to allow some of diagonals of V0 to be 0 and others non zero. Got rid of many of the OMGs. Added pcholinv() function to diaghelpers.r which deals with matrices with 0s on diagonals. This streamlined the filter code.MARSSkem() to allow time-varying parameters. Made changes to MARSSkf(), MARSSkfas() and MARSSsimulate() to allow time-varying parameters. See EMDerivation.pdfMARSShessian() and MARSSparamCIs() to allow one to specify the function used to compute the log-likelihood.MARSShessian()MARSSsettings(), MARSS.marxss(), is.marssm(), is.marssMLE().MARSSkem() and MARSShatyt() to allow some diag.V0=0 and others not 0, so user can mix stochastic and fixed initial x states.MARSSkem(). Removed the OMGs from MARSSkem() since no longer needed given the new pcholinv() function.parmat, pcholinv, pinv, few other functionsMARSSkem() that meant that the maxit-1 kf and logLik were returned when algorithm stopped due to hitting maxit. Par was correct.Major update over 3.9. The main changes have to do with with errors in the Hessian matrix whenever the Cholesky of the R or Q matrix was used (when they weren't diagonal). This affected all the residuals and confidence intervals calculations for non-diagonal R and Q. Hessian for non-diagonal Z was also bad. Version 3.10.8 completely abandons working with the Cholesky transformed variance-covariance matrices for the Hessian calculation. The Cholesky transformation was not necessary for computing the Hessian since the Hessian is computed at the MLEs and localized. Also the default Hessian computation now uses the Harvey et al. analytical algorithm for the Hessian rather than a numerical estimate.
residuals.marssMLE()MARSSinits_marxss() function would give error if U, A, C, or D fixed and user passed in inits. inits ignored in this case so should not throw error.alldefaults could be updated by form. A few functions were neglecting to (re)load alldefaults or to reassign alldefaults when updated: is_marssMLE(), MARSSinits.marxss(), MARSSinits(). The variables in the pkg_globals environment should be (and only be) loaded when needed by a function and only loaded into the function environment.MARSSkf() was not passing optional function args to MARSSkfas().MARSSkfss() miscounting the number of data points when R=0, V0=0, and tinitx=1. When Ft[,,1]=0 (e.g. when R=0, V0=0, and tinitx=1), MARSSkfss() was including the y[1] associated with Ft[,,1]=0 in the # number of data points. These should be excluded since they don't affect x10.MARSSparamCIs() gave the wrong s.e. for variances and covariances when method="hessian". It also gave the wrong CIs for variances and covariances when variance-covariance matrix was non-diagonal. There were a series of issues related to back-transforming from the Hessian of a Cholesky transformed variance-covariance matrix ( Sigma=chol%\*%t(chol) ).MARSSparamCIs(), vrs 3.9 was getting the Hessian matrix numerically using a variance-covariance matrix that had been transformed with a Cholesky decomposition to ensure it stays positive-definite. The upper and lower CIs were computed from the s.e.'s. I back-transformed the Hessian to the original (non-Cholesky transformed) scale the same way I back transformed a variance-covariance matrix. But the variance of s^2 is not the var(s)^2, which is what I was doing, essentially. So the s.e. for R and Q were wrong in all cases. Note, using a Hessian to estimate CIs for variance-covariance matrices is generally a bad idea anyhow however.MARSShessian() in subscripting the d matrix when doing the Cholesky transformation. Caused NAs for cases with non-diagonal matrices. However, had the standard error been returned, they would be wrong for non-diagonal matrices because the elements of the Cholesky transformed matrices do not correspond one-to-one to the non-transformed matrices. E.g. the untransformed [2,2]^2 is Cholesky transformed [1,2]^2+[2,2]^2. The Hessian used was for the Cholesky transformation and the curvature of the LL surface for the Cholesky transformed values is different than the curvature for the untransformed variance-covariance matrix elements.Fix: I completely abandoned working with the Cholesky-transformed variance-covariance matrices for the Hessian calculation. The Cholesky-transformation was not necessary for computing the Hessian since the Hessian is computed at the MLEs and localized.
