renumbering program for the BLUPF90 family now works with SNP info
Ignacy Misztal and Ignacio Aguilar, University of Georgia
August 27, 2001 - Mar 17, 2011

RENUMF90 is a renumbering program for the BLUPF90 family of programs. It supports multiple traits, different effects per trait, alphanumeric and numeric fields. The program provides data statistics, performs comprehensive pedigree checking, and supports unknown parent groups etc.

It accepts files where fields in data and pedigree files are separated by spaces. The program is still in active development so errors are possible and some features may not work or work incorrectly.

Warnings

• input files cannot contain character #.
• missing animals have code 0; 00 may be treated as a known animal

The parameter file contains keywords in capital followed by specifications of a given effect/data item. The keywords need to be typed exactly. Specific keywords need to occur sequentially, as shown below.

IDs starting with “-” may not work

# Parameter file for program renf90; it is translated to parameter # file for BLUPF90 family of programs.

 Lines with # are treated as comments
    

   
DATAFILE
f1

 The data file is f1

   
TRAITS
t1 t2 .. tn

 t1-tn are positions of traits in datafile; n defines the number of traits

FIELDS_PASSED TO OUTPUT
p1 p2 .. pm
<file>
   fields p1-pn are passed to output without changes; can be empty
   
<file>
WEIGHT(S)
w

 w is  position of weight if present; can be empty

   
RESIDUAL_VARIANCE
r

 r is matrix of residual (co)variances  of size n x n

EFFECT
e1.. en type form

 this line defines one group of effects; e1 .. en are positions of this 
 effect for all traits; positions can be different for each trait for fixed
 effects; for random effects, only one position + 0 (misising) efefct are
 possible.
 
 type is 'cross' for crossclassified or 'cov' for covariables
 
 form is 'alpha' for alphanumeric or 'numer' for numeric

NESTED
d1 .. dn form

 optional for covariables only, specifies nesting; form is as above

RANDOM
rtype

 the RANDOM keyword occurs only if the current effect is random;
 rtype is 'diagonal', 'sire' or 'animal'

   
OPTIONAL
o1 o2.. oq
<file>
   causes extra effects appended to the animal effect; current options include
   'pe' for permanent environment, 'mat' for maternal, and 'mped' for maternal 
   permanent environment 

<file>      
FILE
fped

 for animal and sire model only, fped specifies the pedigree file

FILE_POS
an s d alt_dam yob

 for animal effect only; specifies positions in the pedigree file of animal
 an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob; missing
 alt_dam or yob can be replaced by 0; if this line is not given, defaults are 
 1 2 3 0 0. If maternal effect is specified, the maternal effect is due to
 position of d if alt_dam field is 0, or otherwise is due to alt_dam; If
 alt_dam field is not zero, it should include ID of real or recipient
 dam.
 

   
SNP_FILE
fsnp

 optional; fsnp specifies files with ID and SNP information; if present, the 
 relationship matrix will be constructed as in Aguilar et al. (2010) and will
 include the genomic information; file fsnp should start with ID with the
 same format as fped and SNP info needs to start from a fixed column and
 include digits 0, 1, 2 and 5; ID and SNP info need to be separated by
 at leats one space; see info for program PreGSf90 

   
PED_DEPTH
p

   
   optional for animal effect only; p specifies the depth of pedigree search; 
   the default is 3; all pedigrees are loaded if p=0.
   
GEN_INT
min avg max

   optional; specifies minimum, average and maximum generation interval;
   applicable only if year of birth present; minimum and maximum used for
   pedigree checks; average used to predict year of birth of parent with missing
   pedigree.
   
REC_SEX
i

   optional; if only one sex has records, specifies which parent it is; used for
   pedigree checks.
   
UPG_TYPE
t

   optional; 
   if t is 'yob', the asignment is based on year of birth; the
   subsequent line should contain list of years to separate different UPG; 
   
   if t is 'in_pedigrees', the value of a missing parent should be -x, where x is
   UPG number that this missing parent should be allocated to; in this option, 
   all known parents should have pedigree lines, i.e., each parent field should
   contain either the ID of a real parent, or a negative UPG number.
   
   if t is 'internal',  allocation is by a user-written function 
   custom_upg(year_of_birth,sex,ID, parent_code).

