|
Size: 608
Comment:
|
Size: 2678
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
| The [[public/gebvtest.py?action=print|gebvtest.py]] program offers an option (''-m, --mergefiles'') to create a file of merged Cf/Df/Cr/Gr records as a convenience to the user. These files can make it easier to check for the correctness of the input datasets and they can be used for easier |
The [[https://wiki.interbull.org/public/gebvtest_py?action=print|gebvtest.py]] program offers an option (''-m, --mergefiles'') to create a file of merged Cf/Df/Cr/Gr records as a convenience to the user. These files can make it easier to check for the correctness of the input datasets and they can be used perform additional checks and/or statistical analyses, using R for example as in this small [[attachment:test.R]]. |
| Line 6: | Line 5: |
| , either in directDATADIR/merged by By default, the Note: The merged files do not have a _POPBRD extension, so if you would like to create files for more than one population or breed, you should also supply the ''-M, --mergedir'' option with a different destination directory |
One file is created for each trait present in the traits_POPBRD file and the file300Xy_POPBRD files. There is a record for each bull present in the Cf file born in/after the cutoff year specified in the traits_POPBRD file. Flags are supplied to indicate whether the bull qualifies as a candidate or a test bull. Please see the file format below. By default, the files are created in directory DATADIR/merged. The merged files do not have a _POPBRD extension, so if you would like to create files for more than one population or breed, you should also supply the ''-M, --mergedir'' option with a different destination directory for each population/breed. The destination directory can be an absolute path, or it can be relative to the programs directory (eg. ../sample_data/my_merges). The directory will be created automatically if it does not exist. == File format == The file is in comma-separated-variable (csv) format, using commas as the separator. ||'''Column'''||'''Variable'''||'''Type'''||'''Description'''|| ||1||aid||char(19)||animal ID|| ||2||byear||int||Birth year|| ||3||geno||char(1)||Bull has a GEBV (Gr) record (Y/N)|| ||4||cand||char(1)||Bull qualifies as a candidate bull (Y/N)|| ||5||test||char(1)||Bull qualifies as a test bull (Y/N)|| ||6||top||char(2)||Type of proof (from Cf file)|| ||7||off||char(1)||Official proof (Y/N; from Cf file)|| ||8||sta||char(2)||Bull status (from Cf file)|| ||9||Cf||char(2)||Fixed separator for Cf info|| ||10||edc||int||EDC from Cf file|| ||11||rel||real||Reliability from Cf file (x100)|| ||12||ebv||real||Predicted genetic merit ("proof") from Cf file|| ||13||Df||char(2)||Fixed separator for Df info|| ||14||edcd||int||EDC from Df file|| ||15||reld||real||Reliability from Df file (x100)|| ||16||dpgm||real||DD or deregressed proof from Df file|| ||17||Cr||char(2)||Fixed separator for Cr info|| ||18||edcr||int||EDC from Cr file|| ||19||relr||real||Reliability from Cr file (x100)|| ||20||ebvr||real||Predicted genetic merit ("proof") from Cr file|| ||21||Gr||char(2)||Fixed separator for Gr info|| ||18||edcg||int||EDC from Gr file|| ||19||relg||real||Reliability from Gr file (x100)|| ||20||gebv||real||GEBV from Gr file|| |
GEBVtest Merged Files
The gebvtest.py program offers an option (-m, --mergefiles) to create a file of merged Cf/Df/Cr/Gr records as a convenience to the user. These files can make it easier to check for the correctness of the input datasets and they can be used perform additional checks and/or statistical analyses, using R for example as in this small test.R.
One file is created for each trait present in the traits_POPBRD file and the file300Xy_POPBRD files. There is a record for each bull present in the Cf file born in/after the cutoff year specified in the traits_POPBRD file. Flags are supplied to indicate whether the bull qualifies as a candidate or a test bull. Please see the file format below.
By default, the files are created in directory DATADIR/merged. The merged files do not have a _POPBRD extension, so if you would like to create files for more than one population or breed, you should also supply the -M, --mergedir option with a different destination directory for each population/breed. The destination directory can be an absolute path, or it can be relative to the programs directory (eg. ../sample_data/my_merges). The directory will be created automatically if it does not exist.
File format
The file is in comma-separated-variable (csv) format, using commas as the separator.
Column |
Variable |
Type |
Description |
1 |
aid |
char(19) |
animal ID |
2 |
byear |
int |
Birth year |
3 |
geno |
char(1) |
Bull has a GEBV (Gr) record (Y/N) |
4 |
cand |
char(1) |
Bull qualifies as a candidate bull (Y/N) |
5 |
test |
char(1) |
Bull qualifies as a test bull (Y/N) |
6 |
top |
char(2) |
Type of proof (from Cf file) |
7 |
off |
char(1) |
Official proof (Y/N; from Cf file) |
8 |
sta |
char(2) |
Bull status (from Cf file) |
9 |
Cf |
char(2) |
Fixed separator for Cf info |
10 |
edc |
int |
EDC from Cf file |
11 |
rel |
real |
Reliability from Cf file (x100) |
12 |
ebv |
real |
Predicted genetic merit ("proof") from Cf file |
13 |
Df |
char(2) |
Fixed separator for Df info |
14 |
edcd |
int |
EDC from Df file |
15 |
reld |
real |
Reliability from Df file (x100) |
16 |
dpgm |
real |
DD or deregressed proof from Df file |
17 |
Cr |
char(2) |
Fixed separator for Cr info |
18 |
edcr |
int |
EDC from Cr file |
19 |
relr |
real |
Reliability from Cr file (x100) |
20 |
ebvr |
real |
Predicted genetic merit ("proof") from Cr file |
21 |
Gr |
char(2) |
Fixed separator for Gr info |
18 |
edcg |
int |
EDC from Gr file |
19 |
relg |
real |
Reliability from Gr file (x100) |
20 |
gebv |
real |
GEBV from Gr file |