Merge pull request #185 from atsa-es/v3-11-7

V3 11 7 (close) to final changes

Author: eeholmes

.Rbuildignore

@@ -4,32 +4,31 @@
 .Rhistory
 .RData
 .gitignore
-.github
-logo.jpg
-logot.png
+^\.github$
+
+License.md
+tests
+
 hexlogo.png
 mars.png
 favicon.ico
 _config.yml
 _layouts
-License.md
-vignettes/cbe.bst
-vignettes/footmisc.sty
-vignettes/hanging.sty
-vignettes/svmono.cls
-vignettes/versiontest.R
-vignettes/debugger_template.Rnw
-vignettes/debug_manual.R
-tests
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
-^\.github$
+Rplots.*
+
 ^inst/oldtex$
 ^inst/userguide$
 ^inst/derivations$
 ^inst/testing-releases$
-inst/doc/mathdefs.tex
+^inst/Makedoc
+^inst/Makerelease
+^inst/DEVELOPER_NOTES.*
+^inst/Makefile
+
 ^revdep$
 ^cran-comments.md$
-^inst/doc/UserGuide-static\.pdf$
+^doc$
+^Meta$

.gitignore

@@ -10,3 +10,5 @@ tests/testthat/dontruntests/*.*
 inst/.DS_Store
 
 docs
+/doc/
+/Meta/

NEWS.md

@@ -4,19 +4,28 @@ output: html_document
 
 # MARSS 3.11.7 (GitHub)
 
-This release is focused on moving the MARSS User Guide into a separate repository. This will facilitate updating MARSS and converting the User Guide to an eBook.
+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.
 
-* Deleted the `inst/doc` folder
 * Added pkgdown. Note this required special files for MathJax in the `pkgdown` folder.
 * Removed packages in `Suggests:` that were associated with the User Guide and tests and not used in examples.
-* Converted `Quick_Start.Rnw` and `Residuals.Rnw` to Rmd so it works better with pkgdown.
+* Converted `Quick_Start.Rnw` to Rmd so it works better with pkgdown and renders to html for CRAN.
 * Updated DESCRIPTION and README to refer to marssTMB.
 * Added marssTMB to Suggests with `Additional_repositories: https://atsa-es.r-universe.dev`
 
-
 ## BUGS
 
 * In `predict_marssMLE()`, the newdata model.tsp was not being set.
+* In `plot.marssMLE()`, the CIs for the state residuals did not plot correctly because there is always a NA at the end.
+* In `autoplot.marssMLE(), two plots would always be plotted if one plot type was specified.
+
+## DOCUMENTATION
+
+* Added `vignettes/Learning_MARSS.Rmd`
+* Fixed various equation formatting typos (unbolded x's and x's that should have been X's in expectations).
+* Added `MARSS.dfa()` to the manual built by CRAN by removing keyword internal.
+* Added `inst/DEVELOPER_NOTES.md`
+* Minor change to make the v and w in `EMDerivation.Rnw` in slant font as they are random variables.
+
 
 # MARSS 3.11.6 (GitHub)
 
@@ -26,7 +35,7 @@ This release is focused on adding new method `method="TMB"` which uses the packa
 * Added the generic function `MARSSfit()` and methods for "kem" and "BFGS".
 * Added the defaults to `R/onLoad.R` and made it easier to specify new methods and constraints on methods
 * Made changes to `checkMARSSinputs.R`, `is_marssMLE.R` and `is.validvarcov()` so they are not so specific to `method="BFGS"` but work for any methods with similar constraints.
-* Export MARSSvectorizeparam(). Need when writing methods for MARSSfit() generic.
+* Export `MARSSvectorizeparam()`. Need when writing methods for `MARSSfit()` generic.
 * Added {generics} as a dependency and removed {forecast} and {broom} from Suggests. Cleaned up examples and text throughout to remove references to these packages.
 
 ## BUGS
@@ -110,7 +119,7 @@ This is an update based on version 3.11.2 (GitHub release). It is mainly focused
 * Added notation definitions to the Kalman smoother algorithm section for `xtt` and `xtt1` etc.
 * Added information on how to get CIs on rotated loadings to DFA chapter.
 * Cleaned up MARSSkf.Rd sections on initial conditions and cleaned up equation formatting so looks better in pdf format.
-* Added section on normalization calculations to Residuals.Rnw.
+* Added section on normalization calculations to `Residuals.Rnw`.
 * Cleaned up notation for conditional expectations in the man files.
 * Fixed bug in the Covariates chapter which was not showing the B estimates for `kem.plank.4`.
 

