7.2

.gitignore

@@ -48,7 +48,15 @@ po/*~
 # RStudio Connect folder
 rsconnect/
 
+# compiled files
+*.o
+*.so
+*.mod
 
-*.html
 
+*.html
+QuartoBook/_book/*
+QuartoBook/fortran/*
+QuartoBook/*.png
+toc_*
 AquaFortR.Rproj

QuartoBook/_quarto.yml

@@ -3,11 +3,13 @@ project:
 
 book:
   title: "QuartoBook"
-  author: "Norah Jones"
+  author: "Ahmed Homoudi"
   date: "16/08/2023"
   chapters:
     - index.qmd
     - intro.qmd
+    - scripts.qmd
+    - package.qmd
     - summary.qmd
     - references.qmd
 
@@ -16,8 +18,10 @@ bibliography: references.bib
 format:
   html:
     theme: cosmo
+    code-fold: true
   pdf:
     documentclass: scrreprt
+    toc-depth: 2
 
 
 

QuartoBook/index.qmd

@@ -1,9 +1,8 @@
 # Preface {.unnumbered}
 
-This is a Quarto book.
 
-To learn more about Quarto books visit <https://quarto.org/docs/books>.
+## Acknowledgement {.unnumbered}
+This work has been funded by the German Research Foundation (DFG) through the project NFDI4Earth (DFG project no. 460036893, <https://www.nfdi4earth.de/>) within the German National Research Data Infrastructure (NFDI, <https://www.nfdi.de/>).
 
-```{r}
-1 + 1
-```
+## License {.unnumbered}
+This book is licensed under the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) License (<https://creativecommons.org/licenses/by-nc/4.0/>).

QuartoBook/intro.qmd

@@ -1,9 +1,12 @@
 # Introduction
 
-This is a book created from markdown and executable code.
+This chapter briefly introduces the R programming language and how to install R on different operating systems. Furthermore, we will have a look at the installation of RStudio. Finally, we will learn briefly about Fortran. 
 
-See @knuth84 for additional discussion of literate programming.
+The book is designed to cater to individuals with a foundational understanding of programming, irrespective of their familiarity with a specific programming language.
 
-```{r}
-1 + 1
-```
+## R Programming lanaguage 
+## Installing R 
+## Installing Rstudio
+## Fortran 
+
+@intro2rbook

QuartoBook/package.qmd

@@ -0,0 +1,10 @@
+# Accelerate R Packages with Fortran
+
+This chapter will focus on wrapping the developed routines from the previous chapter in an R package.
+
+## Brief Introduction to R Packages
+
+## Developing AquaFortR Package 
+```{r}
+1 + 1
+```

QuartoBook/references.bib

@@ -16,4 +16,11 @@ @article{knuth84
   numpages = {15}
 }
 
-
+@online{intro2rbook,
+  author = {Alex Douglas, Deon Roos, Francesca Mancini, Ana Couto, David Lusseau},
+  title = {{An Introduction to R}},
+  year = 2023,
+  month = 09,
+  url = {https://intro2r.com/},
+  urldate = {2024-01-08}
+}

QuartoBook/summary.qmd

@@ -5,3 +5,15 @@ In summary, this book has no content whatsoever.
 ```{r}
 1 + 1
 ```
+
+Some issues on memory allocation https://masuday.github.io/fortran_tutorial/r.html
+
+OpenMP support https://cran.r-project.org/doc/manuals/R-exts.html#OpenMP-support
+
+using FFTW library
+
+The Need for Speed Part 1: Building an R Package with Fortran (or C) https://www.r-bloggers.com/2018/12/the-need-for-speed-part-1-building-an-r-package-with-fortran-or-c/
+
+Advanced R by Hadley Wickham R’s C interface
+
+Conv and Xcorr shapes https://cran.r-project.org/web/packages/gsignal/gsignal.pdf

README.md

@@ -12,18 +12,15 @@ The repository is structured as follows:
  - RPackage  
  - SwirlCourse
 
+The documentation of the project is rendered [here](https://ahomoudi.github.io/AquaFortR/)
 
+## Installation 
 
+To install the AquaFortR package, please use: 
 
-
-
-
-
-## Documentation
-
-The documentation is of the project is rendered [here](https://ahomoudi.github.io/AquaFortR/)
-
-
+```r
+remotes::install_github("AHomoudi/AquaFortR", subdir = "RPackage")
+```
 ## Acknowledgment
 
 This work has been funded by the German Research Foundation (DFG) through the project NFDI4Earth (DFG project no. 460036893, https://www.nfdi4earth.de/) within the German National Research Data Infrastructure (NFDI, https://www.nfdi.de/). 

