Initial commit

.Rproj.user/4DBB9BEA/sources/s-7A67720/40570541-contents

+# Hello, world!
+#
+# This is an example function named 'hello' 
+# which prints 'Hello, world!'.
+#
+# You can learn more about package authoring with RStudio at:
+#
+#   http://r-pkgs.had.co.nz/
+#
+# Some useful keyboard shortcuts for package authoring:
+#
+#   Build and Reload Package:  'Ctrl + Shift + B'
+#   Check Package:             'Ctrl + Shift + E'
+#   Test Package:              'Ctrl + Shift + T'
+
+hello <- function() {
+  print("Hello, world!")
+}

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+    "type" : "r_markdown"
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.Rproj.user/4DBB9BEA/sources/s-7A67720/4421A5C7-contents

+---
+title: "start"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{start}
+  %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
+editor_options: 
+  chunk_output_type: console
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+
+The package `fdf` allow to work with column-list. When for instance you have a list of time series that you want to include in a `data.frame`.
+
+Since it works only with `data.frame` object, there is no new object, you can use very easily with any package like `dplyr` (and the tidyverse) and spatio-temporal object with package `sf` for instance.
+
+```{r setup}
+library(fdf)
+```
+
+# Add a new column-list with `fd_add`
+
+```{r addData}
+DF = data.frame( A = 1:10)
+
+DFD = fd_add(DF, "B", function(i) rnorm(runif(1, 4,20)))
+DFD
+```
+
+# Filter element in a column-list with `fd_filter`
+
+```{r filter}
+fd_filter(DFD, "B", 1)
+
+fd_filter(DFD, "B", 2)
+
+fd_filter(DFD, "B", 3)
+```
+
+# Find index of element in column-list matching with a key using `fd_match`
+
+```{r}
+DFD = fd_add(DFD, "C", function(i) sample(1:5, 5))
+
+idMatch = fd_match(DFD, "C", 4)
+idMatch
+
+# to check this:
+fd_filter(DFD, "C", idMatch)
+```
+
+# Melting column-list to a classical data.frame with `fd_melt`
+
+```{r meltSimple}
+fd_melt(DFD, "B")
+
+fd_melt(DFD, "B", keep = "A")
+
+fd_melt(DFD, "B", keep = list("A", "C"))
+```
+
+when two column list have the same length for each elements, we can melt in the same time
+
+```{r meltDouble}
+DFD = fd_add(DFD, "B2", function(i) 1:length(DFD$B[[i]]))
+
+fd_melt(DFD, "B", "B2")
+
+fd_melt(DFD, "B", "B2", keep = list("A", "C"))
+```

.Rproj.user/4DBB9BEA/sources/s-7A67720/492CAD8E-contents

+---
+title: "start"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{start}
+  %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
+editor_options: 
+  chunk_output_type: console
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+
+The package `fdf` allow to work with column-list. When for instance you have a list of time series that you want to include in a `data.frame`.
+
+Since it works only with `data.frame` object, there is no new object, you can use very easily with any package like `dplyr` (and the tidyverse) and spatio-temporal object with package `sf` for instance.
+
+```{r setup}
+library(fdf)
+```
+
+# Add a new column-list with `fd_add`
+
+```{r addData}
+DF = data.frame( A = 1:10)
+
+DFD = fd_add(DF, "B", function(i) rnorm(runif(1, 4,20)))
+DFD
+```
+
+# Filter element in a column-list with `fd_filter`
+
+```{r filter}
+fd_filter(DFD, "B", 1)
+
+fd_filter(DFD, "B", 2)
+
+fd_filter(DFD, "B", 3)
+```
+
+# Find index of element in column-list matching with a key using `fd_match`
+
+```{r}
+DFD = fd_add(DFD, "C", function(i) sample(1:5, 5))
+
+idMatch = fd_match(DFD, "C", 4)
+idMatch
+
+# to check this:
+fd_filter(DFD, "C", idMatch)
+```
+
+# Melting column-list to a classical data.frame with `fd_melt`
+
+```{r meltSimple}
+fd_melt(DFD, "B")
+
+fd_melt(DFD, "B", keep = "A")
+
+fd_melt(DFD, "B", keep = list("A", "C"))
+```
+
+when two column list have the same length for each elements, we can melt in the same time
+
+```{r meltDouble}
+DFD = fd_add(DFD, "B2", function(i) 1:length(DFD$B[[i]]))
+
+fd_melt(DFD, "B", "B2")
+
+fd_melt(DFD, "B", "B2", keep = list("A", "C"))
+```

