Merge pull request #55 from cimentadaj/diagonal_matrix

Diagonal matrix

DESCRIPTION

@@ -1,38 +1,39 @@
-Package: corrr
-Type: Package
-Version: 0.2.1.9000
-Title: Correlations in R
-Description: A tool for exploring correlations.
-    It makes it possible to easily perform routine tasks when
-    exploring correlation matrices such as ignoring the diagonal,
-    focusing on the correlations of certain variables against others,
-    or rearranging and visualising the matrix in terms of the
-    strength of the correlations.
-Authors@R: c(
-  person("Simon", "Jackson", email = "drsimonjackson@gmail.com", role = c("aut", "cre"))
-  )
-URL: https://github.com/drsimonj/corrr
-BugReports: https://github.com/drsimonj/corrr/issues
-Depends: 
-    R (>= 3.3.0),
-    dplyr (>= 0.5.0)
-LazyData: yes
-License: MIT + file LICENSE
-RoxygenNote: 6.0.1
-Suggests: 
-    testthat (>= 1.0.2),
-    knitr (>= 1.13),
-    rmarkdown (>= 0.9.6),
-    dbplyr (>= 1.2.1)
-Imports: 
-    magrittr (>= 1.5),
-    tidyr (>= 0.5.1),
-    ggplot2 (>= 2.2.0),
-    seriation (>= 1.2-0),
-    lazyeval (>= 0.2.0),
-    purrr (>= 0.2.2),
-    tibble (>= 1.1),
-    ggrepel (>= 0.6.5),
-    methods (>= 3.4.3), 
-    rlang(>= 0.2.0)
-VignetteBuilder: knitr
+Package: corrr
+Type: Package
+Version: 0.2.1.9000
+Title: Correlations in R
+Description: A tool for exploring correlations.
+    It makes it possible to easily perform routine tasks when
+    exploring correlation matrices such as ignoring the diagonal,
+    focusing on the correlations of certain variables against others,
+    or rearranging and visualising the matrix in terms of the
+    strength of the correlations.
+Authors@R: c(
+  person("Simon", "Jackson", email = "drsimonjackson@gmail.com", role = c("aut", "cre")),
+  person("Jorge", "Cimentada", email = "cimentadaj@gmail.com", role = c("ctb"))
+  )
+URL: https://github.com/drsimonj/corrr
+BugReports: https://github.com/drsimonj/corrr/issues
+Depends: 
+    R (>= 3.3.0),
+    dplyr (>= 0.5.0)
+LazyData: yes
+License: MIT + file LICENSE
+RoxygenNote: 6.0.1
+Suggests: 
+    testthat (>= 1.0.2),
+    knitr (>= 1.13),
+    rmarkdown (>= 0.9.6),
+    dbplyr (>= 1.2.1)
+Imports: 
+    magrittr (>= 1.5),
+    tidyr (>= 0.5.1),
+    ggplot2 (>= 2.2.0),
+    seriation (>= 1.2-0),
+    lazyeval (>= 0.2.0),
+    purrr (>= 0.2.2),
+    tibble (>= 1.1),
+    ggrepel (>= 0.6.5),
+    methods (>= 3.4.3), 
+    rlang(>= 0.2.0)
+VignetteBuilder: knitr