Created a new function MARSSharveyobsFI() which uses the Harvey (1989) recursion to analytically compute the observed Fisher Information matrix. This is the Hessian for the untransformed variance-covariance matrix parameters. So CIs on variances can be negative since the variance of the MLE is being approximated by a MVN (which can lead to negative lower CIs).
Harvey1989 is now the default function when method='hessian'. In later vrs of MARSS, this is changed to Holmes2014.
The user can also select method='hessian' and hessian.fun='fdHess' or hessian.fun='optim'. This will compute the Hessian (of the log-LL function at the MLEs) numerically using these functions. The variance-covariance matrices are NOT Cholesky transformed. These are numerically estimated Hessian matrices of the untransformed variance-covariance matrices.
Added MARSSinfo(26) which discusses the reason for NAs in the Hessian.
MARSShatyt() was setting ytt1 (expected value of y(t) conditioned on data up to t-1) to y(t), which is incorrect. Expected value of y(t) conditioned on y up to t-1 is Z xtt1 + aCSEGriskfigure() panel 2 was wrong when mu>0 (increasing population).CSEGriskfigure() panel 2 CIs were wrong when CI method=hessian since Q had not been back transformed (so was using sqrt(Q)).MARSSkemcheck()'s test that fixed B is in unit circle failed when B was time-varying and some fixed and others estimated. Also when the eigenvalues were complex, it should test the real part only.coef.marssMLE() was not stopping when illegal "what: arg passed in. man page did not say what happens when type=parameter.MARSS.marxss() and MARSS.marss() to allow G, H, and L passed inMARSSkem() to specify star lists with G, H, and L (mathbb(elem) in EM Derivation)MARSSkss() to use Q*=G Q t(G), R*=H R t(H) and V0*=L V0 t(L)MARSSmcinits() and added chapter on searching over the initial conditions into the User Guide. As the MARSS models that MARSS() can fit expanded, MARSSmcinits() was increasing obsolete and it was impossible to come up with good searching distributions. Because MARSSmcinits() was removed, control$MCInits list item was removed also from defaults and from accepted input.MARSS.marxss() to allow c and d to be 3D arrays. This allows one to use inits=fit to set inits and not get a d (or c) must be 2D error.MARSSinfo(4) regarding errors about R=0 and x0 not fixed. Added info to the error warnings to direct user to MARSSinfo().pchol() and psolve() functions to return the Cholesky transformation or inverse (via solve) when there are 0s on the diagonalprint.marssMLE(x, what="par") returned a vector of estimated values instead of the list of par. Changed to return the list.MARSShatyt() output. Needed for residuals.marssMLE().is.validvarcov() so that it returns an error if the user specifies a structurally illegal variance-covariance matrix. Added info to MARSSinfo(25).augment, tidy and glance functions for marssMLElogLik method for marssMLE objectsfitted method for marssMLE objects to return Z xtT + u (model fitted value of y)plot method with diagnosticsnone. resubmission due to missing file
checkMARSSinputs()print.marssMLE() to make sure models are class marssMODEL.summary.marssMODEL() to return the list matrix instead of the marssMODEL passed in. Added tinitx to the returned (and printed) list.is.blockunconst() and is.blockequaltri() functions. Not really used or useful and were buggy.MARSSoption() code to ensure varcov matrices stay positive-definite.MARSS().
MARSSkf() to return kf (so use what user requested), but set Innov, Sigma, Kt etc with MARSSkfss().MARSSkem(). Removed adding of kf and Ey when trace>0. This happens in MARSS().summary.marssMODEL() to use marssMODEL attributes for par.names and model.dims, so it works on non-marss form marssMODEL objects.MARSShessian()MARSShessian()MARSSinfo() to give the user some code to convert pre-3.5 marssMLE object to the 3.5+ form.MARSSkfss(). When Z was not square (number of rows > number of cols), OmgRVtt was not getting set. OmgRVtt sets Vtt diagonals (and corresponding cols and row) to zero when R had 0s on the diagonal.MARSSkfas(). Was returning $Innov and $Sigma using $v and $F, but as detailed in the KFS help page (KFAS package), the ones returned by KFS are not the same as the standard innovations and Sigma for multivariate data. Now, MARSSkfas() returns a text message to use MARSSkfss() to get these.residuals.marssMLE() and MARSSinnovationsboot() were not running MARSSkfss() to get Innov, Kt, and Sigma when R was not diagonal. Problem occurred after I changed MARSSkfss() to return text error instead of NULL for these.This release is focused on adding new method method="TMB" which uses the package {marssTMB}.
