All data files are limited to 80 character lengths. Repeating variables which exceed 80 characters extend to the following line. All integers must be right justified within the field. Real variables may include a decimal or whole numbers may be right justified. Double precision variables have seven digit precision.
NAME DESCRIPTION COLUMN TYPE
Line repeated for each non-founder pedigree member. LPEDGR Pedigree number 1-8 Integer JFATH Father's ID number 9-16 Integer JMOTH Mother's ID number 17-24 Integer JCHLD Pedigree member's ID number 25-32 Integer
Line repeated for each pair of parents. JPED Pedigree number 1-8 Integer IFAMEM(1) Husband's ID number 9-16 Integer IFAMEM(2) Wife's ID number 17-24 Integer
Required first line(s). NDATA Number of variables in phen.dat 1-4 Integer NCOL Number of columns in phen.dat (maximum = 39) 5-8 Integer NAME(I) Name of variable I, I = 1, NDATA 9-16,17-24,etc Character Required line(s). IVARTP(I) Type of variable I, I = 1, NDATA 9-12,17-20,etc Integer = 1, discrete = 2, quantitative = 3, autosomal marker = 4, X-linked marker = 5, autosomal codominant marker specified as alleles = 6, X-linked codominant marker specified as alleles IVARDF(I) Definition of variable I, I = 1, NDATA 13-16,21-24,etc Integer = 0, if IVARTP(I) = 1 and prevalence/incidence rates will not be used or if IVARTP(I) = 2 = location in popln.dat of prevalence/incidence rates if IVARTP(I) = 1 = (-) number of alleles, if IVARTP(I) = 3, 4, 5, or 6 and if no frequency/phenotype information in popln.dat = location in popln.dat of frequency/phenotype information, if IVARTP(I) = 3, 4, 5, or 6 Optional line(s). MISVL(I) = -9999 if not included. -1 Code to indicate line of missing values 1-8 Integer MISVL(I) Missing value code for variable I, I = 1, NDATA 9-16,17-24,etc Real Optional line(s). PHSIM(I) = -99999 if not included. -2 Code to indicate line of simulation indicators 1-8 Integer PHSIM(I) Simulation indicator for variable I, I = 1, NDATA 9-16,17-24,etc Real Optional line(s). Mean(I) = 0 if not included. -3 Code to indicate line of values to subtract 1-8 Integer MEAN(I) Value to subtract from variable I, I = 1, NDATA 9-16,17-24,etc Real Optional line(s). SD(I) = 1 if not included. -4 Code to indicate line of values to divide by 1-8 Integer SD(I) Value by which to divide variable I, I = 1, NDATA 9-16,17-24,etc Real Optional line(s). PW(I) = 1 if not included. -5 Code to indicate line of power terms 1-8 Integer PW(I) p from the power function r/p[(x/r + 1)p - 1] 9-16,17-24,etc Real [MacLean et al 1976] for variable I, I = 1, NDATA, where x represents the individual's quantitative phenotype, r equals 6; the variable is assumed already standardized
Line repeated for each measured individual. ID ID number corresponding to trip.dat 1-8 Integer PHEN Individual's phenotype for column I, I = 1, NCOL 9-16,17-24,etc Real
File popln.dat can contain sets of lines of two types: for traits and for markers.
