change default behavior to include SDs for all variables (#12)

* Update vignette.Rmd

* changing default behavior ...

... to include SD for all variables in `tsdata` by default

* try again

* Update Date in DESCRIPTION

* adding test for adding variances

* adding expect_equal for new test

* strip the version from Matrix/TMB in DESCRIPTION

---------

Co-authored-by: Jim Thorson <James.T.Thorson@gmail.com>

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, dev]
 
 name: R-CMD-check
 
@@ -21,9 +21,21 @@ jobs:
         with:
           use-public-rspm: true
 
+      - name: Install dependencies Ubuntu
+        if: runner.os == 'Linux'
+        run: |
+          install.packages('remotes')
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("knitr")
+          remotes::install_cran("rmarkdown")
+          remotes::install_cran("rcmdcheck")
+          install.packages("Matrix", type = "source")
+          install.packages("TMB", type = "source")
+        shell: Rscript {0}
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - uses: r-lib/actions/check-r-package@v2
+      - uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, dev]
   release:
     types: [published]
   workflow_dispatch:
@@ -30,6 +30,18 @@ jobs:
         with:
           use-public-rspm: true
 
+      - name: Install dependencies Ubuntu
+        if: runner.os == 'Linux'
+        run: |
+          install.packages('remotes')
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("knitr")
+          remotes::install_cran("rmarkdown")
+          remotes::install_cran("rcmdcheck")
+          install.packages("Matrix", type = "source")
+          install.packages("TMB", type = "source")
+        shell: Rscript {0}
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::pkgdown, local::.

.github/workflows/test-coverage.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, test_codecov]
+    branches: [main, dev]
   pull_request:
-    branches: [main, master, test_codecov]
+    branches: [main, dev]
 
 name: test-coverage
 
@@ -21,6 +21,18 @@ jobs:
         with:
           use-public-rspm: true
 
+      - name: Install dependencies Ubuntu
+        if: runner.os == 'Linux'
+        run: |
+          install.packages('remotes')
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("knitr")
+          remotes::install_cran("rmarkdown")
+          remotes::install_cran("rcmdcheck")
+          install.packages("Matrix", type = "source")
+          install.packages("TMB", type = "source")
+        shell: Rscript {0}
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::covr

DESCRIPTION

@@ -2,16 +2,16 @@ Package: dsem
 Type: Package
 Title: Fit Dynamic Structural Equation Models
 Version: 1.0.2
-Date: 2024-01-17
+Date: 2024-02-01
 Authors@R: 
     c(person(given = "James",
              family = "Thorson",
              role = c("aut", "cre"),
              email = "James.Thorson@noaa.gov")
     )
 Imports:
-    TMB (>= 1.9.7),
-    Matrix (>= 1.6.3),
+    TMB,
+    Matrix,
     sem,
     igraph,
     methods

NEWS.md

@@ -2,6 +2,8 @@
 
 * Eliminate `eval` usage
 * Add codecov Action and badge
+* Change default behavior so that all variables in `tsdata` have a standard
+  deviation by default
 
 # dsem 1.0.1
 

R/dsem.R

@@ -122,6 +122,7 @@ function( sem,
   out = make_dsem_ram( sem,
                   times = as.numeric(time(tsdata)),
                   variables = colnames(tsdata),
+                  covs = colnames(tsdata),
                   quiet = control$quiet )
   ram = out$ram
 

R/make_dsem_ram.R

@@ -5,6 +5,7 @@
 #' @inheritParams dsem
 #' @param times A character vector listing the set of times in order
 #' @param variables A character vector listing the set of variables
+#' @param covs A character vector listing variables for which to estimate a standard deviation
 #' @param quiet Boolean indicating whether to print messages to terminal
 #' @param remove_na Boolean indicating whether to remove NA values from RAM (default) or not.
 #'            \code{remove_NA=FALSE} might be useful for exploration and diagnostics for
@@ -193,6 +194,7 @@ make_dsem_ram <-
 function( sem,
           times,
           variables,
+          covs = NULL,
           quiet = FALSE,
           remove_na = TRUE ){
   # Docs : https://roxygen2.r-lib.org/articles/formatting.html
@@ -284,24 +286,25 @@ function( sem,
   model$par[model$par == ""] <- NA
   model <- cbind( "path"=model$path, "lag"=model$lag, "name"=model$par, "start"=model$start)
 
-  #if( !is.null(covs) ){
-  #  for (cov in covs) {
-  #    vars <- strsplit(cov, "[ ,]+")[[1]]
-  #    nvar <- length(vars)
-  #    for (i in 1:nvar) {
-  #    for (j in i:nvar) {
-  #      p1 = paste(vars[i], "<->", vars[j])
-  #      p2 = if (i==j) paste("V[", vars[i], "]", sep = "") else paste("C[",vars[i], ",", vars[j], "]", sep = "")
-  #      p3 = NA
-  #      row <- c(p1, 0, p2, p3)
-  #      if( any((row[1]==model[,1]) & (row[2]==model[,2])) ){
-  #        next
-  #      }else{
-  #        model <- rbind(model, row, deparse.level = 0)
-  #      }
-  #    }}
-  #  }
-  #}
+  # Adding a SD automatically
+  if( !is.null(covs) ){
+    for (cov in covs) {
+      vars <- strsplit(cov, "[ ,]+")[[1]]
+      nvar <- length(vars)
+      for (i in 1:nvar) {
+      for (j in i:nvar) {
+        p1 = paste(vars[i], "<->", vars[j])
+        p2 = if (i==j) paste("V[", vars[i], "]", sep = "") else paste("C[",vars[i], ",", vars[j], "]", sep = "")
+        p3 = NA
+        row <- c(p1, 0, p2, p3)
+        if( any((row[1]==model[,1]) & (row[2]==model[,2])) ){
+          next
+        }else{
+          model <- rbind(model, row, deparse.level = 0)
+        }
+      }}
+    }
+  }
 