.Rproj.user/4DBB9BEA/sources/s-7A67720/54C76FF4-contents

+Package: fdf
+Type: Package
+Title: Functions for Functional Data Frame 
+Version: 0.1.0
+Author: Virgile Baudrot [aut, cre]
+Maintainer: Virgile Baudrot <virgile.baudrot@posteo.net>
+Description: A set of function to work with functional data in data frame. 
+URL: https://gitlab.paca.inra.fr/biosp/fdf
+BugReports: https://gitlab.paca.inra.fr/biosp/fdf/issues
+License: GPL (>= 2)
+Encoding: UTF-8
+LazyData: true
+Suggests: 
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr
+RoxygenNote: 6.1.1

.Rproj.user/4DBB9BEA/sources/s-7A67720/9999D0BB-contents

+#' @title find index
+#'
+#' @param x a data.frame
+#' @param key character string. name of the column to select
+#' @param value value of the element to return index from the column defined by key
+#'
+#' @return vector if not all index are equal. scalar if all equal.
+#'
+#' @export
+#'
+fd_match <- function(x, key, value){
+  returnID = sapply(1:nrow(x), function(i){ match(value, x[[key]][[i]])  })
+  if(length(unique(returnID)) == 1){ returnID = unique(returnID) }
+  return(returnID)
+}

.Rproj.user/4DBB9BEA/sources/s-7A67720/DB0ECF10-contents

+#' @title Convert list.column data.frame into scalar.column data.frame
+#'
+#' @description Convert data.frame with 2 column.list into data.frame with only column.scalar
+#'
+#' @name fd_melt
+#'
+#' @param x A data.frame
+#' @param key1 character string. The name of the column to select
+#' @param key2 icharacter string. The name of the column to select
+#' @param id name of the replicate for the id. As to be of the same length as the number of row of the x object
+#'
+#' @export
+#'
+fd_melt_DOUBLE <- function(x, key1, key2, id = NULL){
+  lgth_key1 = sapply(x[[key1]], length)
+  lgth_key2 = sapply(x[[key2]], length)
+  if(any(lgth_key1 != lgth_key2)){ stop("length of element from 'key1' and 'key2' differ.")}
+  if(is.null(id)) {
+    id = 1:length(lgth_key1)
+  } else{
+    id = x[[id]]
+  }
+  df = data.frame(
+    id = do.call("c", lapply(1:length(id), function(i) rep(id[i], lgth_key1[[i]])))
+  )
+  df[[key1]] = do.call("c", x[[key1]])
+  df[[key2]] = do.call("c", x[[key2]])
+  return(df)
+}
+
+#' @name fd_melt
+#'
+#'
+#' @export
+#'
+fd_melt_SINGLE <- function(x, key1, id = NULL){
+  lgth_key1 = sapply(x[[key1]], length)
+  if(is.null(id)) {
+    id = 1:length(lgth_key1)
+  } else{
+    id = x[[id]]
+  }
+  df = data.frame(
+    id = do.call("c", lapply(1:length(id), function(i) rep(id[i], lgth_key1[[i]])))
+  )
+  df[[key1]] = do.call("c", x[[key1]])
+  return(df)
+}
+
+#' @name fd_melt
+#'
+#' @param keep vector of column name to keep
+#'
+#' @export
+#'
+fd_melt <- function(x, key1, key2 = NULL, id = NULL, keep = NULL){
+
+  if(is.null(key2)){
+    DF = fd_melt_SINGLE(x, key1, id)
+  } else{
+    DF = fd_melt_DOUBLE(x, key1, key2, id)
+  }
+
+  # --- keep
+  if(!is.null(keep)) {
+    for(i in 1:length(keep)){
+      DF[[keep[[i]]]] = fd_melt_STICK(x, key1, keep[[i]])
+    }
+  }
+  return(DF)
+}
+
+#' @name fd_melt
+#'
+#' @export
+#'
+fd_melt_STICK = function(x, key1, keep){
+  vec = do.call("c", lapply(1:nrow(x),
+                          function(i){ rep(x[[keep]][i], length(x[[key1]][[i]]))}))
+  return(vec)
+}
+
+#' @title Combine list of data.frame by Rows
+#'
+#' @description Function used to filter functional data in data.frame.
+#'
+#' @return Return a data.frame
+#'
+#' @param ls A list of data.frame
+#' @param id id to provide to each data.frame. Must be the length of the list
+#'
+#' @export
+#'
+fd_rbindLStoDF <- function(ls, id = NULL){
+  df <- do.call("rbind", ls)
+  nrow_df <- sapply(ls, nrow)
+  if(is.null(id)) { id = 1:length(nrow_df) }
+  df[["id"]] = do.call("c", lapply(1:length(nrow_df), function(i) rep(id[i], nrow_df[[i]])))
+  return(df)
+}

