26 add namibia data and regional allele frequencies to the package #27
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
… vignette with code to use the new datasets. Add new datasets namibia_data and regional_allele_frequencies. Update vignette with code to use the new datasets. - Added new datasets namibia_data and regional_allele_frequencies. - Updated vignette with code to use the new datasets.
m-murphy
deleted the
26-add-namibia-data-and-regional-allele-frequencies-to-the-package
branch
m-murphy
added a commit
that referenced
this pull request
Aug 1, 2024
* implement logging of latent genotypes (#14) * Fix NA values in allele frequency vector (#20) The code now checks for NA values in the allele frequency vector and replaces them with 0. A warning message is displayed if NA values are detected, indicating a potential problem with the MCMC chain or loci with no diversity. * Add start_profiler and stop_profiler functions (#24) - Added start_profiler function to R/RcppExports.R - Added stop_profiler function to R/RcppExports.R - Modified src/Makevars to include ENABLE_PROFILER flag and link with -lprofiler - Added start_profiler and stop_profiler functions to src/RcppExports.cpp - Created new file src/profiler.cpp containing the implementation of start_profiler and stop_profiler functions * restore accidentally removed openmp library to compilation * Add new datasets namibia_data and regional_allele_frequencies. Update vignette with code to use the new datasets. (#27) Add new datasets namibia_data and regional_allele_frequencies. Update vignette with code to use the new datasets. - Added new datasets namibia_data and regional_allele_frequencies. - Updated vignette with code to use the new datasets. * minor update documentation * fix typo in Namibia vignette * minor cleanup * update documentation * Increment version number to 3.4.0
m-murphy
added a commit
that referenced
this pull request
Oct 30, 2024
* implement logging of latent genotypes (#14) * Fix NA values in allele frequency vector (#20) The code now checks for NA values in the allele frequency vector and replaces them with 0. A warning message is displayed if NA values are detected, indicating a potential problem with the MCMC chain or loci with no diversity. * Add start_profiler and stop_profiler functions (#24) - Added start_profiler function to R/RcppExports.R - Added stop_profiler function to R/RcppExports.R - Modified src/Makevars to include ENABLE_PROFILER flag and link with -lprofiler - Added start_profiler and stop_profiler functions to src/RcppExports.cpp - Created new file src/profiler.cpp containing the implementation of start_profiler and stop_profiler functions * restore accidentally removed openmp library to compilation * Add new datasets namibia_data and regional_allele_frequencies. Update vignette with code to use the new datasets. (#27) Add new datasets namibia_data and regional_allele_frequencies. Update vignette with code to use the new datasets. - Added new datasets namibia_data and regional_allele_frequencies. - Updated vignette with code to use the new datasets. * minor update documentation * fix typo in Namibia vignette * minor cleanup * update documentation * Increment version number to 3.4.0
m-murphy
added a commit
that referenced
this pull request
Oct 30, 2024
* implement logging of latent genotypes (#14) * Fix NA values in allele frequency vector (#20) The code now checks for NA values in the allele frequency vector and replaces them with 0. A warning message is displayed if NA values are detected, indicating a potential problem with the MCMC chain or loci with no diversity. * Add start_profiler and stop_profiler functions (#24) - Added start_profiler function to R/RcppExports.R - Added stop_profiler function to R/RcppExports.R - Modified src/Makevars to include ENABLE_PROFILER flag and link with -lprofiler - Added start_profiler and stop_profiler functions to src/RcppExports.cpp - Created new file src/profiler.cpp containing the implementation of start_profiler and stop_profiler functions * Refactor Chain class to include methods for calculating likelihood, prior, and posterior for a specific sample. (#33) - Add `get_llik(int sample)` method to calculate the likelihood for a specific sample. - Add `get_prior(int sample)` method to calculate the prior for a specific sample. - Add `get_posterior(int sample)` method to calculate the posterior for a specific sample. These changes allow for more granular calculations of likelihood, prior, and posterior values based on individual samples. * Implement maximum runtime (#34) * Implement maximum runtime * log chain runtime * add utility to detect if openmp is enabled * ungroup input data when loading long form (#37) * fix memory crash in prob_any_missing (#38) The code fix addresses a memory crash issue in the `prob_any_missing` function. The fix includes adding a condition to check if `maxNumEvents` is less than `totalEvents`. If true, it fills the `probVec` vector with 1.0 and returns it. This prevents the memory crash and ensures proper execution of the function. * restore accidentally removed openmp library to compilation * Add new datasets namibia_data and regional_allele_frequencies. Update vignette with code to use the new datasets. (#27) Add new datasets namibia_data and regional_allele_frequencies. Update vignette with code to use the new datasets. - Added new datasets namibia_data and regional_allele_frequencies. - Updated vignette with code to use the new datasets. * update citation and manuscript
# for free
to join this conversation on GitHub.
Already have an account?
# to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.