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eguidotti · Sep 26, 2022 · 63d7603 · 63d7603
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,9 @@
 Package: calculus
 Type: Package
 Title: High Dimensional Numerical and Symbolic Calculus
-Version: 0.3.4
+Version: 1.0.0
 Authors@R: person(given = "Emanuele", family = "Guidotti", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-8961-6623"))
-Description: Efficient C++ optimized functions for numerical and symbolic calculus as described in Guidotti (2020) <arXiv:2101.00086>. It includes basic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, high-order derivatives, ordinary differential equations, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors. 
+Description: Efficient C++ optimized functions for numerical and symbolic calculus as described in Guidotti (2022) <doi:10.18637/jss.v104.i05>. It includes basic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, high-order derivatives, ordinary differential equations, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors. 
 License: GPL-3
 URL: https://calculus.guidotti.dev
 BugReports: https://github.com/eguidotti/calculus/issues

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# calculus 1.0.0
+
+- JSS publication
+
 # calculus 0.3.4
 
 - fix CRAN check

diff --git a/R/contraction.R b/R/contraction.R
@@ -35,7 +35,7 @@
 #' @family tensor algebra
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 

diff --git a/R/delta.R b/R/delta.R
@@ -17,7 +17,7 @@
 #' @family tensor algebra
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #'

diff --git a/R/derivative.R b/R/derivative.R
@@ -82,7 +82,7 @@
 #' @family differential operators
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 

diff --git a/R/einstein.R b/R/einstein.R
@@ -23,7 +23,7 @@
 #' @family tensor algebra
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 

diff --git a/R/epsilon.R b/R/epsilon.R
@@ -16,7 +16,7 @@
 #' @family tensor algebra
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #'

diff --git a/R/evaluate.R b/R/evaluate.R
@@ -38,7 +38,7 @@
 #' @family utilities
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 

diff --git a/R/hermite.R b/R/hermite.R
@@ -48,7 +48,7 @@
 #' @family polynomials
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 

diff --git a/R/integral.R b/R/integral.R
@@ -73,7 +73,7 @@
 #' @family integrals
 #'  
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #'      
 #' @export
 #' 

diff --git a/R/mxdet.R b/R/mxdet.R
@@ -18,7 +18,7 @@
 #' @family matrix algebra
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 

diff --git a/R/mxinv.R b/R/mxinv.R
@@ -18,7 +18,7 @@
 #' @family matrix algebra
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 

diff --git a/R/mxtr.R b/R/mxtr.R
@@ -18,7 +18,7 @@
 #' @family matrix algebra
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 

diff --git a/R/ode.R b/R/ode.R
@@ -80,7 +80,7 @@
 #' @family integrals
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 

diff --git a/R/operators.R b/R/operators.R
@@ -24,7 +24,7 @@
 #' @family basic arithmetic
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -74,7 +74,7 @@
 #' @family basic arithmetic
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -131,7 +131,7 @@
 #' @family basic arithmetic
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -188,7 +188,7 @@
 #' @family basic arithmetic
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -250,7 +250,7 @@
 #' @family matrix algebra
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -336,7 +336,7 @@ mx <- function(x, y){
 #' @family basic arithmetic
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -382,7 +382,7 @@ mx <- function(x, y){
 #' @family basic arithmetic
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -435,7 +435,7 @@ mx <- function(x, y){
 #' @family basic arithmetic
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -477,7 +477,7 @@ mx <- function(x, y){
 #' @family basic arithmetic
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -518,7 +518,7 @@ mx <- function(x, y){
 #' @family vector algebra
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -622,7 +622,7 @@ cross <- function(...){
 #' @family differential operators
 #'
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #'      
 #' @export
 #' 
@@ -717,7 +717,7 @@ gradient <- function(f, var, params = list(), coordinates = 'cartesian', accurac
 #' @family differential operators
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -793,7 +793,7 @@ jacobian <- function(f, var, params = list(), coordinates = 'cartesian', accurac
 #' @family differential operators
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -910,7 +910,7 @@ hessian <- function(f, var, params = list(), accuracy = 4, stepsize = NULL, drop
 #' @family differential operators
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -1085,7 +1085,7 @@ divergence <- function(f, var, params = list(), coordinates = 'cartesian', accur
 #' @family differential operators
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #'
@@ -1244,7 +1244,7 @@ curl <- function(f, var, params = list(), coordinates = 'cartesian', accuracy =
 #' @family differential operators
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 