MARSS() to recognize these.MARSSfit() and methods for "kem" and "BFGS".R/onLoad.R and made it easier to specify new methods and constraints on methodscheckMARSSinputs.R, is_marssMLE.R and is.validvarcov() so they are not so specific to method="BFGS" but work for any methods with similar constraints.MARSSvectorizeparam(). Need when writing methods for MARSSfit() generic.optim() was using number of function calls not number of gradient calls.toLatex() to output the raw tex so that it can directly go into RMarkdown or Quarto.match.arg() for form and method.Ignore. Pre-emptive.
Version 3.5 is mainly concerned with formalizing the internal structure of model objects. marssMODEL objects have been formalized with attributes. A form definition along with associated form functions have been defined. This won't be noticeable to users but makes writing functions that use marssMODEL objects easier and more versatile.
MARSS.dfa() to allow B and Q setting to "diagonal and equal" or "diagonal and unequal"MARSS:::predict.marssMLE(). Further development will be done before exporting to users.)MARSSvectorizeparam() and MARSSapplynames() from the exported list. The former has been replaced by coef(marssMLEObj, type="vector"). The latter is an internal utility function.MARSSkfas() to return Innov and Sigma when R is diagonal. When R is not diagonal, the user is directed to use MARSSkfss() since MARSSkfas() and MARSSkfss() do not agree when R is not diagonal (and I think the error is in KFAS as the Sigma looks off when R not diagonal).MARSShessian() to use a Cholesky transformation on any variances so that the variance covariance matrices stay positive definiteMARSSparamCIs()MARSS()..onLoad() function.MARSSkfas() for version of KFAS. API changes in KFAS 1.0.0, and a line of code was added to use the correct API if KFAS 0.9.11 versus 1.0.0 is installed. MARSS will work with both versions of KFAS.MARSSinfo()MARSSinfo()lakeWAplanktonRaw. Month^2 dropped and month not z-scored. Original raw data for the counts.MARSSboot() was out of date with newest version of MARSShessian()'s returned arguments.is.blockunconst() bug made it break on certain diagonal list matricesVersion 3.10.13 mainly has to do with the predict() and forecast() functions along with plotting and printing methods.
MARSSkfss() and MARSSkfas() Add rownames to the x elements of the list.MARSSkf() Added newdata to allow user to pass in a new dataset to fit with the fitted model.predict.marssMLE() Shows the prediction or confidence intervals for data or states. Forecasts can be done by passing in h. newdata can be passed in also and fitted model will be used to fit these data and show the intervals. Output is same form as a tibble (but not a tibble). Returns a list of class marssPredict.forecast.marssMLE() This does the forward forecasting past the end of the data. Intended to be called by predict.marssMLE. I did not write a marssMLE method for the forecast generic in the forecast package since that would require that the forecast package be required for the MARSS package.plot.marssPredict() plot method for the new marssPredict object. This is designed to look like the plot.forecast() function in the forecast package.print.marssPredict() print method for marssPredict objects.Version 2.9 was a temporary update to deal with a major change to the API of the KFAS package. Needed to disable use of MARSSkfas() until that function was rewritten.