RPackage/.Rbuildignore

@@ -5,3 +5,4 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^data-raw$

RPackage/DESCRIPTION

@@ -11,9 +11,11 @@ License: CC BY 4.0
 Encoding: UTF-8
 LazyData: true
 URL: https://AHomoudi.github.io/AquaFortR/
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: 
     knitr,
     learnr,
     rmarkdown
 VignetteBuilder: knitr
+Depends: 
+    R (>= 2.10)

RPackage/NAMESPACE

@@ -1,2 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+export(conv2D_f)
+export(conv2D_r)
+export(xcorr2D_f)
+export(xcorr2D_r)
+useDynLib(AquaFortR)
+useDynLib(AquaFortR, .registration=TRUE)

RPackage/R/AquaFortR-package.R

@@ -0,0 +1,7 @@
+#' @keywords internal
+"_PACKAGE"
+#' @name AquaFortR
+#' @useDynLib AquaFortR, .registration=TRUE
+## usethis namespace: start
+## usethis namespace: end
+NULL

RPackage/R/conv2D_f.R

@@ -0,0 +1,27 @@
+#' @title 2D Convolution using Fortran.
+#'
+#' @description  This function calculates the 2D Convolution of two matrices
+#'  `a` and `b` using compiled Fortran subroutine.
+#'
+#' @param a A matrix (2D array) of values.
+#' @param b A matrix (2D array) of values.
+#' @return A matrix representing the 2D cross-correlation of the input matrices.
+#' @export
+#' @examples
+#' a <- matrix(c(1, 2, 3, 4), ncol = 2)
+#' b <- matrix(c(5, 6, 7, 8), ncol = 2)
+#' conv2D_f(a, b)
+#' @author Ahmed Homoudi
+#' @useDynLib AquaFortR
+#' @export
+conv2D_f <- function(a, b) {
+  stopifnot(length(dim(a))==2 | length(dim(b))==2)
+  result <- .Call(
+    c_conv2d_f,
+    as.integer(dim(a)),
+    as.double(a),
+    as.integer(dim(b)),
+    as.double(b)
+  )
+  return(result)
+}

RPackage/R/conv2D_r.R

@@ -0,0 +1,55 @@
+#' @title 2D Convolution using R.
+#'
+#' @description  This function calculates the 2D Convolution of two matrices
+#'  `a` and `b` using compiled Fortran subroutine.
+#'
+#' @param a A matrix (2D array) of values.
+#' @param b A matrix (2D array) of values.
+#' @return A matrix representing the 2D cross-correlation of the input matrices.
+#' @export
+#' @examples
+#' a <- matrix(c(1, 2, 3, 4), ncol = 2)
+#' b <- matrix(c(5, 6, 7, 8), ncol = 2)
+#' conv2D_f(a, b)
+#' @author Ahmed Homoudi
+#' @useDynLib AquaFortR
+#' @export
+conv2D_r <- function(a, b) {
+  stopifnot(length(dim(a))==2 | length(dim(b))==2)
+  # the full convolution matrix
+  conv_row <- nrow(a) + nrow(b) - 1
+  conv_col <- ncol(a) + ncol(b) - 1
+  conv <- matrix(1:c(conv_row * conv_col), byrow = FALSE, ncol = conv_col)
+
+  # obtain possible shifts
+  min_row_shift <- -(nrow(b) - 1)
+  max_row_shift <- (nrow(a) - 1)
+  min_col_shift <- -(ncol(b) - 1)
+  max_col_shift <- (ncol(a) - 1)
+
+  # Padded matrix
+  rows_padded <- abs(min_row_shift) + nrow(a) + abs(max_row_shift)
+  cols_padded <- abs(min_col_shift) + ncol(a) + abs(max_col_shift)
+  # a
+  padded_a <- matrix(0, nrow = rows_padded, ncol = cols_padded)
+  padded_a[
+    (abs(min_row_shift) + 1):(abs(min_row_shift) + nrow(a)),
+    (abs(min_col_shift) + 1):(abs(min_col_shift) + ncol(a))
+  ] <- a
+
+  for (icol in 1:conv_col) {
+    for (irow in 1:conv_row) {
+      iconv <- irow + ((icol - 1) * conv_row)
+      cols <- (icol):(icol + ncol(b) - 1)
+      rows <- (irow):(irow + nrow(b) - 1)
+      # b
+      padded_b <- array(0, dim = c(rows_padded, cols_padded))
+      # flip the kernel i.e. b
+      padded_b[rows, cols] <- b[nrow(b):1, ncol(b):1]
+
+      conv[irow, icol] <- sum(padded_a * padded_b)
+    }
+  }
+
+  return(conv)
+}