.Rproj.user/4DBB9BEA/sources/s-7A67720/E90EAA85

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.Rproj.user/4DBB9BEA/sources/s-7A67720/E90EAA85-contents

+Package: fdf
+Type: Package
+Title: Functions for Functional Data Frame 
+Version: 0.1.0
+Author: Virgile Baudrot [aut, cre]
+Maintainer: Virgile Baudrot <virgile.baudrot@posteo.net>
+Description: A set of functions to work with functional data (column-list) in data frame. 
+URL: https://gitlab.paca.inra.fr/biosp/fdf
+BugReports: https://gitlab.paca.inra.fr/biosp/fdf/issues
+License: GPL (>= 2)
+Encoding: UTF-8
+LazyData: true
+Suggests: 
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr
+RoxygenNote: 6.1.1

.Rproj.user/4DBB9BEA/sources/s-7A67720/FCF7DFD1-contents

+#' @name fd_add
+#'
+#' @title Add functional data
+#'
+#' @description Add functional data in data.frame object.
+#'
+#' @param x object of class data.frame.
+#' @param key the name of the new column, as strings or symbols
+#' @param FUN the function to be applied to each element of \code{x}.
+#'  In the case of functions like +, %*%, the function name must be
+#'   backquoted or quoted. See lapply functions for details.
+#' @param \dots optional arguments to FUN. See lapply functions for details.
+#'
+#' @return An object with addition functional data feature (or feature dynamic).
+#'
+#' @export
+#'
+fd_add <- function(x, key, FUN, ...){
+  x[[key]] <- lapply(1:nrow(x), FUN, ...)
+  return(x)
+}
+
+#' @name fd_add
+#'
+#' @export
+#'
+fd_add_NAME <- function(x, key, FUN, ...){
+  x[[key]] <- lapply(1:nrow(x), FUN, ...)
+  # class(x) <- c(class(.x), "xfd")
+  attr(x, "fdFD") <- c(deparse(substitute(key)), attr(x, "fdFD"))
+  return(x)
+}
+
+#' @name fd_add
+#'
+#' @param keyConstraint character string. The reference of the column to be checked
+#'
+#' @export
+#'
+fd_add2 <- function(x, # geometry on which we applied the pollen emission pattern
+                    keyConstraint,
+                    key, # name of the column which is going to be created
+                    FUN,
+                   ...){
+  if("stackTimeline" %in% colnames(x)) {
+    stop("Please rename column 'stackTimeline' in x object.")
+  }
+  # CREATE NEW COLUMN
+  x[["key_temp"]] <- lapply(1:nrow(x), FUN, ...)
+  # check length with timeline
+  if(all(sapply(x[[keyConstraint]], length) != sapply(x[["key_temp"]], length))){
+    stop(paste0("element within list returned by FUN' has not the same length as list element of '", keyConstraint, "' column"))
+  }
+  # ADD StackTimeLine
+  stackTimeline = sort(unique(do.call("c", x[[keyConstraint]])))
+
+  x[[key]] = lapply(1:nrow(x), function(i){
+    index_matching = match(x[[keyConstraint]][[i]], stackTimeline)
+    res = rep(0,length(stackTimeline))
+    res[index_matching] = x[["key_temp"]][[i]]
+    return(res)
+  })
+  # /!\ REPLACE timeline
+  x[[keyConstraint]] = lapply(1:nrow(x), function(i) stackTimeline)
+  warning(paste("The column variable", keyConstraint, "may have changed"))
+  # remove "key_temp"
+  x[["key_temp"]] = NULL
+
+  return(x)
+}
+
+
+