NAMESPACE

@@ -1,43 +1,43 @@
-# Generated by roxygen2: do not edit by hand
-
-S3method(Ops,cor_df)
-S3method(as_matrix,cor_df)
-S3method(correlate,default)
-S3method(correlate,tbl_sql)
-S3method(fashion,data.frame)
-S3method(fashion,default)
-S3method(fashion,matrix)
-S3method(focus_,cor_df)
-S3method(focus_if,cor_df)
-S3method(focus_if,default)
-S3method(network_plot,cor_df)
-S3method(network_plot,default)
-S3method(rearrange,cor_df)
-S3method(rplot,cor_df)
-S3method(rplot,default)
-S3method(shave,cor_df)
-S3method(stretch,cor_df)
-export(as_cordf)
-export(as_matrix)
-export(correlate)
-export(fashion)
-export(first_col)
-export(focus)
-export(focus_)
-export(focus_if)
-export(network_plot)
-export(pair_n)
-export(rearrange)
-export(rplot)
-export(shave)
-export(stretch)
-import(dplyr)
-import(ggplot2)
-import(rlang)
-importFrom(magrittr,"%<>%")
-importFrom(magrittr,"%>%")
-importFrom(purrr,map)
-importFrom(purrr,map_df)
-importFrom(stats,"dist")
-importFrom(tibble,as.tibble)
-importFrom(tibble,tibble)
+# Generated by roxygen2: do not edit by hand
+
+S3method(Ops,cor_df)
+S3method(as_matrix,cor_df)
+S3method(correlate,default)
+S3method(correlate,tbl_sql)
+S3method(fashion,data.frame)
+S3method(fashion,default)
+S3method(fashion,matrix)
+S3method(focus_,cor_df)
+S3method(focus_if,cor_df)
+S3method(focus_if,default)
+S3method(network_plot,cor_df)
+S3method(network_plot,default)
+S3method(rearrange,cor_df)
+S3method(rplot,cor_df)
+S3method(rplot,default)
+S3method(shave,cor_df)
+S3method(stretch,cor_df)
+export(as_cordf)
+export(as_matrix)
+export(correlate)
+export(fashion)
+export(first_col)
+export(focus)
+export(focus_)
+export(focus_if)
+export(network_plot)
+export(pair_n)
+export(rearrange)
+export(rplot)
+export(shave)
+export(stretch)
+import(dplyr)
+import(ggplot2)
+import(rlang)
+importFrom(magrittr,"%<>%")
+importFrom(magrittr,"%>%")
+importFrom(purrr,map)
+importFrom(purrr,map_df)
+importFrom(stats,"dist")
+importFrom(tibble,as.tibble)
+importFrom(tibble,tibble)

NEWS.md

@@ -1,63 +1,67 @@
-# corrr 0.2.1.9000
-
-## New Functions
-
-- `as_cordf` will coerce lists or matrices into correlation data frames if possible.
-- `focus_if` enables conditional variable selection.
-
-
-## New Functionality
-
-- Can use arithmetic operators (e.g., `+` or `-`) with correlation data frames.
-- Plotting functions (`rplot` and `network_plot`) will attempt to coerce objects to a correlation data frame (via `as_cordf`) if needed, making it possible to directly use these functions with other square-matrix-like objects.
-- `repel` option added to `network_plot` (default = `TRUE`).
-- `curved` option added to `network_plot` (default = `TRUE`).
-- `correlate()` now prints a message about the `method` and `use` parameters. Can be silenced with `quiet = TRUE`.
-- `correlate()` now supports data frame with a SQL back-end (`tbl_sql`)
-
-## Fixes
-
-- When `legend = TRUE` (now the default setting), `rplot` and `network_plot` generate a single, unlabelled legend referring to the size of the correlations.
-
-## Other
-
-- `correlate()` is now an S3 method so that it can adapt to `x`'s object type.
-
-- During the development of this version, ggplot v2.2.0 was released. Many changes in the plotting functions have been made to handle new features in the updated version of ggplot2.
-
-# corrr 0.2.1
-
-## New Functionality
-
-- Can keep leading zeros when using `fashion()` with new argument `leading_zeros = TRUE`.
-- New optional arguments added to plotting functions, `network_plot()` and `rplot()`:
-  - `legend` to display a legend mapping correlations to size and colour.
-  - `colours` (or `colors`) to change colours in plot.
-
-## Fixes
-
-- `network_plot()` no longer plots wrong colours if only positive correlations are included.
-- Colour scheme for `network_plot()` changed to match `rplot()`.
-- Other bug fixes.
-
-# corrr 0.2.0
-
-## New Functions
-
-- `network_plot()` the correlations.
-- `focus_()` for standard evaluation version of `focus()`.
-
-## New Functionality
-
-- `fashion()` will now attempt to work on any object (not just `cor_df`), making it useful for printing any data frame, matrix, vector, etc.
-- `print_cor` argument added to `rplot()` to overlay the correlations as text.
-
-## Other
-
-- `na_omit` argument in `stretch()` changed to `na.rm` to match `gather_()`.
-- Bug fixes.
-- Improvements.
-
-# corrr 0.1.0
-
+# corrr 0.2.1.9000
+
+## Small breaking changes
+
+The `diagonal` argument of `as_matrix` and `as_matrix.cor_df` is now an optional argument rather than set to `1` by default [#52](https://github.com/drsimonj/corrr/issues/52)
+
+## New Functions
+
+- `as_cordf` will coerce lists or matrices into correlation data frames if possible.
+- `focus_if` enables conditional variable selection.
+
+## New Functionality
+
+- Can use arithmetic operators (e.g., `+` or `-`) with correlation data frames.
+- Plotting functions (`rplot` and `network_plot`) will attempt to coerce objects to a correlation data frame (via `as_cordf`) if needed, making it possible to directly use these functions with other square-matrix-like objects.
+- `repel` option added to `network_plot` (default = `TRUE`).
+- `curved` option added to `network_plot` (default = `TRUE`).
+- `correlate()` now prints a message about the `method` and `use` parameters. Can be silenced with `quiet = TRUE`.
+- `correlate()` now supports data frame with a SQL back-end (`tbl_sql`)
+
+## Fixes
+
+- When `legend = TRUE` (now the default setting), `rplot` and `network_plot` generate a single, unlabelled legend referring to the size of the correlations.
+
+## Other
+
+- `correlate()` is now an S3 method so that it can adapt to `x`'s object type.
+
+- During the development of this version, ggplot v2.2.0 was released. Many changes in the plotting functions have been made to handle new features in the updated version of ggplot2.
+
+# corrr 0.2.1
+
+## New Functionality
+
+- Can keep leading zeros when using `fashion()` with new argument `leading_zeros = TRUE`.
+- New optional arguments added to plotting functions, `network_plot()` and `rplot()`:
+  - `legend` to display a legend mapping correlations to size and colour.
+  - `colours` (or `colors`) to change colours in plot.
+
+## Fixes
+
+- `network_plot()` no longer plots wrong colours if only positive correlations are included.
+- Colour scheme for `network_plot()` changed to match `rplot()`.
+- Other bug fixes.
+
+# corrr 0.2.0
+
+## New Functions
+
+- `network_plot()` the correlations.
+- `focus_()` for standard evaluation version of `focus()`.
+
+## New Functionality
+
+- `fashion()` will now attempt to work on any object (not just `cor_df`), making it useful for printing any data frame, matrix, vector, etc.
+- `print_cor` argument added to `rplot()` to overlay the correlations as text.
+
+## Other
+
+- `na_omit` argument in `stretch()` changed to `na.rm` to match `gather_()`.
+- Bug fixes.
+- Improvements.
+
+# corrr 0.1.0
+
+>>>>>>> b594f6382f9c21be8ae3b1c3720e76ad2453aefb
 - First corrr release!

