Data preparation with RENUMF90
August 2026
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Animal model with pedigree file
Random effect specification
We consider a mixed model with one or more random effects. Note that, even when random effects are added, the renumbered data file will be the same as the one used for the fixed-effect model. The only differences when considering random effects in RENUMF90 are: (1) the output parameter file contains statements for random effects, and (2) pedigree or related files are processed properly if needed.
First, we reconsider the previous example and assume the second effect (\(S_j\)) is random. \[ y_{ijk} = A_{i} + S_{j} + \beta x_{ijk} + e_{ijk} \] The raw data file is the same as the one used before, but we change the filename.
ID006 A 1 1.0 3.0
ID009 A 2 1.0 2.0
ID012 A 1 2.0 4.0
ID007 B 2 2.0 6.0
ID010 B 1 1.0 3.0
ID013 B 2 2.0 6.0
ID008 C 1 2.0 6.0
ID011 C 2 1.0 6.0
ID014 C 1 1.0 8.0
ID015 C 2 2.0 4.0Assuming that the residual variance is \(\sigma_{e}^{2} = 2.0\) and the random-effect variance is \(\sigma_{s}^{2} = 1.0\), the parameter file is as follows:
DATAFILE
rawdata2.txt
TRAITS
5
FIELDS_PASSED TO OUTPUT
WEIGHT(S)
RESIDUAL_VARIANCE
2.0
EFFECT # 1st effect
2 cross alpha
EFFECT # 2nd effect
3 cross alpha
RANDOM ## treated as a random effect
diagonal
(CO)VARIANCES ## its variance components
1.0
EFFECT # 3rd effect
4 covThis parameter file is also the same as the one used before, except
that we inserted two additional keywords and their corresponding values:
the keyword RANDOM with the value diagonal and
the keyword (CO)VARIANCES with the value 1.0, immediately
after the definition of effect 2. Basically, RENUMF90 treats the effect
as random if RANDOM is placed after the effect
specification; otherwise, the effect is fixed. 1
This produces data and parameter files equivalent to those used in the previous chapter. You can confirm that the generated files provide the same solutions as before.
Animal model
Raw data
RENUMF90 can handle an animal model within the same framework, using
RANDOM and other optional keywords to read a raw pedigree
file. We can use the same data file as before. We duplicate the data
file under a different name.
ID006 A 1 1.0 3.0
ID009 A 2 1.0 2.0
ID012 A 1 2.0 4.0
ID007 B 2 2.0 6.0
ID010 B 1 1.0 3.0
ID013 B 2 2.0 6.0
ID008 C 1 2.0 6.0
ID011 C 2 1.0 6.0
ID014 C 1 1.0 8.0
ID015 C 2 2.0 4.0Raw pedigree
The following is the raw pedigree corresponding to the pedigree shown in the previous chapter.
ID001 0 0
ID002 0 0
ID003 0 0
ID004 0 0
ID005 0 0
ID006 0 0
ID007 ID002 ID005
ID008 ID001 ID004
ID009 ID002 ID003
ID010 ID007 ID006
ID011 ID007 ID004
ID012 ID011 ID008
ID013 ID011 ID010
ID014 ID009 ID013
ID015 ID011 ID010Animal IDs are shared by the raw data and raw pedigree files. A raw pedigree with the following format is allowed for RENUMF90.
- It contains at least 3 columns—animal ID, sire ID, and dam ID—separated by one or more spaces. A tab is not allowed.
- Each ID can be in any position. For example, the animal ID can be in column 4.
- An unknown or missing parent must be
0. Other expressions (like00or00000orNA) are not allowed as missing, and they will be recognized as real animals. - You can also put the date of birth (year of birth) as an additional column. The information should be an integer value.
- Animals do not have to be ordered chronologically or alphabetically. Any order is allowed.
- Although an animal appears in the sire or dam column, it does not necessarily appear in the animal column. Such an animal is assumed to have unknown parents (both sire and dam unknown).
