Merge branch 'develop' of https://github.com/rjdverse/rjd3toolkit int…

…o develop

# Conflicts:
#	.gitignore
#	R/modellingcontext.R
#	README.Rmd
#	README.md
#	man/modelling_context.Rd

.Rbuildignore

@@ -17,4 +17,4 @@ TO_DO
 ^\.github$
 .DS_Store
 ^reconf\.sh$
-^rjd3toolkit-java-deps\.xml$
+^pom\.xml$

.gitignore

@@ -1,7 +1,58 @@
-.Rproj.user
+# History files
 .Rhistory
+.Rapp.history
+
+# Session Data files
 .RData
+.RDataTmp
+
+# User-specific files
 .Ruserdata
 
-TO_DO
-docs
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+Meta/
+inst/doc/
+doc/
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/
+
+# Hidden file from mac-os
+.DS_Store
+
+# produced README.html
+README.html

.lintr

@@ -1,9 +1,6 @@
 linters: linters_with_defaults(
         indentation_linter = NULL,
-        trailing_blank_lines_linter = NULL,
-        trailing_whitespace_linter = NULL,
         assignment_linter = NULL,
-        whitespace_linter = NULL,
         brace_linter = NULL,
         infix_spaces_linter = NULL,
         paren_body_linter = NULL,
@@ -12,9 +9,8 @@ linters: linters_with_defaults(
         spaces_left_parentheses_linter = NULL,
         commas_linter = NULL,
         quotes_linter = NULL,
-        spaces_inside_linter = NULL,
-        vector_logic_linter = NULL,
-        seq_linter = NULL,
+        #spaces_inside_linter = NULL,
+        #vector_logic_linter = NULL,
         object_length_linter = NULL,
         semicolon_linter = NULL,
         cyclocomp_linter = NULL,

R/arima.R

@@ -16,7 +16,7 @@ NULL
 #' @return A `"JD3_SARIMA"` model.
 #' @export
 sarima_model<-function(name="sarima", period, phi=NULL, d=0, theta=NULL, bphi=NULL, bd=0, btheta=NULL){
-  return (structure(
+  return(structure(
     list(name = name, period = period, phi = phi, d = d, theta = theta,
                          bphi = bphi, bd = bd, btheta = btheta), class="JD3_SARIMA"))
 }
@@ -35,7 +35,7 @@ sarima_properties<-function(model, nspectrum=601, nacf=36){
   jmodel<-.r2jd_sarima(model)
   spectrum<-.jcall("jdplus/toolkit/base/r/arima/SarimaModels", "[D", "spectrum", jmodel, as.integer(nspectrum))
   acf<-.jcall("jdplus/toolkit/base/r/arima/SarimaModels", "[D", "acf", jmodel, as.integer(nacf))
-  return (list(acf=acf, spectrum=spectrum))
+  return(list(acf=acf, spectrum=spectrum))
 }
 
 
@@ -58,7 +58,7 @@ sarima_properties<-function(model, nspectrum=601, nacf=36){
 sarima_random<-function(model, length, stde=1, tdegree=0, seed=-1){
   if (!inherits(model, "JD3_SARIMA"))
     stop("Invalid model")
-  return (.jcall("jdplus/toolkit/base/r/arima/SarimaModels", "[D", "random",
+  return(.jcall("jdplus/toolkit/base/r/arima/SarimaModels", "[D", "random",
          as.integer(length),
          as.integer(model$period),
          .jarray(as.numeric(model$phi)),
@@ -91,8 +91,8 @@ sarima_decompose<-function(model, rmod=0, epsphi=0){
   jmodel<-.r2jd_sarima(model)
   jucm<-.jcall("jdplus/toolkit/base/r/arima/UcarimaModels", "Ljdplus/toolkit/base/core/ucarima/UcarimaModel;", "decompose",
          jmodel, as.numeric(rmod), as.numeric(epsphi))
-  if (is.jnull(jucm)) return (NULL)
-  return (.jd2r_ucarima(jucm))
+  if (is.jnull(jucm)) return(NULL)
+  return(.jd2r_ucarima(jucm))
 
 }
 
@@ -109,25 +109,25 @@ sarima_decompose<-function(model, rmod=0, epsphi=0){
 #'
 #' @examples
 arima_model<-function(name="arima", ar=1, delta=1, ma=1, variance=1){
-  return (structure(list(name=name, ar=ar, delta=delta, ma=ma, var=variance), class="JD3_ARIMA"))
+  return(structure(list(name=name, ar=ar, delta=delta, ma=ma, var=variance), class="JD3_ARIMA"))
 }
 
