poly3test               package:MCPAN               R Documentation

_A_p_p_r_o_x_i_m_a_t_e _s_i_m_u_l_t_a_n_e_o_u_s _t_e_s_t _f_o_r _p_o_l_y-_3-_a_d_j_u_s_t_e_d _t_u_m_o_u_r _r_a_t_e_s

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

     P-value of maximum test and adjusted p-values for M contrasts of I
     groups in a one-way layout. Based on approximation of the true
     distribution of the M test statistics by an M-variate normal
     distribution.

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

     poly3test(time, status, f, type = "Dunnett", cmat = NULL, method = "BP", alternative = "two.sided")

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

    time: a numeric vector of times of death of the individuals

  status: a logical (or numeric, consisting of 0,1 only) vector giving
          the tumour status at time of death of each individual, where
          TRUE (1) = tumour present, FALSE (0) = no tumour present  

       f: a factor of the same length as 'time' 'status', giving the
          levels of a grouping variable in a one-way layout 

    type: a character string specifying the contrast type 

    cmat: an optional user defined contrast matrix of dimension MxI

  method: a single charcter string, specifying the method for
          adjustment, with options: "BP" (Bailer Portier: assuming
          poly-3-adjusted rates are binomial variables), "BW" (Bieler,
          Williams: delta method as in Bieler-Williams (1993)) "ADD1"
          (as Bailer Portier, including an add1-adjustment on the raw
          tumour rates) "ADD2" (as Bailer Portier, including an
          add2-adjustment on the raw tumour rates following Agresti
          Caffo (2000) for binomials) 

alternative: a character string specifying the direction of the
          alternative hypothesis

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

     Please note

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

     An object of class "poly3test", a list containing:

teststat: a numeric vector of teststatistics of length M

    pval: a single numeric p-value, the p-value of the maximum test
          (minimum p-value)

p.val.adj: a vector of length M, the adjusted p-values of the single
          contrasts

alternative: a single character vector, as the input

    time: as input

  status: as input

       f: as input

  method: as input

    cmat: used contrast matrix

sample.est: a list containing sample estimates

_N_o_t_e:

     Please note that all methods here described are only
     approximative, and might violate the nominal level in certain
     situations. Please note further that appropriateness of the point
     estimates, and consequently of tests and confidence intervals is
     based on the assumptions in Bailer and Portier (1988), which might
     be a matter of controversies.

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

     Frank Schaarschmidt

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

     Assumption with regard to data as in: Bailer, J.A. and Portier,
     C.J. (1988): Effects of treatment-induced mortality and
     tumor-induced mortality on tests for carcinogenicity in small
     samples. Biometrics 44, 417-431.

     Peddada, S.D., Dinse, G.E., and Haseman, J.K. (2005): A
     survival-adjusted quantal response test for comparing tumor
     incidence rates. Applied Statistics 54, 51-61.

     Statistical procedures and characterization of coverage
     probabilities are described in: Sill, M. (2007): .... Master
     thesis, Institute of Biostatistics, Leibniz University Hannover.

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

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

     # poly-3-adjusted tumour rates with a potential
     # down-turn effect for the highest dose group "4":

     data(methyl)

     # many-to-one:
     methylD<-poly3test(time=methyl$death, status=methyl$tumour, f=methyl$group, type = "Dunnett", method = "ADD1" )
     methylD

     # Williams-Contrast:
     methylW<-poly3test(time=methyl$death, status=methyl$tumour, f=methyl$group, type = "Williams", method = "ADD1" )
     methylW

     # Changepoint-Contrast:
     methylCh<-poly3test(time=methyl$death, status=methyl$tumour, f=methyl$group, type = "Change", method = "ADD1" )
     methylCh