R/autoplot_marssMLE.R

@@ -172,7 +172,7 @@ autoplot.marssMLE <-
       }
       plts[[i]] <- p1
       if (length(plot.type) == 1) {
-        invisible(plts)
+        return(plts[[1]])
       }
     }
 
@@ -246,7 +246,7 @@ autoplot.marssMLE <-
       }
       plts[[i]] <- p1
       if (length(plot.type) == 1) {
-        invisible(plts)
+        return(plts[[1]])
       }
     }
 
@@ -292,7 +292,7 @@ autoplot.marssMLE <-
       }
       plts[[i]] <- p1
       if (length(plot.type) == 1) {
-        invisible(plts)
+        return(plts[[1]])
       }
     }
 
@@ -355,7 +355,7 @@ autoplot.marssMLE <-
       }
       plts[[i]] <- p1
       if (length(plot.type) == 1) {
-        invisible(plts)
+        return(plts[[1]])
       }
     }
 
@@ -393,6 +393,7 @@ autoplot.marssMLE <-
       if (conf.int) {
         if (grepl("std", i)) {
           df$sigma <- 1
+          df$sigma[is.na(df$value)] <- 0
         } else {
           df$sigma <- df$.sigma
           df$sigma[is.na(df$value)] <- 0 # will never be the case for x so not really needed here
@@ -416,7 +417,7 @@ autoplot.marssMLE <-
       }
       plts[[i]] <- p1
       if (length(plot.type) == 1) {
-        invisible(plts)
+        return(plts[[1]])
       }
     }
 
@@ -489,9 +490,7 @@ autoplot.marssMLE <-
         p1 <- p1 + ggplot2::labs(caption = paste0(strwrap(note), collapse = "\n")) + ggplot2::theme(plot.caption = ggplot2::element_text(size = 7.5, hjust = 0))
       }
       plts[[i]] <- p1
-      if (length(plot.type) == 1) {
-        invisible(plts)
-      }
+      if (length(plot.type) == 1) return(plts[[1]])
     }
 
     # ACF plots
@@ -574,9 +573,7 @@ autoplot.marssMLE <-
         p1 <- p1 + ggplot2::labs(caption = paste0(strwrap(note), collapse = "\n")) + ggplot2::theme(plot.caption = ggplot2::element_text(size = 7.5, hjust = 0))
       }
       plts[[i]] <- p1
-      if (length(plot.type) == 1) {
-        invisible(plts)
-      }
+      if (length(plot.type) == 1) return(plts[[1]])
     }
 
     for (i in names(plts)) {
@@ -595,6 +592,5 @@ autoplot.marssMLE <-
         if (!silent) cat("Finished plots.\n")
       }
     }
-
-    invisible(plts)
+    if(silent) invisible(plts)
   }

R/plot_marssMLE.R

@@ -228,6 +228,7 @@ plot.marssMLE <-
       # need to adjust sigma for making a polygon
       if (grepl("std", i)) {
         df$.sigma <- 1
+        df$.sigma[is.na(df$value)] <- 0
       } else {
         df$.sigma[is.na(df$value)] <- 0
       }
@@ -251,7 +252,9 @@ plot.marssMLE <-
             cex = plotpar$point.size
           )
           if (conf.int) {
-            polygon(c(t, rev(t)), c(ymin, rev(ymax)), col = plotpar$ci.col, border = plotpar$ci.border, lwd = plotpar$ci.lwd, lty = plotpar$ci.lty)
+            df2 <- data.frame(x=c(t, rev(t)), y=c(ymin, rev(ymax)))
+            df2 <- na.omit(df2)
+            polygon(df2$x, df2$y, col = plotpar$ci.col, border = plotpar$ci.border, lwd = plotpar$ci.lwd, lty = plotpar$ci.lty)
             points(t, .resids, col = plotpar$point.col, pch = plotpar$point.pch, cex = plotpar$point.size)
           }
           title(plt)

README.md

@@ -2,9 +2,9 @@
 
 MARSS stands for Multivariate Auto-Regressive(1) State-Space. The MARSS R package estimates the parameters of linear MARSS models with Gaussian errors.  This class of model is extremely important in the study of linear stochastic dynamical systems, and these models are important in many different fields, including economics, engineering, genetics, physics and ecology.  The model class has different names in different fields, for example in some fields they are termed dynamic linear models (DLMs) or vector autoregressive (VAR) state-space models.  The MARSS package allows you to easily fit time-varying constrained and unconstrained MARSS models with or without covariates via maximum-likelihood using an EM algorithm or BFGS. Fast fitting with TMB is available with the companion package [marssTMB](https://atsa-es.github.io/marssTMB/).
 
-[![cran version](http://www.r-pkg.org/badges/version/MARSS)](https://cran.r-project.org/package=MARSS)
+[![cran version](https://www.r-pkg.org/badges/version/MARSS)](https://cran.r-project.org/package=MARSS)
 [![github](https://img.shields.io/github/v/release/atsa-es/MARSS?color=brightgreen&label=GitHub)](https://github.com/atsa-es/MARSS/releases/latest)
-[![rstudio mirror downloads](http://cranlogs.r-pkg.org/badges/grand-total/MARSS?)](https://github.com/r-hub/cranlogs.app)
+[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/grand-total/MARSS?)](https://github.com/r-hub/cranlogs.app)
 [![](https://cranlogs.r-pkg.org/badges/MARSS?color=FFD700)](https://www.r-pkg.org/pkg/MARSS)
 [![License: CC0-1.0](https://img.shields.io/badge/License-CC0%201.0-lightgrey.svg)](https://creativecommons.org/publicdomain/zero/1.0/)
 
@@ -69,6 +69,9 @@ Type `citation("MARSS")` at the command line to get the most up to data citation
 
 To see our publications using MARSS models, see the [Applied Time Series Analysis website](https://atsa-es.github.io/).
 
+### Developers
+
+See `inst/DEVELOPER_NOTES.md` for instructions on creating a release from the repository.
 
 ### NOAA Disclaimer