MARSSboot() so that MLE objects with method=BFGS can be used; changed the param.gen argument to take "MLE" and "hessian" instead of "KalmanEM" and "hessian". Updated MARSSboot.R and MARSSboot.Rd.MARSSkfas() until MARSS can be made compatible with new version of KFAS package. Removed importFrom(KFAS, kf) and importFrom(KFAS, ks) from the NAMESPACE. Removed MARSSkfas from the export list in NAMESPACE. Removed KFAS in the depends line of DESCRIPTION.MARSSaic() and MARSSparamCIs() so that MARSSboot() call uses param.gen="MLE". This fixes the bug that stopped MLE objects from BFGS calls to fail.Version 2.8 improved default initial conditions functions and fixed bugs in the Shumway and Stoffer Kalman filter/smoother function.
MARSSkf() when R=0, kf.x0=x10, and V0=0. The algorithm was not setting x(1) via y(1) in this special case.MARSSinits(), got rid of the linear regression to get inits for x0; using instead solution of pi from y(1)=Z*(D*pi+f)+A; This stops MARSS from complaining about no inits when Z is not a design matrix. NOTE NB: This means the default initial x0 are different for 2.7 and 2.8, which leads to slightly different answers for MARSS(dat) in 2.7 and 2.8. The answers are not really different, just they started with slightly different initial values so have slightly different values when the algorithm reaches its convergence limit.MARSSkemcheck() to allow lag-p models. I worked on the derivation of the degenerate models (with 0 on diag of Q) to better define the needed constraints on B.0 and B.plus sub matrices. This led to changes in MARSSkemcheck.r so that lag-p models written as MARSS model are now allowed. There are still problems though in x0 estimation in the EM algorithm when there are zeros on R and B diagonals, so best to method=``BFGS'' until I redo the degenerate EM algorithm.MARSSkf() function instead of MARSSkfas. If kf.x0="x10", default was to use MARSSkfas() function which is much faster, but it doesn't like 0s on B diagonal if V0 is 0. So I added the option to force use of slower MARSSkf() function using method="BFGSkf". Required adding stuff to MARSSsettings.r and MARSSoptim.r. This is mainly for debugging since MARSSoptim() will now check if optim failed and try using MARSSkf() if MARSSkfas() was used. Added line to output that says which function used for likelihood calculation; again for debugging.MARSSmcinit() to improve random B generation. There is nothing to guarantee that random Bs in mcinit routine will be within the unit circle, however it is probably a good idea if they are. Default bounds for B changed to -1,1 and random B matrix rescaled by dividing by max(abs(Re(eigen(B)))/runif(1) to get the max abs eigenvalue between 0 and 1. This works unless the user has fixed some B values to non-zero values. This required change to is_marssMLE.r also to remove constraint that B bounds be greater than 0.MARSSmcinit() to allow fixed and shared values in random Qs and Rs. The random Wishart draw is rescaled based on the fixed and shared structure in R or Q. As part of this, I cleaned up how fixed and shared values are specified in the random draws of other parameters. This change doesn't change the end effect, but the code is cleaner.MARSSoptim() did not allow unconstrained Q or R. The problem had to do with temporarily resetting the upper triangle of tmp fixed matrices to 0 when using tmp.par as the Cholesky matrix.MARSSkf() when there were 0s on diagonal of Q. The algorithm only worked if B was diagonal. Fix required changes to Kalman smoother bit of MARSSkf(). I rewrote the pertinent section in EMDerivation.pdf.Versions 2.7 and 2.6 focused on misc. bugs.
MARSSPopWrap(). Some of the allowable cases for Z and m were missing.MARSSsimulate() bug. MARSSsimulate() was broken for multivariate simulation since I forgot that rmvnorm returns a 1 x p matrix even if the mean is p x 1. Wrapped the rmvnorm call in a array() to fix the dim setting.Version 2.5 focused on switching model specification to use list matrices.
MARSS(). Same functionality is provided via list matricesMARSS(). Just the name of the argument was changed to be more intuitiveVersion 3.10.12 update mainly has to do with the tidy(), fitted() and augment() enhancements which clarify ytT, xtT and residual intervals for MARSS models. This was a major update though probably users will not notice much as it only affects residuals output. A few minor bugs were fixed which caused errors to be thrown in some rare time-varying cases. One bug that affected bootstrap confidence intervals was fixed. The documentation got a major clean-up. The Residuals report has been heavily edited to improve precision and clarity (with added verbosity). The help files and automated manual from the help files were cleaned-up and some of the internal functions moved out of the manual.