TRAIT SET: Initial line. NCATEG Number of age groups or severity categories 1-4 Integer TRAIT SET: Line repeated NCATEG times. IRANG1(I) Lower limit of age group or severity category 1-4 Integer IRANG2(I) Upper limit of age group or severity category 5-8 Integer RATE(1, I) Incidence/prevalence in males for a sex-specific model in both genders combined for a non-sex-specific model RATE(2, I) Incidence/prevalence 17-24 Real in females for a sex-specific model unused if for a non-sex-specific model MARKER SET: Initial line. NLINES Number of additional lines in the set 1-4 CONPN Phenotype/genotype correspondent indicator 5-6 Logical = T, phenotype/genotype correspondences will follow = F, codominant inheritance XLINK Inheritance indicator 7-8 Logical = T, X-linked inheritance = F, autosomal inheritance MARKER SET: Second line. NALL Number of marker alleles 1-3 Integer FR(I) Frequency of allele I, I = 1, NALL 4-18,19-33,etc Real MARKER SET: Included if CONPN = T. NGNT Number of marker genotypes 1-4 Integer NMKPHN Number of marker phenotypes 5-8 Integer MARKER SET: Repeated NMKPHN time if CONPN = T. IP(I) Phenotype/genotype correspondent for marker genotype I, 1-2,3-4,etc Integer I = 1, NGNT = 1, genotype possible for phenotype = 0, genotype not possible for phenotype
First line. NDATA Number of variables 1-8 Integer IASCR Ascertainment correction indicator 9-10 Logical = T, ascertainment correction = F, no ascertainment correction Second line(s) (taken from header.dat). NAMEV(I) Name of variable I, I = 1, NDATA 1-8,9-16,etc Character Following line(s) (taken from header.dat). IVARTP(I) Type of variable I, I = 1, NDATA 1-4,9-12,etc Integer IVARDF(I) Definition of variable I, I = 1, NDATA 5-8,13-16,etc Integer Repeated for each pedigree. NUMPED Pedigree number (taken from trip.dat) 1-8 Integer NINDPD Number of individuals in the pedigree 9-16 Integer NFAMPD Number of nuclear families in the pedigree 17-24 Integer IDNMBR(I) ID of individual assigned pedigree location I, I=1,NINDPD 25-32,49-56,etc Integer LOCFTH(I) Pedigree location of father of I, I = 1, NINDPD 33-40,57-64,etc Integer LOCMTH(I)Pedigree location of mother of I, I = 1, NINDPD 41-48,65-72,etc Integer Repeated NFAMPD times. IFATH Family location of father 1-8 Integer IMOTH Family location of mother 9-16 Integer NCHJT Number of offspring requiring joint likelihoods 17-24 Integer ICH(I) Family location of offspring, I = 1, NCHJT 25-32,+ Integer NCS Number in the cutset 33-40 Integer NMEMJT Number requiring joint likelihoods 41-48 Integer NFAMEM Number in the family 49-56 Integer LOCID(I) Pedigree location for family location I, I = 1, NFAMEM 57-64,65-72,etc Integer Repeated NINDPD times. PH(I) Phenotype for variable I, I = 1, NDATA 1-13,14-26,etc Double
First line. NAMEMD Name to identify the file 2-11 Character IFRSBR Number of frequency subroutine selected 12-14 Integer ITRSBR Number of transmission subroutine selected 15-17 Integer IMDSBR Number of major locus discrete subroutine selected 18-20 Integer IMQSBR Number of major locus quantitative subroutine selected 21-23 Integer IWGSBR Number of within genotype subroutine selected 24-26 Integer IPNSBR Number of penetrance subroutine assigned 27-29 Integer IVTPMD Code designating quantitative/discrete 30-32 Integer = 0, neither discrete nor quantitative = 1, discrete only = 2, quantitative only = 3, both discrete and quantitative Second line. FRNAME Name of frequency subroutine selected 2-11 Character TRNAME Name of transmission subroutine selected 13-22 Character MDNAME Name of major locus discrete subroutine selected 24-33 Character MQNAME Name of major locus quantitative subroutine selected 35-44 Character