Class: Statsample::Reliability::ICC

Inherits:
Object
  • Object
show all
Includes:
Summarizable
Defined in:
lib/statsample/reliability/icc.rb

Overview

Intra-class correlation

According to Shrout & Fleiss (1979, p.422): “ICC is the correlation between one measurement (either a single rating or a mean of several ratings) on a target and another measurement obtained on that target”

Usage

require 'statsample'
size = 1000
a = Daru::Vector.new(size.times.map {rand(10)})
b = a.recode{|i|i+rand(4)-2}
c = a.recode{|i|i+rand(4)-2}
d = a.recode{|i|i+rand(4)-2}
ds = Daru::DataFrame.new({:a => a,:b => b,:c => c,:d => d})
# Use :type attribute to set type to summarize
icc=Statsample::Reliability::ICC.new(ds, :type=>:icc_1_k)
puts icc.summary

Reference

  • Shrout,P. & Fleiss, J. (1979). Intraclass Correlation: Uses in assessing rater reliability. Psychological Bulletin, 86(2), 420-428

  • McGraw, K. & Wong, S.P. (1996). Forming Inferences About Some Intraclass Correlation Coefficients. Psychological methods, 1(1), 30-46.

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Summarizable

#summary

Constructor Details

#initialize(ds, opts = Hash.new) ⇒ ICC

Returns a new instance of ICC.



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# File 'lib/statsample/reliability/icc.rb', line 98

def initialize(ds, opts=Hash.new)
  @ds=ds.reject_values(*Daru::MISSING_VALUES)
  @vectors=@ds.map { |e| e }
  @n=@ds.nrows
  @k=@ds.ncols
  compute
  @g_rho=0
  @alpha=0.05
  @icc_name=nil
  opts_default={:name=>"Intra-class correlation", :type=>:icc_1}
  @opts=opts_default.merge(opts)
  @opts.each{|k,v| self.send("#{k}=",v) if self.respond_to? k }
end

Instance Attribute Details

#alpha ⇒ Object

Returns the value of attribute alpha.



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# File 'lib/statsample/reliability/icc.rb', line 96

def alpha
  @alpha
end

#df_bj ⇒ Object (readonly)

Returns the value of attribute df_bj.



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# File 'lib/statsample/reliability/icc.rb', line 33

def df_bj
  @df_bj
end

#df_bt ⇒ Object (readonly)

Create a ICC analysis for a given dataset Each vector is a different measurement. Only uses complete data (listwise deletion).



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# File 'lib/statsample/reliability/icc.rb', line 31

def df_bt
  @df_bt
end

#df_residual ⇒ Object (readonly)

Returns the value of attribute df_residual.



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# File 'lib/statsample/reliability/icc.rb', line 34

def df_residual
  @df_residual
end

#df_wt ⇒ Object (readonly)

Returns the value of attribute df_wt.



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# File 'lib/statsample/reliability/icc.rb', line 32

def df_wt
  @df_wt
end

#f ⇒ Object (readonly)

Returns the value of attribute f.



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# File 'lib/statsample/reliability/icc.rb', line 91

def f
  @f
end

#g_rho ⇒ Object

Returns the value of attribute g_rho.



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# File 'lib/statsample/reliability/icc.rb', line 95

def g_rho
  @g_rho
end

#icc_1 ⇒ Object (readonly)

:section: McGraw and Wong ICC denominations



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# File 'lib/statsample/reliability/icc.rb', line 61

def icc_1
  @icc_1
end

#icc_1_1 ⇒ Object (readonly)

:section: Shrout and Fleiss ICC denominations



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# File 'lib/statsample/reliability/icc.rb', line 52

def icc_1_1
  @icc_1_1
end

#icc_1_k ⇒ Object (readonly)

Returns the value of attribute icc_1_k.



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# File 'lib/statsample/reliability/icc.rb', line 55

def icc_1_k
  @icc_1_k
end

#icc_2_1 ⇒ Object (readonly)

Returns the value of attribute icc_2_1.



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# File 'lib/statsample/reliability/icc.rb', line 53

def icc_2_1
  @icc_2_1
end

#icc_2_k ⇒ Object (readonly)

Returns the value of attribute icc_2_k.



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# File 'lib/statsample/reliability/icc.rb', line 56

def icc_2_k
  @icc_2_k
end

#icc_3_1 ⇒ Object (readonly)

Returns the value of attribute icc_3_1.



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# File 'lib/statsample/reliability/icc.rb', line 54

def icc_3_1
  @icc_3_1
end

#icc_3_k ⇒ Object (readonly)

Returns the value of attribute icc_3_k.