 .jd2r_doubleseq<-function(jobj, jprop){
   jseq<-.jcall(jobj, "Ljdplus/toolkit/base/api/data/DoubleSeq;", jprop)
-  return (.jcall(jseq, "[D", "toArray"))
+  return(.jcall(jseq, "[D", "toArray"))
 }
 
 
 .jd2r_sarima<-function(jsarima){
   q<-.jcall("jdplus/toolkit/base/r/arima/SarimaModels", "[B", "toBuffer", jsarima)
   rq<-RProtoBuf::read(modelling.SarimaModel, q)
-  return (.p2r_sarima(rq))
+  return(.p2r_sarima(rq))
 }
 
 #' @export
 #' @rdname jd3_utilities
 .r2jd_sarima<-function(model){
-  return (.jcall("jdplus/toolkit/base/r/arima/SarimaModels", "Ljdplus/toolkit/base/core/sarima/SarimaModel;", "of",
+  return(.jcall("jdplus/toolkit/base/r/arima/SarimaModels", "Ljdplus/toolkit/base/core/sarima/SarimaModel;", "of",
                  as.integer(model$period),
                  .jarray(as.numeric(model$phi)),
                  as.integer(model$d),
@@ -142,11 +142,11 @@ arima_model<-function(name="arima", ar=1, delta=1, ma=1, variance=1){
 .jd2r_arima<-function(jarima){
   q<-.jcall("jdplus/toolkit/base/r/arima/ArimaModels", "[B", "toBuffer", jarima)
   rq<-RProtoBuf::read(modelling.ArimaModel, q)
-  return (.p2r_arima(rq))
+  return(.p2r_arima(rq))
 }
 
 .r2jd_arima<-function(model){
-  return (.jcall("jdplus/toolkit/base/r/arima/ArimaModels", "Ljdplus/toolkit/base/core/arima/ArimaModel;", "of",
+  return(.jcall("jdplus/toolkit/base/r/arima/ArimaModels", "Ljdplus/toolkit/base/core/arima/ArimaModel;", "of",
                  .jarray(as.numeric(model$ar)),
                  .jarray(as.numeric(model$delta)),
                  .jarray(as.numeric(model$ma)),
@@ -176,13 +176,13 @@ arima_model<-function(name="arima", ar=1, delta=1, ma=1, variance=1){
 #' @export
 arima_sum<-function(...){
   components<-list(...)
-  return (arima_lsum(components))
+  return(arima_lsum(components))
 }
 
 arima_lsum<-function(components){
   q<-.jarray(lapply(components, .r2jd_arima), "jdplus/toolkit/base/core/arima/ArimaModel")
   jsum<-.jcall("jdplus/toolkit/base/r/arima/ArimaModels", "Ljdplus/toolkit/base/core/arima/ArimaModel;", "sum", q)
-  return (.jd2r_arima(jsum))
+  return(.jd2r_arima(jsum))
 }
 
 #' Remove an arima model from an existing one
@@ -205,7 +205,7 @@ arima_difference<-function(left, right, simplify=TRUE){
   jleft<-.r2jd_arima(left)
   jright<-.r2jd_arima(right)
   jdiff<-.jcall(jleft, "Ljdplus/toolkit/base/core/arima/ArimaModel;", "minus", jright, as.logical(simplify))
-  return (.jd2r_arima(jdiff))
+  return(.jd2r_arima(jdiff))
 }
 
 
@@ -223,7 +223,7 @@ arima_properties<-function(model, nspectrum=601, nacf=36){
   jmodel<-.r2jd_arima(model)
   spectrum<-.jcall("jdplus/toolkit/base/r/arima/ArimaModels", "[D", "spectrum", jmodel, as.integer(nspectrum))
   acf<-.jcall("jdplus/toolkit/base/r/arima/ArimaModels", "[D", "acf", jmodel, as.integer(nacf))
-  return (list(acf=acf, spectrum=spectrum))
+  return(list(acf=acf, spectrum=spectrum))
 }
 
 #' Title
@@ -242,24 +242,24 @@ ucarima_model<-function(model=NULL, components, complements=NULL, checkmodel=FAL
   else if (! is(model, "JD3_ARIMA") && ! is(model, "JD3_SARIMA")) stop("Invalid model")
 
   # TODO: checkmodel
-  return (structure(list(model=model, components=components, complements=complements), class="JD3_UCARIMA"))
+  return(structure(list(model=model, components=components, complements=complements), class="JD3_UCARIMA"))
 }
 
