liebke

(use '(incanter core stats charts))

;; Overlay a xy-plot on a histogram 

;; Plot a histogram of a normal sample of size 1000, using the :density option
;; so that the y-axis represents density instead of the default frequency.
;; Then plot a pdf curve for the normal distribution on the same chart.

(def x (range -3 3 0.01))
(doto (histogram (sample-normal 1000) :density true)

liebke

(use '(incanter core stats charts datasets))
;; load the iris dataset
(def iris (to-matrix (get-dataset :iris)))
;; run the pca on the first four columns only
(def pca (principal-components (sel iris :cols (range 4))))
;; extract the first two principal components
(def pc1 (sel (:rotation pca) :cols 0))
(def pc2 (sel (:rotation pca) :cols 1))

;; project the first four dimension of the iris data onto the first

liebke

(use '(incanter stats charts))

;; plot the normal pdf function
(def x (range -3 3 0.1))
(view (xy-plot x (pdf-normal x)))

liebke

(use '(incanter core stats charts))

;; generate a sample from a bi-variate normal distribution
(def mvn-samp (sample-mvn 1000 :mean [7 5] :sigma (matrix [[2 1.5] [1.5 3]])))
(def x (sel mvn-samp :cols 0))
(def y (sel mvn-samp :cols 1))

;; add regression line to scatter plot
(def lm (linear-model y x))

liebke

(use '(incanter core datasets stats bayes charts))

(def survey-data (to-matrix (get-dataset :survey)))
(def x (sel survey-data (range 0 2313) (range 1 10)))
(def y (sel survey-data (range 0 2313) 10))
(def sample-params (sample-model-params 5000 (linear-model y x :intercept false)))
(view (trace-plot (:var sample-params))) 

(view (trace-plot (sel (:coefs sample-params) :cols 0)))

liebke

(use '(incanter stats charts))

;; qq-plot of normal distributed sample data
(view (qq-plot (sample-normal 100)))

;; qq-plot of exponential distributed sample data
(view (qq-plot (sample-exp 100)))

liebke

(use '(incanter core datasets charts io))
(def flow-meter (to-matrix (get-dataset :flow-meter)))
(def x1 (sel flow-meter :cols 1))
(def x2 (sel flow-meter :cols 3))

(doto (bland-altman-plot x1 x2)
      view
      clear-background
      (save "/tmp/bland_altman_plot.png"))

liebke

;; Examples of plots from the Gamma Distribution page at
;; Wikipedia (http://en.wikipedia.org/wiki/Gamma_distribution)

(use '(incanter stats charts io))

(def x (range 0 20 0.1))
(def gamma-plot (xy-plot x (pdf-gamma x :shape 1 :rate 2) 
                           :legend true
                           :title "Gamma PDF"
                           :y-label "Density"))

liebke

(use '(incanter core stats charts io))

;; make a histogram of a sample of 1000 Gamma deviates
(doto (histogram (sample-gamma 1000 :shape 1 :rate 2) 
                 :title "Gamma Histogram")
      view
      clear-background
      (save "/tmp/gamma_hist.png"))

liebke

(use '(incanter stats charts io))

(doto (box-plot (sample-gamma 1000 :shape 1 :rate 2) 
                              :title "Gamma Boxplot"
                              :legend true) 
      (add-box-plot (sample-gamma 1000 :shape 2 :rate 2))
      (add-box-plot (sample-gamma 1000 :shape 3 :rate 2))
      (add-box-plot (sample-gamma 1000 :shape 5 :rate 1))
      (add-box-plot (sample-gamma 1000 :shape 9 :rate 0.5))
      clear-background