Diagonal matrix

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: corrr
 Type: Package
-Version: 0.2.1.9000
+Version: 0.3.0.9999
 Title: Correlations in R
 Description: A tool for exploring correlations.
     It makes it possible to easily perform routine tasks when
@@ -9,7 +9,8 @@ Description: A tool for exploring correlations.
     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("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
@@ -31,4 +32,4 @@ Imports:
     tibble (>= 1.1),
     ggrepel (>= 0.6.5),
     methods (>= 3.4.3)
-VignetteBuilder: knitr
+VignetteBuilder: knitr

NEWS.md

@@ -1,59 +1,63 @@
-# 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`.
-
-## 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
-
-- 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 0.3.0.9999
+
+## 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`.
+
+## 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
+
+- 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
+
 - 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