   exog.variances = endog.variances = TRUE
   model = add.variances()

scratch/Upload_to_CRAN.R

@@ -1,5 +1,4 @@
 
-root_dir = R'(C:\Users\James.Thorson\Desktop\Work files\Collaborations\2023 -- DSEM\CRAN submission)'
 
 library(devtools)
 setwd( R'(C:\Users\James.Thorson\Desktop\Git\dsem)' )
@@ -66,6 +65,7 @@ if( FALSE ){
 }
 
 # Build for uploading via web interface
+root_dir = R'(C:\Users\James.Thorson\Desktop\Git\dsem\scratch)'
 # https://cran.r-project.org/submit.html
 build( path=root_dir, manual=TRUE )
 

tests/testthat/test-platform.R

@@ -77,3 +77,21 @@ test_that("dsem example is working ", {
   residuals(fit1, type="response")
 })
 
+test_that("dsem adds variances ", {
+  data(isle_royale)
+  data = ts( log(isle_royale[,2:3]), start=1959)
+
+  sem = "
+    wolves <-> wolves, 0, sd1
+    moose <-> moose, 0, sd2
+  "
+  # initial first without delta0 (to improve starting values)
+  fit1 = dsem( sem = "",
+               tsdata = data )
+  # initial first without delta0 (to improve starting values)
+  fit2 = dsem( sem = sem,
+               tsdata = data )
+  # Check objective function
+  expect_equal( as.numeric(fit1$opt$obj), as.numeric(fit2$opt$obj), tolerance=1e-2 )
+})
+

vignettes/vignette.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Demonstration of selected features"
-author: "Anonymous"
+author: "James Thorson"
 output: rmarkdown::html_vignette
 #output: rmarkdown::pdf_document
 vignette: >
@@ -35,7 +35,7 @@ library(phylopath)
 
 We first demonstrate that `dsem` gives identical results to `dynlm` for a well-known econometric model, the Klein-1 model.
 
-```{r, echo=TRUE, message=FALSE, fig.width=7, fig.height=5}
+```{r, echo=TRUE, message=FALSE, fig.width=7, fig.height=7}
 data(KleinI, package="AER")
 TS = ts(data.frame(KleinI, "time"=time(KleinI) - 1931))
 
@@ -148,7 +148,7 @@ This dataset was previously analyzed by in Chapter 14 of the User Manual for the
 
 Here, we compare fits using `dsem` with `dynlm`, as well as a vector autoregressive model package `vars`, and finally with `MARSS`.
 
-```{r, echo=TRUE, message=FALSE, fig.width=7, fig.height=5}
+```{r, echo=TRUE, message=FALSE, fig.width=5, fig.height=7}
 data(isle_royale)
 data = ts( log(isle_royale[,2:3]), start=1959)
 
@@ -242,7 +242,7 @@ Results again show that `dsem` can estimate parameters for a vector autoregressi
 
 We next replicate an analysis involving climate, forage fishes, stomach contents, and recruitment of a predatory fish.
 
-```{r, echo=TRUE, message=FALSE, fig.width=7, fig.height=5}
+```{r, echo=TRUE, message=FALSE, fig.width=7, fig.height=7}
 data(bering_sea)
 Z = ts( bering_sea )
 family = rep('fixed', ncol(bering_sea))
@@ -277,7 +277,8 @@ fit = dsem( sem = sem,
             control = dsem_control(use_REML=FALSE, quiet=TRUE) )
 ParHat = fit$obj$env$parList()
 # summary( fit )
-
+```
+```{r, echo=TRUE, message=FALSE, fig.width=7, fig.height=7}
 # Timeseries plot
 oldpar <- par(no.readonly = TRUE)
 par( mfcol=c(3,3), mar=c(2,2,2,0), mgp=c(2,0.5,0), tck=-0.02 )
@@ -296,7 +297,8 @@ for(i in 1:ncol(bering_sea)){
            y=c(tmp[,3],rev(tmp[,4])), col=rgb(0,0,1,0.2), border=NA )
 }
 par(oldpar)
-
+```
+```{r, echo=TRUE, message=FALSE, fig.width=8, fig.height=8}
 #
 library(phylopath)
 library(ggplot2)
@@ -333,7 +335,7 @@ These results are further discussed in the paper describing dsem.
 
 Finally, we replicate an analysis involving a trophic cascade involving sea stars predators, sea urchin consumers, and kelp producers.
 
-```{r, echo=TRUE, message=FALSE, fig.width=7, fig.height=5}
+```{r, echo=TRUE, message=FALSE, fig.width=5, fig.height=7}
 data(sea_otter)
 Z = ts( sea_otter[,-1] )