   
RANDOM_REGRESSION 
r_type

   Specifies that random regressions should be applied to the animal and
   corresponding effects (mat, pe and mpe), this keyword also could be 
   applied to set covariables for fixed effects; r_type is 'data' if covariables for
   random regressions are in the data, or "legendre' if legendre plynomials are
   to be generated from a single data variable; not yet implemented
   
RR_POSITION
r1 .. rq
   for random regressions, r1-rq specifies positions of covariables if
   r_type='data', or r1 is order of legendre polynomial and r2 is position of
   covariable if r_type='legendre'; not yet implemented
   
(CO)VARIANCES
g

   g are (co)variances for the animal effect; the dimensions of g should 
   account for the maternal effect if present
   
(CO)VARIANCES_PE
gpe

   gpe are (co)variances for the PE effect if present

(CO)VARIANCES_MPE
gmpe

   gmpe are (co)variances for the MPE effect if present


Sections starting from EFFECTS can be repeated any number of types.
If (Co)variances for any effect are missing, they are substituted with matrices containing 1.0 
on diagonals and 0.1 on off-diagonals. 

Warning: for variance estimation by EM REML,usually there is improved 
convergence rate if the starting values for (co)variances are too large 
than too small. 

The sequence of keywords should be as above although optional fields can be
skipped. Keywords out of order may not be recognized.

The following options can added at the end of the parameter file to redefine
parameter used to read the input file:

 - the default size of character fields
	OPTION alpha size nn
   where nn is the new size.

 - the size of th record length 
	OPTION max_string_readline nn
   where nn is the new size.

 - the maximun number of fields  
        OPTION max_field_readline nn
   where nn is the number of fields. 

 
The end of the parameter file for RENUMF90 can contain many lines beginning with OPTION. 
All of these lines are passed to parameter file renf90.par to be used by 
application programs. 


Combining fields or interactions
================================
Several fields in the data file can be combined into one using a COMBINE keyword. 
	COMBINE a b c ....
catenates b c ... into c. Keywords COMBINE need to be on top of the parameter
file, but possibly after comments. There may be many combined fields. 
For example:
	COMBINE 7 2 3 4
combines content of fields 2 3 4 into field 7; the data file is not changed,
only the program treats field 7 as fields 2 3 4 put together (without spaces). 
The combined fields can be treated as "numeric", if they are composed of numbers
and if their total length is <9. Otherwise, they need to be used as "alpha". 
Please note that the maximum size of the combined variable is limited by the
largest size of the "alpha" field.  



Additive Pedigree File
======================

The additive pedigree file(s) renadd* has the following structure:
   1) animal number (from 1)                                        
   2) parent 1 number or unknown parent group number for parent 1   
   3) parent 2 number or unknown parent group number for parent 2   
   4) 3 minus number of known parents                               
   5) known or estimated year of birth (0 if not provided)          
   6) number of known parents (parents might be eliminated if not   
      contributing; if animal has genotype 10+number of know parents                                                  
   7) number of records             
   8) number of progenies (before elimination due to other effects) 
      as parent 1
   9) number of progenies (before elimination due to other effects) 
      as parent 2  
  10) original animal id                                            



Extensions
==========

The program is being modified to support inbreeding, dominance, random
regressions with automatic calculations of Legendre polynomials,...


Example
========

data file - data.test
---------------------
1 aa 34.5 11 12 zz
3 bb 21.333 22 23 xx
8 cc 23.666 33 34 yy
1 dd 29 44 45 xx 
3 aa  30 55 56 yy
5 bb 1234567.890 66 67 zz

pedigree file - test.ped
------------------------
qq 0 0
aa 0 0
bb qq aa
cc qq 0
dd 0 aa

parameter file - testpar1
-------------------------
# Parameter file for program renf90; it is translated to parameter
# file for BLUPF90 family f programs.
DATAFILE
data.test
TRAITS
3 4
FIELDS_PASSED TO OUTPUT
2 1 # passing alphanumeric
WEIGHT(S)

RESIDUAL_VARIANCE
5 2
2 4
EFFECT
1 1 cross alpha
EFFECT
2 2 cross alpha
RANDOM
animal
OPTIONAL
mat mpe pe
FILE
test.ped
(CO)VARIANCES
10 3 2 1
3 11 4 5
2 4 12 6
1 5 6 13.01
(CO)VARIANCES_PE
5.3 2.1
2.1 4.85
(CO)VARIANCES_MPE
1.03 .27
.27 .85
EFFECT
5 0 cov
NESTED
 1 0 alpha
EFFECT
6 6 cross alpha
RANDOM
diagonal


printout (temporary; the amount of details may change)
------------------------------------------------------
 RENUMF90 version 1.93
 name of parameter file? testpar1                                
 datafile:data.test                                         
 traits:           3           4
 fields passed:           2           1
 R
   5.000       2.000    
   2.000       4.000    

 Processing effect  1 of type cross     
 item_kind=alpha     

 Processing effect  2 of type cross     
 item_kind=alpha     
 Optional maternal effect
 Optional maternal permanent environment
 Optional permanent environment
 pedigree file name  "test.ped"
 positions of animal, sire, dam, alternate dam and yob    1    2    3    0    0
 Reading (CO)VARIANCES:           4 x           4
 Reading (CO)VARIANCES_PE:           2 x           2
 Reading (CO)VARIANCES_MPE:           2 x           2