Parameter file
We assume a mixed model: \[
y_{ijk} = A_{i} + S_{j} + \beta x_{ijk} + u_{k} + e_{ijk}
\] where \(A_{i}\) and \(S_{j}\) are fixed effects, \(\beta\) is a fixed regression coefficient,
\(u_{k}\) is the additive genetic
effect, and \(e_{ijk}\) is the random
residual. The variances are assumed to be \(\sigma_{e}^2 = 2.0\) and \(\sigma_u^2 = 0.5\). We add an
EFFECT statement to the previous instruction to specify the
additive genetic effect with the RANDOM keyword.
DATAFILE
rawdata3.txt
TRAITS
5
FIELDS_PASSED TO OUTPUT
WEIGHT(S)
RESIDUAL_VARIANCE
2.0
EFFECT # 1st effect fixed
2 cross alpha
EFFECT # 2nd effect fixed
3 cross alpha
EFFECT # 3rd effect fixed
4 cov
EFFECT # 4th effect
1 cross alpha
RANDOM ## treated as a random effect
animal
FILE ## pedigree file
rawpedigree3.txt
FILE_POS ## animal, sire and dam IDs, and two 0s
1 2 3 0 0
(CO)VARIANCES ## its variance component
0.5We can see two new keywords here.
FILE: the name of the raw pedigree file.rawpedigree3.txt
FILE_POS: the positions of IDs in the raw pedigree file; 5 items are needed.- 1st item = the position of animal ID (1 for the 1st column)
- 2nd item = the position of sire ID (2 for the 2nd column)
- 3rd item = the position of dam ID (3 for the 3rd column)
- 4th item = usually 0 (explained later)
- 5th item = usually 0 (explained later)
Be careful about the order of keywords for random effects. RENUMF90 only accepts the keywords when they are properly ordered in the instruction file. In this example, the order should be:
RANDOMFILEFILE_POS(CO)VARIANCES
There are many more keywords related to random effects. The keywords should be ordered so that RENUMF90 can read them. We will review the proper ordering later.
Output files
After running RENUMF90, you can find several files in the same
directory: renf90.dat, renf90.par,
renf90.tables, and renadd04.ped. The last one
is the renumbered pedigree. Why 4? This 4 comes from the position of the
effect in the instruction file; the additive genetic effect was defined
as the 4th EFFECT statement. If your additive genetic
effect is declared as the 6th effect, the pedigree file will be named
renadd06.ped.
The renumbered pedigree file (renadd04.ped) contains 10
columns.
1 7 5 1 0 2 1 0 0 ID015
13 0 0 3 0 0 0 0 2 ID004
11 0 0 3 0 0 0 0 1 ID005
2 0 0 3 0 0 1 0 1 ID006
3 12 11 1 0 2 1 2 0 ID007
4 14 13 1 0 2 1 0 1 ID008
5 3 2 1 0 2 1 0 2 ID010
6 12 15 1 0 2 1 1 0 ID009
7 3 13 1 0 2 1 3 0 ID011
8 7 4 1 0 2 1 0 0 ID012
14 0 0 3 0 0 0 1 0 ID001
9 7 5 1 0 2 1 0 1 ID013
12 0 0 3 0 0 0 2 0 ID002
10 6 9 1 0 2 1 0 0 ID014
15 0 0 3 0 0 0 0 1 ID003Column 1 contains the renumbered animal ID, column 2 contains the sire ID, and column 3 contains the dam ID. The remaining columns contain additional information. The last (10th) column is the original ID. Many of these columns are ignored by BLUPF90. 2 The official manual explains the meaning of each column.
- animal number (from 1)
- parent 1 number or unknown parent group number for parent 1
- parent 2 number or unknown parent group number for parent 2
- 3 minus number of known parents
- known or estimated year of birth (0 if not provided)
- number of known parents (parents might be eliminated if they do not contribute; if the animal has a genotype, this is 10 + the number of known parents)
- number of records
- number of progeny (before elimination due to other effects) as parent 1
- number of progeny (before elimination due to other effects) as parent 2
- original animal ID
The conversion table for animal ID is not saved in
renf90.tables. The correspondence can be found only in the
renumbered pedigree file (columns 1 and 10).
Test run with the renumbered data
You can run BLUPF90 with the generated parameter file and obtain the solutions of the equations. The analysis is the same as the previous one, so the results should be identical (apart from numerical error). You will find that the BLUE and the estimated breeding values (BLUPs) are also the same, but the order of the animals is different. The following combines the previous results (left) and the current results (right).