.Rproj.user/4DBB9BEA/sources/s-7A67720/FEF2E3E9-contents

+#' @name fd_filter
+#'
+#' @title Function used to filter functional data in data.frame object.
+#'
+#' @param x a data.frame object.
+#' @param key character string. The name of the column to select.
+#' @param index integer (or vector). The index of the functional data.
+#'
+#' @export
+#'
+fd_filter1 <- function(x, key, index){
+  x[[key]] <- do.call("c", lapply(x[[key]] , `[[`, index) )
+  return(x)
+}
+
+#' @name fd_filter
+#'
+#' @export
+#'
+
+fd_filter_ <- function(x, key, index){
+  if(length(index) == 1){ index = rep(index, nrow(x)) }
+  if(length(index) != nrow(x)){ stop("length of vector index is different of 1 and nrow(x).")}
+  x[[key]] <- do.call("c", lapply(1:nrow(x), function(i) x[[key]][[i]][index[i]] ))
+  return(x)
+}
+
+#' @name fd_filter
+#'
+#' @param key1 character string. The name of the column to select
+#' @param key2 character string. The name of the column to select
+#'
+#' @export
+#'
+fd_filter2 <- function(x, key1, key2, index){
+  x[[key1]] <- do.call("c", lapply(x[[key1]] , `[[`, index) )
+  x[[key2]] <- do.call("c", lapply(x[[key2]] , `[[`, index) )
+  return(x)
+}
+
+#' @name fd_filter
+#'
+#' @param key3 character string. The name of the column to select
+#'
+#' @export
+#'
+fd_filter3 <- function(x, key1, key2, key3, index){
+  x[[key1]] <- do.call("c", lapply(x[[key1]] , `[[`, index) )
+  x[[key2]] <- do.call("c", lapply(x[[key2]] , `[[`, index) )
+  x[[key3]] <- do.call("c", lapply(x[[key3]] , `[[`, index) )
+  return(x)
+}
+
+
+#' @name fd_filter
+#'
+#' @param keys list of names of the column to select
+#'
+#' @export
+#'
+fd_filter <- function(x, keys, index){ # need multi-dispatch !!!!
+  if(length(index) == 1){ index = rep(index, nrow(x)) }
+  if(length(index) != nrow(x)){ stop("length of vector index is different of 1 and nrow(x).")}
+  for(i in 1:length(keys)){
+    x[[keys[[i]]]] <- do.call("c", lapply(1:nrow(x), function(j) x[[keys[[i]]]][[j]][index[j]] ))
+    #x[[keys[[i]]]] <- do.call("c", lapply(x[[keys[[i]]]] , `[[`, index[i]) )
+  }
+  return(x)
+}

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+/home/vbaudrot/Documents/PACKAGES/fdf/R/filter.R="E96533C1"
+/home/vbaudrot/Documents/PACKAGES/fdf/R/match.R="CA02FEED"
+/home/vbaudrot/Documents/PACKAGES/fdf/R/melt.R="9115648E"
+/home/vbaudrot/Documents/PACKAGES/fdf/vignettes/start.Rmd="C55DB299"

.gitignore

+inst/doc

DESCRIPTION

+Package: fdf
+Type: Package
+Title: Functions for Functional Data Frame 
+Version: 0.1.0
+Author: Virgile Baudrot [aut, cre]
+Maintainer: Virgile Baudrot <virgile.baudrot@posteo.net>
+Description: A set of functions to work with functional data (column-list) in data frame. 
+URL: https://gitlab.paca.inra.fr/biosp/fdf
+BugReports: https://gitlab.paca.inra.fr/biosp/fdf/issues
+License: GPL (>= 2)
+Encoding: UTF-8
+LazyData: true
+Suggests: 
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr
+RoxygenNote: 6.1.1

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(fd_add)
+export(fd_add2)
+export(fd_add_NAME)
+export(fd_filter)
+export(fd_filter1)
+export(fd_filter2)
+export(fd_filter3)
+export(fd_filter_)
+export(fd_match)
+export(fd_melt)
+export(fd_melt_DOUBLE)
+export(fd_melt_SINGLE)
+export(fd_melt_STICK)
+export(fd_rbindLStoDF)

R/add.R

+#' @name fd_add
+#'
+#' @title Add functional data
+#'
+#' @description Add functional data in data.frame object.
+#'
+#' @param x object of class data.frame.
+#' @param key the name of the new column, as strings or symbols
+#' @param FUN the function to be applied to each element of \code{x}.
+#'  In the case of functions like +, %*%, the function name must be
+#'   backquoted or quoted. See lapply functions for details.
+#' @param \dots optional arguments to FUN. See lapply functions for details.
+#'
+#' @return An object with addition functional data feature (or feature dynamic).
+#'
+#' @export
+#'
+fd_add <- function(x, key, FUN, ...){
+  x[[key]] <- lapply(1:nrow(x), FUN, ...)
+  return(x)
+}
+
+#' @name fd_add
+#'
+#' @export
+#'
+fd_add_NAME <- function(x, key, FUN, ...){
+  x[[key]] <- lapply(1:nrow(x), FUN, ...)
+  # class(x) <- c(class(.x), "xfd")
+  attr(x, "fdFD") <- c(deparse(substitute(key)), attr(x, "fdFD"))
+  return(x)
+}
+
+#' @name fd_add
+#'
+#' @param keyConstraint character string. The reference of the column to be checked
+#'
+#' @export
+#'
+fd_add2 <- function(x, # geometry on which we applied the pollen emission pattern
+                    keyConstraint,
+                    key, # name of the column which is going to be created
+                    FUN,
+                   ...){
+  if("stackTimeline" %in% colnames(x)) {
+    stop("Please rename column 'stackTimeline' in x object.")
+  }
+  # CREATE NEW COLUMN