R/cor_df.R

@@ -1,13 +1,13 @@
 # Utility --------------------------------------------------------------
 
 #' @export
-as_matrix.cor_df <- function(x, diagonal = 1) {
+as_matrix.cor_df <- function(x, diagonal) {
 
   # Separate rownames
   row_names <- x$rowname
   x %<>% dplyr::select_("-rowname")
   # Return diagonal to 1
-  diag(x) <- diagonal
+  if (!missing(diagonal)) diag(x) <- diagonal
 
   # Convert to matrix and set rownames
   class(x) <- "data.frame"
@@ -43,7 +43,7 @@ shave.cor_df <- function(x, upper = TRUE) {
 rearrange.cor_df <- function(x, method = "PCA", absolute = TRUE) {
 
   # Convert to original matrix
-  m <- x %>% as_matrix()
+  m <- x %>% as_matrix(diagonal = 1)
 
   if (absolute) {
     m %<>% abs()
@@ -218,7 +218,7 @@ network_plot.cor_df <- function(rdf,
   if (!missing(colors))
     colours <- colors
 
-  rdf %<>% as_matrix()
+  rdf %<>% as_matrix(diagonal = 1)
   distance <- sign(rdf) * (1 - abs(rdf))
 
   # Use multidimensional Scaling to obtain x and y coordinates for points.

R/utility.R

@@ -84,6 +84,6 @@ pair_n <- function(x, y = NULL) {
 #' @examples
 #' x <- correlate(mtcars)
 #' as_matrix(x)
-as_matrix <- function(x, diagonal = 1) {
+as_matrix <- function(x, diagonal) {
   UseMethod("as_matrix")
 }

corrr.Rproj

@@ -1,18 +1,18 @@
-Version: 1.0
-
-RestoreWorkspace: Default
-SaveWorkspace: Default
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
-BuildType: Package
-PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace