add imageMat

.Rbuildignore

@@ -1,3 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^misc$
+^.*\.o$
+^.*\.so$

DESCRIPTION

@@ -22,6 +22,7 @@ Depends:
     data.table,
     lme4,
     Matrix,
+    methods,
     Rcpp,
     stats
 License: GPL-3 | AGPL-3
@@ -55,7 +56,6 @@ Suggests:
     lmerTest,
     loo,
     MASS,
-    methods,
     MuMIn,
     nlme,
     pdftools,

NAMESPACE

@@ -120,6 +120,7 @@ export(h2v2WX2019)
 export(haplosAlleles2num)
 export(haplosList2Matrix)
 export(hinton)
+export(imageMat)
 export(imageWithScale)
 export(imputeGenosWithMean)
 export(imputeGenosWithMeanPerPop)
@@ -311,3 +312,4 @@ import(Rcpp)
 import(data.table)
 import(lme4)
 import(stats)
+importFrom(methods,is)

R/misc.R

@@ -1,6 +1,7 @@
 ##' @import data.table
 ##' @import lme4
 ##' @import Matrix
+##' @importFrom methods is
 ##' @import Rcpp
 ##' @import stats
 

R/plotting.R

@@ -225,6 +225,25 @@ hinton <- function(m, main="", max.sqrt.m=NULL){
   on.exit(graphics::par(def.par))
 }
 
+##' Image of a matrix
+##'
+##' Plots an image of a matrix.
+##' @param mat matrix
+##' @param title optional title of the plot
+##' @param col colors
+##' @return nothing
+##' @author Timothee Flutre
+##' @export
+imageMat <- function(mat, title,
+                     col=grDevices::grey.colors(length(table(c(mat))), rev=TRUE)){
+  if(missing(title)){
+    title <- deparse(substitute(mat))
+    title <- paste0(title, " (", nrow(mat), " x ", ncol(mat), ")")
+  }
+  graphics::image(t(mat)[,nrow(mat):1], axes=FALSE, main=title,
+                  col=col)
+}
+
 ##' Plot a scale, e.g. to add on the side of image()
 ##'
 ##' Takes some time to draw (there is one polygon per break...)

R/stats.R

@@ -106,6 +106,7 @@ rmsre <- function(rel_error){
 ##' Returns the relative root mean squared error (RRMSE) as defined in \href{https://doi.org/10.3354/cr030079}{Willmott and Matsuura (2005)}.
 ##' @param error vector \eqn{(\hat{\theta}_i - \theta_i)}
 ##' @param theta vector \eqn{\theta_i}
+##' @param perc if TRUE, the return value will be a percentage
 ##' @return numeric
 ##' @author Timothee Flutre
 ##' @seealso \code{\link{rmse}}, \code{\link{rmsre}}

misc/intro-het-GxE.Rmd

@@ -32,6 +32,7 @@ suppressPackageStartupMessages(library(emmeans))
 suppressPackageStartupMessages(library(lme4))
 suppressPackageStartupMessages(library(nlme))
 suppressPackageStartupMessages(library(MM4LMM))
+suppressPackageStartupMessages(library(MegaLMM))
 ```
 
 Execution time (see the appendix):
@@ -830,6 +831,12 @@ cor(tmp[,"true"], tmp[,"estim"])
 plot(tmp[,"estim"], tmp[,"true"], las=1, asp=1, xlab="estimated value", ylab="true value", main="Error variances (gls het)", pch=19); abline(a=0, b=1, lty=2)
 ```
 
+### `MegaLMM`
+
+Details: https://github.com/deruncie/MegaLMM/blob/master/vignettes/MultiEnvironmentTrial.Rmd
+
+TODO
+
 ### `MMEst` from `MM4LMM`
 
 The `MMEst` from the `MM4LMM` package performs inference via ReML, and can handle both random variables and heteroscedasticity.