diff --git a/R/partitions.R b/R/partitions.R
@@ -37,7 +37,7 @@
 #' partitions(3, equal = FALSE, length = 2, fill = TRUE, perm = TRUE) 
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 

diff --git a/R/taylor.R b/R/taylor.R
@@ -40,7 +40,7 @@
 #' @family derivatives
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #'    
 #' @export
 #' 

diff --git a/R/utils.R b/R/utils.R
@@ -22,7 +22,7 @@
 #' @family utilities
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -53,7 +53,7 @@ wrap <- function(x){
 #' @family utilities
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -88,7 +88,7 @@ e2c <- function(x){
 #' @family utilities
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -125,7 +125,7 @@ c2e <- function(x){
 #' @family tensor algebra
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 
@@ -182,7 +182,7 @@ index <- function(x){
 #' @family tensor algebra
 #' 
 #' @references 
-#' Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". \url{https://arxiv.org/abs/2101.00086}
+#' Guidotti E (2022). "calculus: High-Dimensional Numerical and Symbolic Calculus in R." Journal of Statistical Software, 104(5), 1-37. \doi{10.18637/jss.v104.i05}
 #' 
 #' @export
 #' 

diff --git a/README.md b/README.md
@@ -43,19 +43,20 @@ Several [unit tests](https://github.com/eguidotti/calculus/tree/master/tests/tes
 
 ## Cite as
 
-*Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". https://arxiv.org/abs/2101.00086*
+Guidotti E (2022). “calculus: High-Dimensional Numerical and Symbolic Calculus in R.” _Journal of Statistical Software_, *104*(5), 1-37. [doi:10.18637/jss.v104.i05](https://doi.org/10.18637/jss.v104.i05)
 
 A BibTeX entry for LaTeX users is
 
-```latex
-@Misc{,
-    title = {calculus: High Dimensional Numerical and Symbolic Calculus in R},
-    author = {Emanuele Guidotti},
-    year = {2020},
-    eprint = {2101.00086},
-    archiveprefix = {arXiv},
-    primaryclass = {cs.MS},
-    url = {https://arxiv.org/abs/2101.00086}
+```bibtex
+@Article{,
+  title = {{calculus}: High-Dimensional Numerical and Symbolic Calculus in {R}},
+  author = {Emanuele Guidotti},
+  journal = {Journal of Statistical Software},
+  year = {2022},
+  volume = {104},
+  number = {5},
+  pages = {1--37},
+  doi = {10.18637/jss.v104.i05},
 }
 ```
 
diff --git a/inst/CITATION b/inst/CITATION
@@ -1,12 +1,13 @@
-bibentry(
-	bibtype = "Misc",
-	header = "Cite as:",
-	title = "calculus: High Dimensional Numerical and Symbolic Calculus in R",
-	author = "Emanuele Guidotti",
-	year = "2020",
-	eprint = "2101.00086",
-	archivePrefix = "arXiv",
-	primaryClass = "cs.MS",
-	url = "https://arxiv.org/abs/2101.00086",
-	textVersion = 'Guidotti, E. (2020). "calculus: High dimensional numerical and symbolic calculus in R". https://arxiv.org/abs/2101.00086'
+bibentry(bibtype = "Article",
+  title        = "{calculus}: High-Dimensional Numerical and Symbolic Calculus in {R}",
+  author       = person(given = "Emanuele",
+                        family = "Guidotti",
+                        email = "[email protected]"),
+  journal      = "Journal of Statistical Software",
+  year         = "2022",
+  volume       = "104",
+  number       = "5",
+  pages        = "1--37",
+  doi          = "10.18637/jss.v104.i05",
+  header       = "To cite calculus in publications use:"
 )
diff --git a/man/c2e.Rd b/man/c2e.Rd