Clean up items involving matrix exp.

Rename miscAlgorithm.r to .R.

Author: paciorek

UserManual/src/tables/functionTableMatrixLong.md

@@ -23,3 +23,5 @@ provided in NIMBLE.
   `pmin(x, y), pmax(x,y)` vector of mins (maxs) of elements of                                        yes
                           `x` and `y`
   `interp.lin(x, v1, v2)` linear interpolation                                                        no
+  `expm(A)`               matrix exponential                         $e^A$; $A$ non-negative diags    yes
+  `expAv(A,v)`            matrix exponential multiplied by vector    $e^A v$; $A$ non-neg. diags      yes

packages/nimble/DESCRIPTION

@@ -30,7 +30,7 @@ Authors@R: c(
     person("Wei", "Zhang", role = "aut", comment = "Laplace approximation"),
     person("Sally", "Paganin", role = "aut", comment = "reversible jump MCMC"),
     person("Joshua", "Hug", role = "aut", comment = "WAIC"),
-    person("Paul", "van Dam-Bates", role = "aut", comment = "P\u00f3lya-Gamma sampler, nimIntegrate"),
+    person("Paul", "van Dam-Bates", role = "aut", comment = "P\u00f3lya-Gamma sampler, nimIntegrate, matrix exponential"),
     person("Jagadish", "Babu", role = "ctb", comment = "code for the compilation system for an early version of NIMBLE"),
     person("Lauren", "Ponisio", role = "ctb", comment = "contributions to the cross-validation code"),
     person("Peter", "Sujan", role = "ctb", comment = "multivariate t distribution code")
@@ -150,5 +150,6 @@ Collate:
     registration.R
     nimble-package.r
     QuadratureGrids.R
+    miscAlgorithms.R
     zzz.R
 RoxygenNote: 7.3.2

packages/nimble/R/miscAlgorithms.r packages/nimble/R/miscAlgorithms.Rpackages/nimble/R/miscAlgorithms.r renamed to packages/nimble/R/miscAlgorithms.R

@@ -29,10 +29,10 @@ spectrumBound <- nimbleFunction(
     Min <- Inf
     Max <- -Inf
     for( i in 1:q[1] ){
-      centre <- A[i,i]
-      radius <- sum(abs(A[i,])) - abs(centre)
-      minC <- centre - radius
-      maxC <- centre + radius
+      center <- A[i,i]
+      radius <- sum(abs(A[i,])) - abs(center)
+      minC <- center - radius
+      maxC <- center + radius
       if(minC < Min) Min <- minC
       if(maxC > Max) Max <- maxC
     }
@@ -94,7 +94,7 @@ expAv <- nimbleFunction(
     if(q[2] != q[1])      stop("A must be a square matrix.")
     if(length(v) != q[1]) stop("Length of v must be equal to the number of columns of A.")
 
-    ## Only centre, perform uniformization, if no diag > 0.
+    ## Only center, perform uniformization, if no diag > 0.
     CR <- spectrumBound(A)
     diag(A) <- diag(A) - CR[1]
     ans <- v
@@ -209,7 +209,7 @@ expm <- nimbleFunction(
     if(dim(A)[1] != dim(A)[2]) stop("`A' must be a square matrix")
     # if(dim(tol)[1] > 1)  stop("`tol' must be a scalar.")
 
-    ## Only centre, perform uniformization, if no diag > 0.
+    ## Only center, perform uniformization, if no diag > 0.
     CR <- spectrumBound(A)
     Niter <- 1L
     C <- CR[1]
@@ -249,5 +249,5 @@ expm <- nimbleFunction(
 
     for( i in 1:s ) expMsmall <- expMsmall %*% expMsmall
     return(expMsmall)
-  }#, buildDerivs = TRUE
+  } #, buildDerivs = TRUE
 )