MARSSsimulate() missing values were placed in the wrong positions in simulated data. This would affect all simulated data with missing values and thus any function that used MARSSboot(), for example bootstrap confidence intervals for a data set with missing values. Default is to use Hessian so the user would not normally have encountered this bug and it had little effect on the CIs.fitted.marssMLE() Fixed bug in fitted.marssMLE for states when one.step.ahead=TRUE. It was using xtt1[,t-1] instead of xtt[,t-1]. The former meant it only used data up to t-2.degen.test() in MARSSkem() was not catching when R or Q was time-varying (and thus degeneracy should not be allowed). Changed to test the 3D of model.dims == 1 or not.residuals.marssMLE(..., Harvey=TRUE) would fail if Q, B, or G was time-varying because parmat() called with t+1. Changed to only call parmat() when t<TT. Q, B, and G do not appear in the recursion when t=TT so parmat() with t=t+1 is never needed.MARSS_dfa() used form="dfa" in MARSS.call list. Just info. Never used.is.design().toLatex.marssMODEL() Fixed some old bugs in toLatex_marssMODEL.R. Added S3 class declaration in NAMESPACE for toLatex. fixed equation attribute in MARSS_marxss. G{t} was used instead of G_{t}. Only affected toLatex_marssMODEL(). Had extra line in build.mat.tex() that removed last line of matrices. This function was not exported so users would never have run into these bugs.MARSSkfss() To limit propagation of numerical errors when R=0, the row/col of Vtt for the fully determined x (determined from data) need to be set to 0. My algorithm for finding these x was not robust and zero-d out Vtt row/cols when it should not have if Z was under-determined. MARSSkfss() is not used for fitting and only affected underdetermined models (such as models with a stochastic trend and AR-1 errors). To fix I added a function fully.det.x() to the utility functions. This returns the x that are fully determined by the data. Note, MARSkfss() is the classic Kalman filter/smoother. The MARSS algorithm does not use this normally. Normally MARSSkfas(), build off the Koopman et al algorithm which avoids unneeded matrix inverses, is used. MARSSkfas() uses the Kalman filter/smoother in the KFAS package.MARSShatyt() Added ytt, ytt1, Ott, Ott1 to MARSShatyt() so that tidy.marssMLE() can more easily return the one-step-ahead predictions for Y(t). Also added var.ytT and var.EytT so you can easily get the estimates, CI and prediction intervals for missing data. Added only.kem to MARSShatyt() so that only values conditioned on 1:T as needed by MARSS kem are returned. This makes the Ey part of a MARSS object smaller and speeds up MARSShatyt() a little.tidy.marssMLE() Changed type for tidy() to xtT, ytT and fitted.ytT. tidy() exclusively gives estimates of things (parameters, X, Y, fitted Y) conditioned on all the data.fitted.marssMLE() Added interval=c("none", "confidence", "prediction") to fitted() and returns a list with se's (or sd's if prediction) and intervals. Also added conditioning argument to fitted.marssMLE which gives fitted values with different conditioning. Changed default output to tibble.augment.marssMLE() Changed standard errors output for augment() to .se.fit for std error of fitted y and .sigma to std error of residuals. This matches what augment.lm outputs.plot.marssMLE() and autoplot.marssMLE(). Added plot.par to plot.marssMLE and autoplot.marssMLE so that the plots can be customized. Added plot of ytT to both functions. Changed the residuals plots to use the CIs for the residuals not the loess CIs.MARSSinfo() Added "AZR0" to MARSSinfo() to give info if user gets error that A cannot be estimated with R=0. Added more informative message to MARSSkemcheck() for that case.residuals.marssMLE(). This is now a helper function which calls MARSSresiduals.tT() or MARSSresiduals.tt1(). The former is smoothation residuals and the latter is innovations (one-step-ahead) residuals.? or help.search.Version 2.2 focused on incorporating the KFAS Kalman filter/smoother functions which are faster and more stable.