WGNAME Name of within genotype subroutine selected 46-55 Character PNNAME Name of penetrance subroutine assigned 57-66 Character CRNAME Name of correlated penetrance subroutine assigned 68-77 Character Third line. IXACOD Genotype-assignment code 1-3 Integer NLOCI Number of loci 4-6 Integer NLOCIX Number of X-linked loci 7-9 Integer NALL(I) Number of alleles, I = 1, NLOCI 10-12,13-15,etc Integer Fourth line. NVAR Number of variables in the model 1-3 Integer NMARKR Number of markers in the model 4-6 Integer NTRAIT Number of traits in the model 7-9 Integer NCNTP(1) Number of types of concomitants for discrete traits 10-12 Integer NCN(I,1) Number of concomitants of type I, I = 1,NCNTP(1) 13-15,+ Integer NCNTP(2) Number of types of concomitants for quantitative traits 16-18 Integer NCN(I,2) Number of concomitants of type, I = 1, NCNTP(2) 19-21,+ Integer NCNTP(3) Number of types of concomitants for within genotypes 22-24 Integer NCN(I,3) Number of concomitants of type, I = 1, NCNTP(3) 25-27,+ Integer LOCVAR(I) Location of variable in phen.dat, I = 1, NVAR 28-30,31-33,etc Integer IVARTP(0) Type of simulated variable 31-33 Integer Line included if NMARKR > 0. KMARKR(I) Position in LOCVAR of marker I, I = 1, NMARKR 1-3,7-9,etc Integer LMARKR(I) Locus of marker I, I = 1, NMARKR 4-6,10-12,etc Integer Line included if NTRAIT > 0. KTRAIT(I) Position in LOCVAR of trait I, I = 1, NTRAIT 1-3,10-12,etc Integer LTRAIT(I) First locus of trait I, I = 1, NTRAIT 4-6,13-15,etc Integer JTRAIT(I) Last locus of trait I, I = 1, NTRAIT 7-9,16-18,etc Integer Line included if NTRAIT > 0. KCNML(I,J) Major locus concomitant locations, I = 1, NCNTP(L), 1-3,+ Integer J = 1, NTRAIT KCNWG(I) Within genotype concomitant locations, I = 1, NCNTP(3) 4-6,+ Integer Repeated for each parameter type for each discrete trait. NPR Number of major locus discrete parameters 1-3 Integer PARMD(I) Values of major locus discrete parameters, I = 1, NPR 4-18,19-33,etc Double Repeated for each parameter type for each quantitative trait. NPR Number of major locus quantitative parameters 1-3 Integer PARMQ(I) Values of major locus quantitative parameters, I = 1, NPR 4-18,19-33,etc Double Repeated for each parameter type for each trait. NPR Number of within genotype parameters 1-3 Integer PARWG(I) Values of within genotype parameters, I = 1, NPR 4-18,19-33,etc Double Determined by the frequency subroutine selected. NFREQS Number of sets of frequencies 1-3 Integer Line repeated NFREQS times. NFREQ Number of frequencies (negative indicates in popln.dat) 1-3 Integer FREQ(I) Frequency of classification I, I = 1, NFREQ 4-18,19-33,etc Double If NLOCI > 1. N Number of probabilities = NLOCI - 1 1-3 Integer RCMMTH(I) Female probability of recombination between locus I-1 4-18,19-33,etc Real and locus I, I = 2, NLOCI If NLOCI > NLOCIX + 1. N Number of probabilities = NLOCI - NLOCIX - 1 1-3 Integer RCMFTH Male probability of recombination between locus I-1 4-18,19-33,etc Real and locus I, I = NLOCIX + 1, NLOCI If NLOCI = 1 and NALL = 2. N Number of probabilities = NGENTL 1-3 Integer TRNDAU(I) Probability allele transmitted to daughter if 4-18,19-33,etc Real parent genotype I, I = 1, NGENTL If NLOCI = 1, NALL = 2, and IAXCOD 1 or 3. N Number of probabilities = NGENTL 1-3 Integer TRNSON(I) Probability allele transmitted to son if 4-18,19-33,etc Real parent genotype I, I = 1, NGENTL Following line. NPARAM Number of parameters to maximize, grid or 1-3 Integer compute standard errors Repeated NPARAM times for each parameter to maximize, standard error or grid. X Parameter value 1-15 Double BOUND1 Lower bound for grid or maximization 16-30 Double BOUND2 Upper bound for grid or