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# File 'lib/statsample/reliability/icc.rb', line 57

def icc_3_k
  @icc_3_k
end

#icc_a_1 ⇒ Object (readonly)

Returns the value of attribute icc_a_1.



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# File 'lib/statsample/reliability/icc.rb', line 63

def icc_a_1
  @icc_a_1
end

#icc_a_k ⇒ Object (readonly)

Returns the value of attribute icc_a_k.



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# File 'lib/statsample/reliability/icc.rb', line 66

def icc_a_k
  @icc_a_k
end

#icc_c_1 ⇒ Object (readonly)

Returns the value of attribute icc_c_1.



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# File 'lib/statsample/reliability/icc.rb', line 62

def icc_c_1
  @icc_c_1
end

#icc_c_k ⇒ Object (readonly)

Returns the value of attribute icc_c_k.



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# File 'lib/statsample/reliability/icc.rb', line 65

def icc_c_k
  @icc_c_k
end

#icc_k ⇒ Object (readonly)

Returns the value of attribute icc_k.



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# File 'lib/statsample/reliability/icc.rb', line 64

def icc_k
  @icc_k
end

#k ⇒ Object (readonly)

Returns the value of attribute k.



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# File 'lib/statsample/reliability/icc.rb', line 69

def k
  @k
end

#lbound ⇒ Object (readonly)

Returns the value of attribute lbound.



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# File 'lib/statsample/reliability/icc.rb', line 92

def lbound
  @lbound
end

#ms_bj ⇒ Object (readonly) Also known as: jms, msc

Returns the value of attribute ms_bj.



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# File 'lib/statsample/reliability/icc.rb', line 38

def ms_bj
  @ms_bj
end

#ms_bt ⇒ Object (readonly) Also known as: bms, msr

Returns the value of attribute ms_bt.



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# File 'lib/statsample/reliability/icc.rb', line 36

def ms_bt
  @ms_bt
end

#ms_residual ⇒ Object (readonly) Also known as: ems, mse

Returns the value of attribute ms_residual.



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# File 'lib/statsample/reliability/icc.rb', line 39

def ms_residual
  @ms_residual
end

#ms_wt ⇒ Object (readonly) Also known as: wms, msw

Returns the value of attribute ms_wt.



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# File 'lib/statsample/reliability/icc.rb', line 37

def ms_wt
  @ms_wt
end

#n ⇒ Object (readonly)

Returns the value of attribute n.



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# File 'lib/statsample/reliability/icc.rb', line 69

def n
  @n
end

#name ⇒ Object

Returns the value of attribute name.



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# File 'lib/statsample/reliability/icc.rb', line 97

def name
  @name
end

#r ⇒ Object (readonly)

ICC value, set with :type



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# File 'lib/statsample/reliability/icc.rb', line 90

def r
  @r
end

#total_mean ⇒ Object (readonly)

Returns the value of attribute total_mean.



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# File 'lib/statsample/reliability/icc.rb', line 70

def total_mean
  @total_mean
end

#type ⇒ Object

Type of analysis, for easy summarization By default, set to :icc_1

  • Shrout & Fleiss(1979) denominations

    • :icc_1_1

    • :icc_2_1

    • :icc_3_1

    • :icc_1_k

    • :icc_2_k

    • :icc_3_k

  • McGraw & Wong (1996) denominations

    • :icc_1

    • :icc_k

    • :icc_c_1

    • :icc_c_k

    • :icc_a_1

    • :icc_a_k



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# File 'lib/statsample/reliability/icc.rb', line 88

def type
  @type
end

#ubound ⇒ Object (readonly)

Returns the value of attribute ubound.



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# File 'lib/statsample/reliability/icc.rb', line 93

def ubound
  @ubound
end

Instance Method Details

#compute ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 196

def compute
  @df_bt=n-1
  @df_wt=n*(k-1)
  @df_bj=k-1
  @df_residual=(n-1)*(k-1)
  @total_mean=@vectors.inject(0){|ac,v| ac+v.sum}.quo(n*k)
  vm=@ds.vector_mean
  
  @ss_bt=k*vm.ss(@total_mean)
  @ms_bt=@ss_bt.quo(@df_bt)
  
  @ss_bj=n*@vectors.inject(0){|ac,v| ac+(v.mean-@total_mean).square}
  @ms_bj=@ss_bj.quo(@df_bj)
  
  @ss_wt=@vectors.inject(0){|ac,v| ac+(v-vm).ss(0)}
  @ms_wt=@ss_wt.quo(@df_wt)
  
