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NEWS.md
In Rfast2: A Collection of Efficient and Extremely Fast R Functions II
*Rfast2*
Version 0.1.5.2 - Zagreus
New
| Function | What's new! |
|:--------:|:-----------------------------------------------------------------------------------:|
| jbtests | Many Jarque–Bera normality tests |
| lm.nonparboot | Non-parametric bootstrap for linear models |
| normal.etest | Energy based normality test |
| batch.logistic | Logistic regression for large scale data |
| colhalfcauchy.mle | Column-wise MLE for the half Cauchy distribution |
| colcenspois.mle | Column-wise MLE for the censored Poisson distribution |
| colcensweibull.mle | Column-wise MLE for the censored Weibull distribution |
| el.cor.test | Empirical likelihood test for the correlation coefficient |
| eel.cor.test | Exponential empirical likelihood test for the correlation coefficient |
| jbtest | Jarque–Bera normality test |
Improved
(by speed, correctness or options)
| Function | What's new! |
|:--------:|:-----------------------------------------------------------------------------------:|
| halfcauchy.mle | Time improvement |
| censpois.mle | Time improvement |
| censweibull.mle | Time improvement |
LinkingTo
(by speed, correctness or options)
| Function/Structure | What's new! |
|:------------------:|:--------------------:|
| | |
Version 0.1.5.1 - Theseus
Improved
(by speed, correctness or options)
| Function | What's new! |
|:--------:|:-----------------------------------------------------------------------------------:|
| TrimMean | Add option for parallelism. Supported only where C++ execution policy is supported. |
| Quantile | Add option for parallelism. Supported only where C++ execution policy is supported. |
LinkingTo
(by speed, correctness or options)
| Function/Structure | What's new! |
|:------------------:|:--------------------:|
| Quantile | Exported for linking |
| rowQuantile | Exported for linking |
| colQuantile | Exported for linking |
| TrimMean | Exported for linking |
| rowTrimMean | Exported for linking |
| colTrimMean | Exported for linking |
| colTrimMean | Exported for linking |
Comments
- All the exported functions for linking to mechanism are in namespace
Rfast.
- We have added the header file
parallel.h which automatically includes the new parallelism policy rules of C++17. If not supported by your system, non-parallel algorithms are automatically used.
Version 0.1.4 - Heracles
New
| Function | What's new! |
|:---------:|:-----------------------------------------------:|
| covrob.lm | Linear regression with robust covariance matrix |
Version 0.1.3
New
| Function | What's new! |
|:-----------:|:-------------------------------------------------------------------------------:|
| Runif | Like R's runif but faster. |
| Sample | Like R's Sample but faster. |
| Sample.int | Like R's Sample.int but faster. |
| colaccs | Column-wise accuracies |
| colsens | Column-wise sensitivities |
| colspecs | Column-wise specificities |
| colprecs | Column-wise precisions |
| colfscores | Column-wise F-scores |
| colfbscores | Column-wise F-beta-scores |
| colfmis | Column-wise Fowlkes--Mallows index |
| colfmses | Column-wise MSEs |
| colmaes | Column-wise MAEs |
| colpkl | Column-wise Kullback-Leibler divergence for percentages |
| colukl | Column-wise Kullback-Leibler divergence for non-negative or non-negative values |
| pinar1 | Poisson INAR(1) model estimation |
| colpinar1 | Column-wise Poisson INAR(1) model estimation |
Improved
(by speed, correctness or options)
| Function | What's new! |
|:---------------------:|:-------------------------------------------------:|
| Quantile, rowQuantile | Optimize algorithm |
| colQuantile | Optimize algorithm and new method for data.frames |
| colTrimMean | Optimize algorithm and new method for data.frames |
Version 0.1.1
New
| Function | What's new! |
|:----------:|:-----------------------------------------------------:|
| mmhc.skel | Skeleton of MMHC Bayesian network learning algorithm |
| fedhc.skel | Skeleton of FEDHC Bayesian network learning algorithm |
| fe.lmfit | Fixed effects linear regression for panel data |
Version 0.0.8
New
| Function | What's new! |
|:--------------:|:--------------------------------------------------:|
| gammareg | Gamma regression |
| gammaregs | Many gamma regressions |
| cor_test | Hypothesis testing for the correlation coefficient |
| cor_test | Hypothesis testing for the correlation coefficient |
| hcf.circaov | ANOVA for circular data |
| het.circaov | ANOVA for circular data |
| lr.circaov | ANOVA for circular data |
| multivm.mle | Fitting many von Mises distributions |
| multispml.mle | Fitting many von SPML distributions |
| depth.mahala | Mahalanobis depth |
| perm.ttest2 | Permutation based 2 sample t-test |
| lm.parboot | Parametric bootstrap for linear models |
| weibull.nb | Weibull Naive Bayes (NB) classifier |
| weibullnb.pred | Prediction using Weibull NB classifier |
| normlog.nb | Gaussian(log-link) NB classifier |
| normlognb.pred | Prediction using Gaussian(log-link) NB classifier |
| laplace.nb | Laplace NB classifier |
| laplacenb.pred | Prediction using Laplace NB classifier |
| vm.nb | von Mises NB classifier |
| vmnb.pred | Prediction using von Mises NB classifier |
| spml.nb | SPML NB classifier |
| spml.pred | Prediction using SPML NB classifier |
Version 0.0.4
Improved
(by speed, correctness or options)
| Function | What's new! |
|:-----------:|:------------------------------------:|
| bic.regs | Addition SPML and Weibull regression |
| pc.sel | Time improvement |
| welch.tests | Time improevement |
New
| Function | What's new! |
|:-----------------:|:---------------------------------------------------:|
| cls | Constrained least squares regression |
| cluster.lm | Linear regression with clustered data |