maximization 31-45 Double NPARSM Number of parameters held to value 46-48 Integer LPARAM Array element of parameter 49-52 Integer KPARAM Code identifying parameter 53-55 Integer = 1, FREQ = 2, TRNDAU = 3, TRNSON = 4, RCMMTH = 5, RCMFTH = 6 to 5+NTRAIT, PARMD = 6+NTRAIT to 5+2 NTRAIT, PARMQ = 6+2 NTRAIT to 5+3 NTRAIT, PARWG Next line. NCLIN Number of linear constraints 1-3 Integer Repeated NCLIN times. BOUND1 Lower bound for constraint 1-15 Double BOUND2 Upper bound for constraint 16-30 Double CONLIN(I) Weight for parameter I, I = 1, NPARAM 31-45,46-60,etc Double
Initial line of the set repeated for each papfq
NUMSBR Number stored as JFRSBR in papfq 1-3 Integer NLDESC Number of lines of description 4-6 Integer NLTOTL Number of additional lines in set 7-9 Integer JXACOD Genotype-assignment code indicator 10-12 Integer > 0, equals the code allowed = 0, unrestricted < 0, equals the negative of the code not allowed NUMLOC Number of loci indicator 13-15 Integer > 0, equals the number allowed = 0, unrestricted NUMALL Number of alleles indicator 16-18 Integer > 0, equals the number allowed = 0, unrestricted IFRTYP Frequency parameter code 19-21 Integer = 1, alleles = 2, haplotypes = 3, genotypes = 4, conditional alleles Second line. FRNAME Name of frequency subroutine 2-11 Character Line repeated NLDESC lines. DESCR Description of subroutine 1-50 Character Next line. IFRTYP Frequency parameter code 1-3 Integer = 1, alleles = 2, conditional alleles = 3, haplotypes = 4, genotypes NFRPR Number of frequency parameters 4-6 Integer Repeated NPARFR times. IFRNG Range code for frequency parameter 1-3 Integer = 1, -infinity to infinity = 2, 0 to infinity = 3, 0.01 to infinity = 4, 0 to 1 = 5, -.99 to .99 = 6, -.99 to .99, not equivalent = 7, 0 to 1, sum restricted DSFR Name of frequency parameter 5-24 Character
Initial line of set for each version of paptc. NUMSBR Number stored as JTRSBR in paptc 1-3 Integer NLDESC Number of lines of description 4-6 Integer NLTOTL Number of additional lines in the set 7-9 Integer JXACOD Genotype-assignment code indicator > 0, equals the code allowed = 0, unrestricted < 0, equals the negative of the code not allowed NUMLOC Number of loci indicator 10-12 Integer > 0, equals the number allowed = 0, unrestricted NUMALL Number of alleles indicator 13-15 Integer > 0, equals the number allowed = 0, unrestricted IRQHW Hardy-Weinberg requirement indicator 16-18 Integer = 0, doesn't require Hardy-Weinberg for the frequencies = 1, requires Hardy-Weinberg for the frequencies Second line. TRNAME Name of subroutine 1-10 Character Repeated NLDESC times. DESCR Description of subroutine 1-50 Character Following line. INDTRP Transmission probability indicator 1-3 Integer = 0, TRNDAU, TRNSON not used = 1, TRNDAU, TRNSON used = 2, TRNDAU, TRNSON used except for heterozygotes INDRCM Recombination probability indicator 4-6 Integer = 0, RCMMTH, RCMFTH not used = 1, RCMMTH, RCMFTH used B.10. Major Locus Discrete Subroutine List: dmlp.dat Initial line of set for each dmlpr. NUMSBR Number stored as JMDSBR in dmlpr 1-3 Integer NLDESC Number of lines of description 4-6 Integer NLTOTL Number of additional lines in the set 7-9 Integer NUMLOC Number of loci indicator 10-12 Integer > 0, equals the number allowed = 0, unrestricted NUMALL Number of alleles indicator 13-15 Integer > 0, equals the number allowed = 0, unrestricted IXA Mode of inheritance indicator 16-18 Integer = 0, unspecified = 1, X-linked inheritance = 2, autosomal inheritance IPOPN Population data indicator 19-21 Integer = 0, population data not necessary = 1, population data required Second line. MDNAME Name of subroutine 1-10 Character Repeated NLDESC times. DESCR