MARSSkfas() function.MARSSkfas() to deal with 0s on diag of Ft[,,1] so can do R=0show.doc() with RShowDoc() (base)Version 2.0 implements changes to allow B and Z estimation and more element sharing in Q and R matrices.
MARSSkem() algorithm changed to allow B and Z estimation.MARSSkem() algorithm changed to allow constrained B and Z estimation. This was the second main objective of MARSS 2.0. This allows you to have fixed values or shared values in your B or Z matrices.MARSSkem(). There is no iter.V0 control element anymore.MARSSkem() changed to a more general way to deal with missing values. This is described in the EMDerivation.pdf. It doesn't affect the user, but allows the code to be expanded to more types of models much more easily.This version update is mainly concerned with adding generic functions (coef, residuals, predict), hooking back up KFAS package filters into MARSS functions, and customizing print functions for different model forms.
MARSSkfas() was changed to work with the new KFAS version released July 2012. This led to a 10-20 fold decrease in computation time for method="BFGS" and 2 fold for method="kem".MARSSkf() changed to MARSSkfss(); MARSSkf() is now a utility function that picks MARSSkfas() or MARSSkfss() based on MLEobj$fun.kfMARSSkfas() using the algorithm given on page 321 in Shumway and Stoffer (2000), Time Series Analysis and Its Applications (note the 2000 edition not 2006). The algorithm is given in the User Guide also. The EM Algorithm requires the lag-one covariance smoother but this is not one of the outputs of the KFS() function in the KFAS package.MARSSkfas() to be strictly 0 when it is supposed to be (when R has 0 on the diagonals); KFS() output has ~0 not actually 0.coef() method for marssMLE objects. Added $coef to marssMLE object.parmat() to be hidden (not exported). Instead its functionality is through the standard R function for this purpose, coef().residuals() method for marssMLE objects by changing MARSSresids() to residuals.marssMLE().predict() method for marssMLE objects.toLatex.marssMODEL() function to create latex and pdf output of modelsMARSS.dfa() did not allow user to pass in Z as matrix.parmat(). When t was a vector, parmat() only returned the value at max(t).MARSSkemcheck() crashed when the test "when u^{0} or xi^{0} are estimated, B adjacency matrix must be time invariant" was started.MARSS_marxss() threw an error when Z was passed in as a matrix and A="scaling"describe.marss() bug caused diagonal matrices with 1 estimated value and fixed values to not be identified as diagonalMARSSmcinit(). MCMC init function would crash for anything except the default model.is.design() function. A design matrix must have more or equal rows than columns.MARSSkf(). R has a flaw in terms of how it behaves when you subscript a matrix and the new matrix has a dimension length of 1 for one (or more dimensions). For example, if a=array(0,dim=c(1,2,4)), then a[,,1] is no longer a matrix but instead is a vector and dim(a[,,1]) is NULL. This can cause all sorts of mysterious bugs. Sometimes adding drop=FALSE will prevent this unpleasant behavior. If b=matrix(0,2,2), dim(b[,1,drop=FALSE]) is c(2,1) while dim(b[,1]) is NULL. drop=FALSE works great with 2-dimensional matrices, but with 3-dimensional matrices it doesn't work. If a=array(0,dim=c(1,2,4)), dim(a[,,1,drop=FALSE]) is c(1,2,1) instead of c(1,2) which is what you want if a[,,1] is what is going to appear in some matrix operation. This problem came up in the Kt[,,t] %*% innov[,t] line in MARSSkf. Normally Kt[,,t] is square and a square matrix or a scalar is returned, but if Kt[,,t] happened to be something like dim=c(1,3,20) then Kt[,,t] returned a VECTOR of length 3. In this case, Kt[, , t] %*% innov[, t] crashed the code. I had to use a kluge to force R to keep the dimensions after subscripting. This bug only occurred in models where Z is not a design matrix.summary(marssMLE object).MARSSoptions(). This allows you to change the defaults for the MARSS() function. See ?MARSSoptions.MARSSLLprofile(). This allows you to plot some basic log-likelihood profiles. See ?MARSSLLprofile.