  @ss_residual=@ss_wt-@ss_bj
  @ms_residual=@ss_residual.quo(@df_residual)
  ###
  # Shrout and Fleiss denomination
  ###
  # ICC(1,1) / ICC(1)
  @icc_1_1=(bms-wms).quo(bms+(k-1)*wms) 
  # ICC(2,1) / ICC(A,1)
  @icc_2_1=(bms-ems).quo(bms+(k-1)*ems+k*(jms - ems).quo(n))  
  # ICC(3,1) / ICC(C,1)
  @icc_3_1=(bms-ems).quo(bms+(k-1)*ems) 
  
  
  
  # ICC(1,K) / ICC(K)
  @icc_1_k=(bms-wms).quo(bms) 
  # ICC(2,K) / ICC(A,k)
  @icc_2_k=(bms-ems).quo(bms+(jms-ems).quo(n))
  # ICC(3,K) / ICC(C,k) = Cronbach's alpha
  @icc_3_k=(bms-ems).quo(bms) 
  
  ###
  # McGraw and Wong
  ###
  
end

#icc_1_1_ci(alpha = 0.05) ⇒ Object

Intervale of confidence for ICC (1,1)



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# File 'lib/statsample/reliability/icc.rb', line 312

def icc_1_1_ci(alpha=0.05)
  per=1-(0.5*alpha)
 
  fu=icc_1_f.f*Distribution::F.p_value(per, @df_wt, @df_bt)
  fl=icc_1_f.f.quo(Distribution::F.p_value(per, @df_bt, @df_wt))
  
  [(fl-1).quo(fl+k-1), (fu-1).quo(fu+k-1)]
end

#icc_1_f(rho = 0.0) ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 240

def icc_1_f(rho=0.0)
  num=msr*(1-rho)
  den=msw*(1+(k-1)*rho)
  Statsample::Test::F.new(num, den, @df_bt, @df_wt)
end

#icc_1_f_shrout ⇒ Object

F test for ICC Case 1. Shrout and Fleiss



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# File 'lib/statsample/reliability/icc.rb', line 307

def icc_1_f_shrout
  Statsample::Test::F.new(bms, wms, @df_bt, @df_wt)
end

#icc_1_k_ci(alpha = 0.05) ⇒ Object

Intervale of confidence for ICC (1,k)



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# File 'lib/statsample/reliability/icc.rb', line 322

def icc_1_k_ci(alpha=0.05)
  per=1-(0.5*alpha)
  fu=icc_1_f.f*Distribution::F.p_value(per, @df_wt, @df_bt)
  fl=icc_1_f.f.quo(Distribution::F.p_value(per, @df_bt, @df_wt))
  [1-1.quo(fl), 1-1.quo(fu)]
end

#icc_1_k_f(rho = 0) ⇒ Object

One way random F, type k



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# File 'lib/statsample/reliability/icc.rb', line 246

def icc_1_k_f(rho=0)
  num=msr*(1-rho)
  den=msw
  Statsample::Test::F.new(num, den, @df_bt, @df_wt)
end

#icc_2_1_ci(alpha = 0.05) ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 350

def icc_2_1_ci(alpha=0.05)
  icc_2_1_ci_mcgraw
end

#icc_2_1_ci_mcgraw(alpha = 0.05) ⇒ Object

Confidence interval ICC(A,1), McGawn



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# File 'lib/statsample/reliability/icc.rb', line 356

def icc_2_1_ci_mcgraw(alpha=0.05)
  fd,fu=icc_2_1_fs(icc_2_1,alpha)
  cl=(n*(msr-fd*mse)).quo(fd*(k*msc+(k*n-k-n)*mse)+n*msr)
  cu=(n*(fu*msr-mse)).quo(k*msc+(k*n-k-n)*mse+n*fu*msr)
  [cl,cu]
end

#icc_2_1_fs(pp, alpha = 0.05) ⇒ Object

F* for ICC(2,1) and ICC(2,k)



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# File 'lib/statsample/reliability/icc.rb', line 338

def icc_2_1_fs(pp,alpha=0.05)
  fj=jms.quo(ems)
  per=1-(0.5*alpha)
  vn=(k-1)*(n-1)*((k*pp*fj+n*(1+(k-1)*pp)-k*pp)**2)
  vd=(n-1)*(k**2)*(pp**2)*(fj**2)+((n*(1+(k-1)*pp)-k*pp)**2)
  v=vn.quo(vd)
  f1=Distribution::F.p_value(per, n-1,v)
  f2=Distribution::F.p_value(per, v, n-1)
  [f1,f2]
end