Description of subroutine 1-50 Character Following line. NCNTP Number of concomitant types 1-3 Integer NPRTP Number of parameter types 4-6 Integer Repeated NCNTP times. NC Number of concomitants 1-3 Integer > 0, equals the number required < 0, equals the negative of the corresponding parameter DSCN Name of concomitant 5-24 Character Repeated NPARPN times. IPRCD Number of parameter values 1-3 Integer > 0, number of values = -99, equal to the number of trait genotypes = -98, equal to the trait number - 1 = -97, # of trait loci if not sex-specific, twice otherwise = -96, # of trait loci if not parent-specific, twice otherwise < 0, user queried for number IPRNG Range code for parameter 4-6 Integer = 1, -infinity to infinity = 2, 0 to infinity = 3, 0.01 to infinity = 4, 0 to 1 = 5, -.99 to .99 = 6, -.99 to .99, not equal = 7, 0 to 1, sum restricted DSPR Name of parameter 8-27 Character
Initial line of set for each qmlpr. NUMSBR Number stored as JMQSBR in qmlpr 1-3 Integer NLDESC Number of lines of description 4-6 Integer NLTOTL Number of additional lines in the set 7-9 Integer NUMLOC Number of loci indicator 10-12 Integer > 0, equals the number allowed = 0, unrestricted NUMALL Number of alleles indicator 13-15 Integer > 0, equals the number allowed = 0, unrestricted IXA Mode of inheritance indicator 16-18 Integer = 0, unspecified = 1, X-linked inheritance = 2, autosomal inheritance IPOPN Population data indicator 19-21 Integer = 0, population data not necessary = 1, population data required Second line. MQNAME Name of subroutine 1-10 Character Repeated NLDESC times. DESCR Description of subroutine 1-50 Character Following line. IVRTP Discrete data indicator 1-3 Integer = 0, no discrete data = 1, discrete data for some individuals Following line. NCNTP Number of concomitant types 1-3 Integer NPRTP Number of parameter types 4-6 Integer Repeated NCNTP times. NCN Number of concomitants 1-3 Integer > 0, equals number < 0, equals negative of corresponding parameter DSCN Name of concomitant 5-24 Character Repeated NPARPN times. IPRCD Number of parameter values 1-3 Integer > 0, number of values = -99, equals number of trait genotypes = -98, equals trait number - 1 = -97, 1 if not sex-specific, 2 if sex-specific < 0, user queried for number IPRNG Range code for parameter 4-6 Integer = 1, -infinity to infinity = 2, 0 to infinity = 3, 0.01 to infinity = 4, 0 to 1 = 5, -.99 to .99 = 6, -.99 to .99, not equal = 7, 0 to 1, sum restricted DSPR Name of parameter 8-27 Character
Initial line of set for each papwg. NUMSBR Number stored as JWGSBR in papwg 1-3 Integer NLDESC Number of lines of description 4-6 Integer NLTOTL Number of additional lines in the set 7-9 Integer Second line. WGNAME Name of subroutine 1-10 Character Repeated NLDESC times. DESCR Description of subroutine 1-50 Character Following line. MLMX Major locus/mixed model indicator 1-3 Integer 0 = major locus 1 = mixed Following line. NCNTP Number of concomitant types 1-3 Integer NPRTP Number of parameter types 4-6 Integer Repeated NCNTP times. NCN Number of concomitants 1-3 Integer > 0, equals number < 0, equals negative of corresponding parameter DSCN Name of concomitant 5-24 Character Repeated NPARPN times. IPRCD Number of parameter values 1-3 Integer > 0, equals number of values = -99, equals number of trait genotypes = -98, equals trait number - 1 = -97, equals 1 if not sex-specific, 2 if sex-specific < 0, user-specified number IPRNG Range code for parameter 4-6 Integer = 1, -infinity to infinity = 2, 0 to infinity = 3, 0.01 to infinity = 4, 0 to 1 = 5, -.99 to .99 = 6, -.99 to .99, not equal = 7, 0 to 1, sum restricted DSPR Name of parameter 8-27 Character