 .r2jd_ucarima<-function(ucm){
   jmodel<-.r2jd_arima(ucm$model)
   jcmps<-.jarray(lapply(ucm$components, .r2jd_arima), "jdplus/toolkit/base/core/arima/ArimaModel")
-  return (.jcall("jdplus/toolkit/base/r/arima/UcarimaModels", "Ljdplus/toolkit/base/core/ucarima/UcarimaModel;", "of", jmodel, jcmps))
+  return(.jcall("jdplus/toolkit/base/r/arima/UcarimaModels", "Ljdplus/toolkit/base/core/ucarima/UcarimaModel;", "of", jmodel, jcmps))
 }
 
 #' @export
 #' @rdname jd3_utilities
 .jd2r_ucarima<-function(jucm){
 #  model<-.jcall(jucm, "Ljdplus/toolkit/base/core/arima/ArimaModel;", "sum")
 #  jcmps<-.jcall(jucm, "[Ljdplus/toolkit/base/core/arima/ArimaModel;", "getComponents")
-#  return (ucarima_model(.jd2r_arima(model), lapply(jcmps, .jd2r_arima)))
+#  return(ucarima_model(.jd2r_arima(model), lapply(jcmps, .jd2r_arima)))
   q<-.jcall("jdplus/toolkit/base/r/arima/UcarimaModels", "[B", "toBuffer", jucm)
   rq<-RProtoBuf::read(modelling.UcarimaModel, q)
-  return (.p2r_ucarima(rq))
+  return(.p2r_ucarima(rq))
 }
 
 
@@ -284,7 +284,7 @@ ucarima_wk<-function(ucm, cmp, signal=TRUE, nspectrum=601, nwk=300){
   wk<-.jcall("jdplus/toolkit/base/r/arima/UcarimaModels", "[D", "filter", jwk, as.integer(nwk))
   gain<-.jcall("jdplus/toolkit/base/r/arima/UcarimaModels", "[D", "gain", jwk, as.integer(nspectrum))
 
-  return (structure(list(spectrum=spectrum, filter=wk, gain2=gain*gain), class="JD3_UCARIMA_WK"))
+  return(structure(list(spectrum=spectrum, filter=wk, gain2=gain*gain), class="JD3_UCARIMA_WK"))
 }
 
 #' Title
@@ -300,7 +300,7 @@ ucarima_canonical<-function(ucm, cmp=0, adjust=TRUE){
   jucm<-.r2jd_ucarima(ucm)
   jnucm<-.jcall("jdplus/toolkit/base/r/arima/UcarimaModels", "Ljdplus/toolkit/base/core/ucarima/UcarimaModel;", "doCanonical",
                jucm, as.integer(cmp-1), as.logical(adjust))
-  return (.jd2r_ucarima(jnucm))
+  return(.jd2r_ucarima(jnucm))
 }
 
 #' Estimate UCARIMA Model
@@ -317,7 +317,7 @@ ucarima_estimate<-function(x, ucm, stdev=TRUE){
   jucm<-.r2jd_ucarima(ucm)
   jcmps<-.jcall("jdplus/toolkit/base/r/arima/UcarimaModels", "Ljdplus/toolkit/base/api/math/matrices/Matrix;", "estimate",
                 as.numeric(x), jucm, as.logical(stdev))
-  return (.jd2r_matrix(jcmps))
+  return(.jd2r_matrix(jcmps))
 }
 
 #' Estimate SARIMA Model
@@ -373,7 +373,7 @@ sarima_estimate<-function(x, order=c(0,0,0), seasonal = list(order=c(0,0,0), per
                                  sprintf("btheta(%i)", seq_len(seasonal$order[3])))
   res$orders <- list(order = order, seasonal = seasonal)
   class(res) <- c("JD3_SARIMA_ESTIMATE", "JD3_REGARIMA_RSLTS")
-  return (res)
+  return(res)
 }
 
 #' Title
@@ -402,5 +402,5 @@ sarima_hannan_rissanen<-function(x, order=c(0,0,0), seasonal = list(order=c(0,0,
     seasonal$period <- frequency(x)
   jmodel<-.jcall("jdplus/toolkit/base/r/arima/SarimaModels", "Ljdplus/toolkit/base/core/sarima/SarimaModel;", "hannanRissanen",
                  as.numeric(x), as.integer(order), as.integer(seasonal$period), as.integer(seasonal$order), as.character(initialization), as.logical(biasCorrection), as.logical(finalCorrection))
-  return (.jd2r_sarima(jmodel))
+  return(.jd2r_sarima(jmodel))
 }