 Processing effect  3 of type cov       
 item_kind=alpha     

 Processing effect  4 of type cross     
 item_kind=alpha     

 Maximum size of character fields: 20

 Maximum size of record (max_string_readline): 800

 Maximum number of fields innput file (max_field_readline): 100

 hash tables for effects set up
 read            6  records
 table with            4  elements sorted
 added count
 Effect group            1  of column            1  with            4  levels
 table expanded from        10000  to        10000  records
 added count
 Effect group            2  of column            1  with            4  levels
 table with            4  elements sorted
 added count
 Effect group            3  of column            1  with            4  levels
 table expanded from        10000  to        10000  records
 table with            3  elements sorted
 added count
 Effect group            4  of column            1  with            3  levels
 table expanded from        10000  to        10000  records
 wrote statistics in file "renf90.tables"

 Basic statistics for input data  (missing value code is 0)
 Pos  Min         Max         Mean        SD                 N
   3    21.333     0.12346E+07 0.20578E+06 0.50400E+06       6
   4    11.000      66.000      38.500      20.579           6
   5    12.000      67.000      39.500      20.579           6

 Correlation matrix
        3     4     5
  3   1.00  0.65  0.65
  4   0.65  1.00  1.00
  5   0.65  1.00  1.00

 Counts of nonzero values (order as above)
          6         6         6
          6         6         6
          6         6         6

 random effect   2
 type:animal    
 opened output pedigree file "renadd02.ped"
 read            5  pedigree records
 loaded            3  parent(s) in round            1

 Pedigree checks
 
 Number of animals with records:           4
 Number of parents without records:           1
 Number of phantom dams:           2
 Total number of animals:           7

 random effect   4
 type:diag      

 Wrote parameter file "renf90.par"
 Wrote renumbered data "renf90.dat"


new parameter file - renf90.par
-------------------------------
# BLUPF90 parameter file created by RENF90
DATAFILE
 renf90.dat
NUMBER_OF_TRAITS
           2
NUMBER_OF_EFFECTS
           7
OBSERVATION(S)
    1    2
WEIGHT(S)
 
EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT[EFFECT NESTED]
  3  3         4 cross 
  4  4         7 cross 
  5  5         7 cross
  5  5         7 cross
  4  4         7 cross
  6  0         4 cov   7  0
  8  8         3 cross 
RANDOM_RESIDUAL VALUES
   5.000       2.000    
   2.000       4.000    
 RANDOM_GROUP
     2     3
 RANDOM_TYPE
 add_animal
 FILE
renadd02.ped                                                
(CO)VARIANCES
   10.00       3.000       2.000       1.000    
   3.000       11.00       4.000       5.000    
   2.000       4.000       12.00       6.000    
   1.000       5.000       6.000       13.01    
 RANDOM_GROUP
     4
 RANDOM_TYPE
 diagonal  
 FILE
                                                            
(CO)VARIANCES
   1.030      0.2700    
  0.2700      0.8500    
 RANDOM_GROUP
     5
 RANDOM_TYPE
 diagonal  
 FILE
                                                            
(CO)VARIANCES
   5.300       2.100    
   2.100       4.850    
 RANDOM_GROUP
     7
 RANDOM_TYPE
 diagonal  
 FILE
                                                            
(CO)VARIANCES
   1.000      0.1000    
  0.1000       1.000



data file - renf90.dat
----------------------
 34.5 11 1 3 5 12 1 3 aa 1
 21.333 22 2 1 3 23 2 1 bb 3
 23.666 33 4 4 7 34 4 2 cc 8
 29 44 1 2 3 45 1 1 dd 1
 30 55 2 3 5 56 2 2 aa 3
 1234567.890 66 3 1 3 67 3 3 bb 5

 
 Pedigree file (same format as from renum) - renadd02.ped
 --------------------------------------------------------
 1 6 3 1 0 2 2 0 0 bb
 6 0 0 1 0 0 0 2 0 qq
 2 0 3 1 0 1 1 0 0 dd
 7 0 0 1 0 0 0 0 1 D@@0000002
 5 0 0 1 0 0 0 0 1 D@@0000001
 3 0 5 1 0 1 2 0 2 aa
 4 6 7 1 0 2 1 0 0 cc

renumbering tables - renf90.tables
----------------------------------
 Effect group 1 of column 1 with 4 levels
 Value    #    consecutive number
1 2 1 
3 2 2 
5 1 3 
8 1 4 
 Effect group 3 of column 1 with 4 levels
 Value    #    consecutive number
1 2 1 
3 2 2 
5 1 3 
8 1 4 
 Effect group 4 of column 1 with 3 levels
 Value    #    consecutive number
xx 2 1 
yy 2 2 
zz 2 3