sensSpec              package:epibasix              R Documentation

_S_e_n_s_i_t_i_v_i_t_y _a_n_d _S_p_e_c_i_f_i_c_i_t_y _A_n_a_l_y_s_i_s _o_f _a _2_x_2 _M_a_t_r_i_x

_D_e_s_c_r_i_p_t_i_o_n:

     This function provides detailed information regarding the
     comparison of two competing methods, for example self-report and
     gold-standard treatment through a sensitivity/specificity
     analysis.

_U_s_a_g_e:

     sensSpec(X, alpha=0.05, CL=TRUE, digits=3)

_A_r_g_u_m_e_n_t_s:

       X: A 2x2 matrix, with Gold Standard Class A and B in the columns
          and Comparison Method A and B in the rows.

      CL: Logical: If TRUE, Confidence Intervals are calculated and
          displayed in summary method.

   alpha: The desired Type I Error Rate for Hypothesis Tests and
          Confidence Intervals

  digits: Number of Digits to round calculations

_D_e_t_a_i_l_s:

     This function is designed to calculate Sensitivity, Specificity,
     Youden's J and Percent Agreement. These tools are used to assess
     the validity of a new instrument or self-report against the
     current gold standard.  In general, self-report is less expensive,
     but may be subject to information bias.  Computational formulae
     can be found in the reference.

_V_a_l_u_e:

       X: The original input matrix.

    sens: The point estimate of sensitivity

    spec: The point estimate of specificity

      PA: The point estimate of Percent Agreement

 YoudenJ: The point estimate of Youden's J

  sens.s: The standard deviation of sensitivity

  spec.s: The standard deviation of specificity

    PA.s: The standard deviation of Percent Agreement

YoudenJ.s: The standard deviation of Youden's J

sens.CIL: The lower bound of the constructed confidence interval for
          true sensitivity.

sens.CIU: The upper bound of the constructed confidence interval for
          true sensitivity

spec.CIL: The lower bound of the constructed confidence interval for
          true specificity.

spec.CIU: The upper bound of the constructed confidence interval for
          true specificity.

  PA.CIL: The lower bound of the constructed confidence interval for
          Percent Agreement.

  PA.CIU: The upper bound of the constructed confidence interval for
          Percent Agreement.

YoudenJ.CIL: The lower bound of the constructed confidence interval for
          Youden's J.

YoudenJ.CIU: The upper bound of the constructed confidence interval for
          Youden's J.

   alpha: The desired Type I Error Rate for Hypothesis Tests and
          Confidence Intervals

  digits: Number of Digits to round calculations

_N_o_t_e:

     All confidence limits rely on simple asymptotic theory, as such,
     confidence limits may lie outside of [0,1].  A more accurate
     method is available in the twoby2 function of the Epi package,
     which employs a logit transformation.

_A_u_t_h_o_r(_s):

     Michael Rotondi, mrotondi@uwo.ca

_R_e_f_e_r_e_n_c_e_s:

     Szklo M and Nieto FJ.  Epidemiology: Beyond the Basics, Jones and
     Bartlett: Boston, 2007.

_S_e_e _A_l_s_o:

     'kappa'

_E_x_a_m_p_l_e_s:

     ## Not run: From Szklo and Nieto, p. 315
     dat <- cbind(c(18,1), c(19,11));
     summary(sensSpec(dat));