1 1 1 0.20259644 1 1 1 0.20259637
1 1 2 2.21996461 1 1 2 2.21996452
1 1 3 3.16680208 1 1 3 3.16680200
1 2 1 2.27537292 1 2 1 2.27537284
1 2 2 1.71160537 1 2 2 1.71160529
1 3 1 0.52442755 1 3 1 0.52442750
1 4 1 -0.03487115 1 4 1 -0.25707432
1 4 2 0.08280493 1 4 2 -0.17565610
1 4 3 0.03843921 1 4 3 0.10794666
1 4 4 0.04492008 1 4 4 -0.02984647
1 4 5 0.04436203 1 4 5 -0.25282594
1 4 6 -0.17565609 1 4 6 0.09906235
1 4 7 0.10794667 1 4 7 0.15622415
1 4 8 -0.02984646 1 4 8 0.10874295
1 4 9 0.09906236 1 4 9 0.16426464
1 4 10 -0.25282594 1 4 10 0.34296713
1 4 11 0.15622415 1 4 11 0.04436204
1 4 12 0.10874296 1 4 12 0.08280494
1 4 13 0.16426465 1 4 13 0.04492008
1 4 14 0.34296714 1 4 14 -0.03487115
1 4 15 -0.25707431 1 4 15 0.03843922This is because the animals are ordered differently in the pedigree files for the two data sets. RENUMF90 orders pedigree animals as follows.
- First, the program assigns smaller numbers to animals with records. The order of the animals is unpredictable (that is, it does not follow the order found in the data file).
- Then, the program assigns larger numbers to animals found only in the pedigree.
Note that RENUMF90 does not order the pedigree animals chronologically (that is, from oldest to youngest). No options are available to order the animals chronologically. The above rules result from a simplification of the implementation, but this ordering is useful for fitting the permanent environmental effect in the repeatability model.
Usually, you will combine the solutions (estimated breeding values) with the original animal ID. This can be done in several ways, for example, using Linux (Unix) tools, database management systems, statistical languages such as R, or even Microsoft Excel.
More than 1 random effect
As the last demonstration of RENUMF90 in this section, let us assume that the effect \(S_j\) is also random, as is \(u_k\) in the above model. The variance components are \(\sigma_e^2 = 2.0\), \(\sigma_s^2 = 1.0\), and \(\sigma_u^2 = 0.5\). A suggested instruction file is as follows.
DATAFILE
rawdata3.txt
TRAITS
5
FIELDS_PASSED TO OUTPUT
WEIGHT(S)
RESIDUAL_VARIANCE
2.0
EFFECT # 1st effect fixed
2 cross alpha
EFFECT # 2nd effect fixed
3 cross alpha
RANDOM ## treated as a random effect
diagonal
(CO)VARIANCES ## its variance component
1.0
EFFECT # 3rd effect fixed
4 cov
EFFECT # 4th effect
1 cross alpha
RANDOM ## treated as a random effect
animal
FILE ## pedigree file
rawpedigree3.txt
FILE_POS ## animal, sire and dam IDs with two 0s
1 2 3 0 0
(CO)VARIANCES ## its variance component
0.5This is a combination of the first and second examples in this section. You can easily figure out how each statement works.
Summary
- RENUMF90 treats the effect with the
RANDOMkeyword as a random effect. - The
RANDOMkeyword may require other keywords. - If a random effect does not require the pedigree, include only
RANDOMand(CO)VARIANCES. - If a random effect requires the pedigree, include
RANDOM,FILE,FILE_POS, and(CO)VARIANCESin this order. - A raw pedigree file should contain at least 3 columns: animal ID, sire ID, and dam ID. The order of the columns is arbitrary.
- The renumbered pedigree file is named
renaddnn.ped, wherennis the position of this effect in the instruction file. - The renumbered pedigree file has 10 columns including the original
ID. The renumbered ID will not be in
renf90.tables. - The animals with records have smaller numbers than animals found only in pedigree.
- RENUMF90 supports more than one random effect.
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