#icc_2_f ⇒ Object

F test for ICC Case 2



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# File 'lib/statsample/reliability/icc.rb', line 330

def icc_2_f
  Statsample::Test::F.new(bms, ems, @df_bt, @df_residual)
end

#icc_2_k_ci(alpha = 0.05) ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 363

def icc_2_k_ci(alpha=0.05)
  icc_2_k_ci_mcgraw(alpha)
end

#icc_2_k_ci_mcgraw(alpha = 0.05) ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 367

def icc_2_k_ci_mcgraw(alpha=0.05)
  f1,f2=icc_2_1_fs(icc_2_k,alpha)
  [
  (n*(msr-f1*mse)).quo(f1*(msc-mse)+n*msr),
  (n*(f2*msr-mse)).quo(msc-mse+n*f2*msr)
  ]
  
end

#icc_2_k_ci_shrout(alpha = 0.05) ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 375

def icc_2_k_ci_shrout(alpha=0.05)
  ci=icc_2_1_ci(alpha)
  [(ci[0]*k).quo(1+(k-1)*ci[0]), (ci[1]*k).quo(1+(k-1)*ci[1])]
end

#icc_3_1_ci(alpha = 0.05) ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 385

def icc_3_1_ci(alpha=0.05)
  per=1-(0.5*alpha)
  fl=icc_3_f.f.quo(Distribution::F.p_value(per, @df_bt, @df_residual))
  fu=icc_3_f.f*Distribution::F.p_value(per, @df_residual, @df_bt)
  [(fl-1).quo(fl+k-1), (fu-1).quo(fu+k-1)]
end

#icc_3_f ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 381

def icc_3_f
  Statsample::Test::F.new(bms, ems, @df_bt, @df_residual)
end

#icc_3_k_ci(alpha = 0.05) ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 392

def icc_3_k_ci(alpha=0.05)
  per=1-(0.5*alpha)
  fl=icc_3_f.f.quo(Distribution::F.p_value(per, @df_bt, @df_residual))
  fu=icc_3_f.f*Distribution::F.p_value(per, @df_residual, @df_bt)
  [1-1.quo(fl),1-1.quo(fu)]
end

#icc_a_1_f(rho = 0) ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 279

def icc_a_1_f(rho=0)
  fj=jms.quo(ems)
  num=msr
  den=a(rho)*msc+b(rho)*mse
  pp = @icc_2_1
  vn=(k-1)*(n-1)*((k*pp*fj+n*(1+(k-1)*pp)-k*pp)**2)
  vd=(n-1)*(k**2)*(pp**2)*(fj**2)+((n*(1+(k-1)*pp)-k*pp)**2)
  v=vn.quo(vd)
  Statsample::Test::F.new(num, den, @df_bt, v)        
end

#icc_a_k_f(rho = 0) ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 290

def icc_a_k_f(rho=0)
  num=msr
  den=c(rho)*msc+d(rho)*mse
  
  fj=jms.quo(ems)
  
  pp = @icc_2_k
  vn=(k-1)*(n-1)*((k*pp*fj+n*(1+(k-1)*pp)-k*pp)**2)
  vd=(n-1)*(k**2)*(pp**2)*(fj**2)+((n*(1+(k-1)*pp)-k*pp)**2)
  v=vn.quo(vd)
  
  
  Statsample::Test::F.new(num, den, @df_bt,v)        

end

#icc_c_1_f(rho = 0) ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 252

def icc_c_1_f(rho=0)
  num=msr*(1-rho)
  den=mse*(1+(k-1)*rho)
  Statsample::Test::F.new(num, den, @df_bt, @df_residual)
end

#icc_c_k_ci(alpha = 0.05) ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 399

def icc_c_k_ci(alpha=0.05)
  per=1-(0.5*alpha)
  fl=icc_c_k_f.f.quo(Distribution::F.p_value(per, @df_bt, @df_residual))
  fu=icc_c_k_f.f*Distribution::F.p_value(per, @df_residual, @df_bt)
  [1-1.quo(fl),1-1.quo(fu)]
end

#icc_c_k_f(rho = 0) ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 257

def icc_c_k_f(rho=0)
  num=(1-rho)
  den=1-@icc_3_k
  Statsample::Test::F.new(num, den, @df_bt, @df_residual)
end

#report_building(b) ⇒ Object 



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# File 'lib/statsample/reliability/icc.rb', line 405

def report_building(b)
   b.section(:name=>name) do |s|
     s.text @icc_name
     s.text _("ICC: %0.4f") % @r
     s.parse_element(@f)
     s.text _("CI (%0.2f): [%0.4f - %0.4f]") % [(1-@alpha)*100, @lbound, @ubound]
   end
end