RPackage/R/radiosonde.R

@@ -0,0 +1,11 @@
+#' @title Radiosonde data
+#' @description radiosonde example data to calculate CAPE.
+#' The data measured at Stuttgart radiosonde station on 2021-06-01 12:00 mid day.
+#' For more information about about the
+#' variables meaning, please refer to this sheet
+#' \url{https://opendata.dwd.de/climate_environment/CDC/help/Abkuerzung_Spaltenname_CDC_20180914.xlsx}
+#'
+#' @format A data frame with 14 columns and 2962 rows
+#' @source German Weather Service (DWD). (2024). Radiosondes data set.
+#' Climate Data Center (CDC). \url{https://opendata.dwd.de/}
+"radiosonde"

RPackage/R/xcorr2D_f.R

@@ -0,0 +1,27 @@
+#' @title 2D cross-correlation using Fortran.
+#'
+#' @description  This function calculates the 2D cross-correlation of two matrices
+#'  `a` and `b` using compiled Fortran subroutine.
+#'
+#' @param a A matrix (2D array) of values.
+#' @param b A matrix (2D array) of values.
+#' @return A matrix representing the 2D cross-correlation of the input matrices.
+#' @export
+#' @examples
+#' a <- matrix(c(1, 2, 3, 4), ncol = 2)
+#' b <- matrix(c(5, 6, 7, 8), ncol = 2)
+#' xcorr2D_f(a, b)
+#' @author Ahmed Homoudi
+#' @useDynLib AquaFortR
+#' @export
+xcorr2D_f <- function(a, b) {
+  stopifnot(length(dim(a))==2 | length(dim(b))==2)
+  result <- .Call(
+    c_xcorr2d_f,
+    as.integer(dim(a)),
+    as.double(a),
+    as.integer(dim(b)),
+    as.double(b)
+  )
+  return(result)
+}

RPackage/R/xcorr2D_r.R

@@ -0,0 +1,54 @@
+#' @title 2D cross-correlation using R.
+#'
+#' @description  This function calculates the 2D cross-correlation of two matrices
+#'  `a` and `b` using compiled Fortran subroutine.
+#'
+#' @param a A matrix (2D array) of values.
+#' @param b A matrix (2D array) of values.
+#' @return A matrix representing the 2D cross-correlation of the input matrices.
+#' @export
+#' @examples
+#' a <- matrix(c(1, 2, 3, 4), ncol = 2)
+#' b <- matrix(c(5, 6, 7, 8), ncol = 2)
+#' xcorr2D_f(a, b)
+#' @author Ahmed Homoudi
+#' @useDynLib AquaFortR
+#' @export
+xcorr2D_r <- function(a, b) {
+  stopifnot(length(dim(a))==2 | length(dim(b))==2)
+  # the full CC matrix
+  cc_row <- nrow(a) + nrow(b) - 1
+  cc_col <- ncol(a) + ncol(b) - 1
+  cc <- matrix(1:c(cc_row * cc_col), byrow = FALSE, ncol = cc_col)
+
+  # obtain possible shifts
+  min_row_shift <- -(nrow(b) - 1)
+  max_row_shift <- (nrow(a) - 1)
+  min_col_shift <- -(ncol(b) - 1)
+  max_col_shift <- (ncol(a) - 1)
+
+  # Padded matrix
+  rows_padded <- abs(min_row_shift) + nrow(a) + abs(max_row_shift)
+  cols_padded <- abs(min_col_shift) + ncol(a) + abs(max_col_shift)
+  # a
+  padded_a <- matrix(0, nrow = rows_padded, ncol = cols_padded)
+  padded_a[
+    (abs(min_row_shift) + 1):(abs(min_row_shift) + nrow(a)),
+    (abs(min_col_shift) + 1):(abs(min_col_shift) + ncol(a))
+  ] <- a
+
+  for (icol in 1:cc_col) {
+    for (irow in 1:cc_row) {
+      icc <- irow + ((icol - 1) * cc_row)
+      cols <- (icol):(icol + ncol(b) - 1)
+      rows <- (irow):(irow + nrow(b) - 1)
+      # b
+      padded_b <- array(0, dim = c(rows_padded, cols_padded))
+      padded_b[rows, cols] <- b
+
+      cc[irow, icol] <- sum(padded_a * padded_b)
+    }
+  }
+
+  return(cc)
+}