From 60511d7e598919a7006ec4804f7a262cbde73e05 Mon Sep 17 00:00:00 2001 From: Darren Wilkinson Date: Mon, 5 Jun 2017 21:48:39 +0100 Subject: [PATCH] updated docs --- README.md | 20 ++++++--- docs/api/index.js | 2 +- docs/api/scalaglm/Glm.html | 17 -------- docs/api/scalaglm/Lm.html | 67 +++++++++++++++++++++++-------- docs/api/scalaglm/PredictLm.html | 34 ++++++++-------- src/main/scala/scalaglm/Glm.scala | 2 +- 6 files changed, 84 insertions(+), 58 deletions(-) diff --git a/README.md b/README.md index 4cfe496..fb767ff 100644 --- a/README.md +++ b/README.md @@ -10,18 +10,18 @@ If building from source, running `sbt console` should give a Scala REPL with a d To use the pre-built binary, add the following lines to your `build.sbt`: ```scala -libraryDependencies += "darrenjw" %% "scala-glm" % "0.1" +libraryDependencies += "darrenjw" %% "scala-glm" % "0.2" resolvers += "Newcastle mvn repo" at "https://www.staff.ncl.ac.uk/d.j.wilkinson/mvn/" ``` -The current stable release is "0.1". The latest unstable release is "0.2-SNAPSHOT". +The current stable release is "0.2". The latest unstable release is "0.3-SNAPSHOT". -It's currently only published to my own personal repo. I'll figure out how to push it to Sonatype once it's properly tested. +It's currently only published to my own personal repo. I'll figure out how to push it to Sonatype soon. If you just want to try it out without setting up a project, you can do so with a session like: ``` $ sbt > set scalaVersion := "2.12.1" -> set libraryDependencies += "darrenjw" %% "scala-glm" % "0.1" +> set libraryDependencies += "darrenjw" %% "scala-glm" % "0.2" > set resolvers += "Newcastle mvn repo" at "https://www.staff.ncl.ac.uk/d.j.wilkinson/mvn/" > console scala> import scalaglm._ @@ -48,9 +48,15 @@ val pca = Pca(X, List("V1","V2")) pca.sdev pca.loadings pca.scores +pca.plots pca.summary ``` -The final line prints a readable summary of the PCA to the console. +The final line prints a readable summary of the PCA to the console. Note that there is also a utility function for producing a "scatterplot matrix": + +```scala +import scalaglm.Utils.pairs +pairs(X, List("V1", "V2")) +``` ## Linear regression @@ -63,6 +69,7 @@ val y = DenseVector(1.0,2.0,1.0,1.5) val X = DenseMatrix((1.0,1.5),(1.5,2.0),(2.0,1.5),(2.0,1.0)) val lm = Lm(y,X,List("V1","V2")) lm.coefficients +lm.plots lm.summary ``` The final line produces the following output to the console: @@ -78,6 +85,7 @@ Residual standard error: 0.7071 on 1 degrees of freedom Multiple R-squared: 0.2727, Adjusted R-squared: -1.1818 F-statistic: 0.1875 on 2 and 1 DF, p-value: 0.85280 ``` +The plots include a plot of studentised residuals against fitted values and a normal Q-Q plot for the studentised residuals. ## Generalised linear models @@ -93,6 +101,7 @@ val X = DenseMatrix((1.0,1.5),(1.5,2.0),(2.0,1.5),(2.0,1.0)) val glm = Glm(y,X,List("V1","V2"),LogisticGlm) glm.coefficients glm.summary +glm.plots ``` ### Poisson regression @@ -105,6 +114,7 @@ val X = 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Value Members

) -
  • - - - - - - - - - lazy val - - - xtwxi: DenseMatrix[Double] - - -

    Inverse of the final X'WX matrix -

  • diff --git a/docs/api/scalaglm/Lm.html b/docs/api/scalaglm/Lm.html index 5aa0225..45a541a 100644 --- a/docs/api/scalaglm/Lm.html +++ b/docs/api/scalaglm/Lm.html @@ -602,6 +602,23 @@

    Value Members
    Definition Classes
    AnyRef → Any
    +
  • + + + + + + + + + lazy val + + + h: DenseVector[Double] + + +

    Vector containing the leverages (diagonal of the hat matrix) +

  • @@ -955,6 +972,23 @@

    Value Members

    Standard errors for the regression coefficients +

    +
  • + + + + + + + + + lazy val + + + sh: DenseVector[Double] + + +

    Square root of the leverage vector

  • @@ -973,6 +1007,22 @@

    Value Members

    The sum-of-squares of the centred observations

    +
  • + + + + + + + + + lazy val + + + studentised: DenseVector[Double] + + +
  • @@ -1089,23 +1139,6 @@

    Value Members

    ) -
  • - - - - - - - - - lazy val - - - xtxi: DenseMatrix[Double] - - -

    The inverse of X'X (but calculated efficiently) -

  • diff --git a/docs/api/scalaglm/PredictLm.html b/docs/api/scalaglm/PredictLm.html index 555fd7c..5cf7ffd 100644 --- a/docs/api/scalaglm/PredictLm.html +++ b/docs/api/scalaglm/PredictLm.html @@ -562,23 +562,6 @@

    Value Members
    Definition Classes
    AnyRef
    -
  • - - - - - - - - - lazy val - - - rtix: DenseMatrix[Double] - - -

    for internal use (probably should be marked private) -

  • @@ -679,6 +662,23 @@

    Value Members

    ) +
  • + + + + + + + + + lazy val + + + xrti: DenseMatrix[Double] + + +

    for internal use (probably should be marked private) +

    • diff --git a/src/main/scala/scalaglm/Glm.scala b/src/main/scala/scalaglm/Glm.scala index 226793f..ec19c17 100644 --- a/src/main/scala/scalaglm/Glm.scala +++ b/src/main/scala/scalaglm/Glm.scala @@ -169,7 +169,7 @@ case class Glm(y: DenseVector[Double], import breeze.plot._ def plots: Figure = { - val fig = Figure("Linear regression diagnostics") + val fig = Figure("GLM regression diagnostics") val p0 = fig.subplot(1,1,0) p0 += plot(fitted,y,'+') p0 += plot(fitted,fitted)