Science Score: 36.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
5 of 30 committers (16.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (19.2%) to scientific vocabulary
Keywords from Contributors
Repository
AD computation with Template Model Builder (TMB)
Basic Info
Statistics
- Stars: 186
- Watchers: 49
- Forks: 84
- Open Issues: 71
- Releases: 20
Metadata Files
README.md
Template Model Builder (TMB)
TMB is an R package with functionality similar to ADMB. It requires R at least version 3.0.0 and development tools needed to install R packages from source. Standard install instructions are available here.
Install the development version (Linux)
It is recommended to install TMB into your local R package library (if you do not yet have a local R package library, create one by running install.packages("") from the R prompt and follow the instructions).
The package is installed from the command line by entering the adcomp folder and typing
shell
make install
To build the user manual type
shell
make pdf
Once the package is successfully installed it can be tested by starting R and running
R
library(TMB)
runExample(all=TRUE)
To build API-Function reference see instructions here.
Once the documentation is built open dox/html/index.html in your web browser.
Use the search field to find functions and their documentation.
It is recommended to test that models can be changed, re-compiled and re-loaded without problems:
R
setwd("tmb_syntax")
source("test_reload.R")
If everything works as intended this script should display "TRUE". The script has only been observed to fail for certain combinations of Linux and the gcc compiler, see below.
Advanced notes
Metis orderings
For large 3D random field models the ordering algorithms shipping with R's Matrix package are far from optimal. To get better orderings available run the extended TMB install script (Linux/Mac only):
shell
make install-metis-full
The new orderings are available from R through the function runSymbolicAnalysis().
For a quick example of how to use it try the ar1_4D example:
shell
cd tmb_examples
make ar1_4D
You should see a significant speedup.
Issues with library unloading
On recent versions of gcc the following problem may be encountered: When the user cpp file is changed, re-compiled and re-loaded, the changes do not take place. To see if you are affected by this issue, assuming your compiled DLL is called "mymodel.so", try running:
shell
readelf -s mymodel.so | grep UNIQUE
If this gives any output it is not possible to unload the library, and R will have to be restarted every time the model is re-compiled. There are at least two alternative solutions to this problem:
Use gcc with compilation flag
-fno-gnu-unique(version 4.8.3 and newer): AddCXX = g++ -fno-gnu-uniqueto a file~/.R/Makevars(create it if it doesn't exist).Use the clang compiler instead of gcc: Install clang and add
CXX = clang++to a file~/.R/Makevars(create it if it doesn't exist).
Note: If you have precompiled TMB using precompile() prior to (1) or (2) you must repeat the precompilation with the new compiler settings.
Owner
- Login: kaskr
- Kind: user
- Repositories: 19
- Profile: https://github.com/kaskr
GitHub Events
Total
- Issues event: 9
- Watch event: 8
- Delete event: 4
- Issue comment event: 17
- Push event: 17
- Pull request event: 5
- Fork event: 6
- Create event: 11
Last Year
- Issues event: 9
- Watch event: 8
- Delete event: 4
- Issue comment event: 17
- Push event: 17
- Pull request event: 5
- Fork event: 6
- Create event: 11
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Kasper Kristensen | k****r@d****k | 1,349 |
| skaug | h****g@g****m | 43 |
| casperwberg | c****g@g****m | 16 |
| Kasper Kristensen | k****r@k****) | 15 |
| Arni Magnusson | a****a@h****s | 14 |
| mollie brooks | m****s@g****m | 8 |
| colemonnahan | m****c@u****u | 5 |
| Ben Bolker | b****r@g****m | 5 |
| Anders Nielsen | a****i@a****) | 5 |
| Alexandros Kokkalis | a****9@g****m | 3 |
| jgbabyn | j****n@g****m | 3 |
| Kinh Nguyen | 4****t | 2 |
| Christoffer Moesgaard Albertsen | ca@c****k | 2 |
| Anders Nielsen | f****r@g****m | 2 |
| TheoMichelot | t****t@i****r | 2 |
| neverfail23927 | h****1@M****o | 2 |
| brianstock | b****9@g****m | 1 |
| John Sibert | s****t@h****u | 1 |
| Daniel Sabanes Bove | d****e@r****m | 1 |
| Daniel Hocking | d****g@u****u | 1 |
| Hans J. Skaug | h****1@m****o | 1 |
| Kinh Nguyen | f****n@g****m | 1 |
| hskaug | h****g@l****) | 1 |
| unknown | a****a@s****) | 1 |
| kasper kristensen | k****r@k****l | 1 |
| Brad Bell | b****l@s****m | 1 |
| Alex Forrence | a****1@j****u | 1 |
| Jamie Lentin | jm@l****k | 1 |
| Martin Maechler | m****r@r****g | 1 |
| Mikael Jagan | j****n@m****a | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 105
- Total pull requests: 26
- Average time to close issues: over 1 year
- Average time to close pull requests: about 2 months
- Total issue authors: 56
- Total pull request authors: 14
- Average comments per issue: 3.26
- Average comments per pull request: 2.38
- Merged pull requests: 17
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 7
- Pull requests: 6
- Average time to close issues: 5 days
- Average time to close pull requests: 1 day
- Issue authors: 5
- Pull request authors: 2
- Average comments per issue: 0.86
- Average comments per pull request: 2.33
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ghost (8)
- kaskr (7)
- bbolker (7)
- James-Thorson (6)
- jaganmn (6)
- James-Thorson-NOAA (6)
- mebrooks (3)
- skaug (3)
- kklot (3)
- lentinj (3)
- timjmiller (2)
- Craig44 (2)
- BertvanderVeen (2)
- markpayneatwork (2)
- jkbest2 (2)
Pull Request Authors
- kaskr (10)
- bbolker (2)
- jaganmn (2)
- calbertsen (2)
- kklot (2)
- lentinj (2)
- boennecd (1)
- 2039 (1)
- Blunde1 (1)
- lawlerem (1)
- skaug (1)
- jeffeaton (1)
- James-Thorson-NOAA (1)
- danielinteractive (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 31,704 last-month
- Total docker downloads: 671,587
- Total dependent packages: 38
- Total dependent repositories: 180
- Total versions: 45
- Total maintainers: 1
cran.r-project.org: TMB
Template Model Builder: A General Random Effect Tool Inspired by 'ADMB'
- Homepage: https://github.com/kaskr/adcomp/wiki
- Documentation: http://cran.r-project.org/web/packages/TMB/TMB.pdf
- License: GPL-2
-
Latest release: 1.9.17
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.0.0 depends
- Matrix >= 1.0 imports
- graphics * imports
- methods * imports
- stats * imports
- utils * imports
- numDeriv * suggests
- parallel * suggests