| colborel.mle | Column-wise MLE of the Borel distribution |
| collogitnorm.mle | Column-wise MLE of the logistic normal distribution |
| collognorm.mle | Column-wise MLE of the log-normal distribution |
| cospml.mle | Column-wise MLE of the SPML distribution |
| empirical.entropy | Empirical entropy estimation with continuous data |
| fbed.reg | FBED variable selection algorithm |
| gumbel.reg | Gumbel regression |
| moranI | Moran's I measure of spatial autocorrelation |
| multinom.reg | Multinomial regression |
| negbin.reg | Negative binomial regression |
| pca | Principal component analysis |
| refmeta | Random effects meta-analysis estimation |
| simplex.mle | MLE of the simplex distribution |
| weib.regs | Many simple weibull regressions |
| ztp.reg | zero truncated Poisson regression |
| mmpc2 | MMPC variable selection algorithm |
| is.skew.symmetric | Checking if the given matrix is skew-symmetric. |
Version 0.0.3
Improved
(by speed, correctness or options)
| Function | What's new! |
|:---------:|:----------------------------:|
| benchmark | fix a bug in printing names. |
Version 0.0.2
New
| Function | What's new! |
|:--------------:|:---------------------------------------------------------------:|
| gee.reg | Gereneralised estimating equations Gaussian regression |
| halfcauchy.mle | MLE of the half Cauchy distribution |
| kumar.mle | MLE of the Kumaraswamy distribution |
| powerlaw.mle | MLE of the power law distribution |
| reg.mle.lda | Regularised maximum likleihood linear discriminant analysis |
| walter.ci | Confidence interval for the relative risk using Walter's method |
| welch.tests | Many Welch t-tests |
Version 0.0.1
New
| Function | What's new! |
|:---------------:|:----------------------------------------------------------------------------:|
| add.term | Add many single terms to a model. |
| bic.regs | BIC of many univariate regressions. |
| censpois.mle | MLE of the left censored Poisson distribution. |
| cesweibull.mle | MLE of the censored Weibull distribution. |
| circ.cor1 | Circurlar correlations between two circular variables. |
| circ.cors1 | Circurlar correlations between a circular and many circular variables. |
| colmeansvars | Column-wise means and variances of a matrix. |
| covar | Covariance betweeen a vector and a matrix. |
| diffic | Difficulty of items (psychometric theory). |
| discrim | Discrimination of items (psychometric theory). |
| gammapois.mle | MLE of the gamma-Poisson distribution. |
| km | Kaplan-Meier estimate of a survival function. |
| logiquant.regs | Many simple quantile regressions using logistic regressions. |
| mle.lda | Maximum likelihood linear discriminant analysis. |
| pc.sel | Variable selection using the PC-simple algorithm. |
| pooled.colVars | Column-wise pooled variances across groups. |
| purka.mle | MLE of the Purkayastha distribution. |
| sp.logiregs | Many approximate simple logistic regressionss. |
| trunccauchy.mle | MLE of the truncated Cauchy distribution. |
| truncexpmle | MLE of the truncated exponential distribution. |
| wald.poisrat | Wald confidence interval for the ratio of two Poisson variables. |
| col.waldpoisrat | Column-wise Wald confidence interval for the ratio of two Poisson variables. |
| welch.tests | Many Welch tests. |
| zigamma.mle | MLE of the zero inflated Gamma distribution. |
| ziweibull.mle | MLE of the zero inflated Weibull distribution. |
| zil.mle | MLE of the zero inflated logistic normal distribution. |
| Intersect | Intersect as R's. |
| is.lower.tri | Check if a matrix is lower triangular. |
| is.upper.tri | Check if a matrix is upper triangular. |
| lud | Split a matrix to a lower,upper matrix and diagonal vector. |
| Merge | Merge 2 sorted vectors to a sorted vector. |
| benchmark | Measure code's execution time. |
| colGroup | Apply Rfast's gorup function to each column with some restrictions. |
| Quantile | Quantile(s) of a vector. |
| colQuantile | Column-wise quantile(s) of a matrix. |
| rowQuantile | Row-wise quantile(s) of a matrix. |
| trim.mean | Trimmed mean of a vector. |
| colTrimMean | Column-wise trimmed mean of a matrix. |
| rowTrimMean | Row-wise trimmed mean of a matrix. |
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Rfast2 documentation built on May 29, 2024, 8:45 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
*Rfast2*
Version 0.1.5.2 - Zagreus
New
| Function | What's new! | |:--------:|:-----------------------------------------------------------------------------------:| | jbtests | Many Jarque–Bera normality tests | | lm.nonparboot | Non-parametric bootstrap for linear models | | normal.etest | Energy based normality test | | batch.logistic | Logistic regression for large scale data | | colhalfcauchy.mle | Column-wise MLE for the half Cauchy distribution | | colcenspois.mle | Column-wise MLE for the censored Poisson distribution | | colcensweibull.mle | Column-wise MLE for the censored Weibull distribution | | el.cor.test | Empirical likelihood test for the correlation coefficient | | eel.cor.test | Exponential empirical likelihood test for the correlation coefficient | | jbtest | Jarque–Bera normality test |
Improved
(by speed, correctness or options)| Function | What's new! | |:--------:|:-----------------------------------------------------------------------------------:| | halfcauchy.mle | Time improvement | | censpois.mle | Time improvement | | censweibull.mle | Time improvement |
LinkingTo
(by speed, correctness or options)| Function/Structure | What's new! | |:------------------:|:--------------------:| | | |
Version 0.1.5.1 - Theseus
Improved
(by speed, correctness or options)| Function | What's new! | |:--------:|:-----------------------------------------------------------------------------------:| | TrimMean | Add option for parallelism. Supported only where C++ execution policy is supported. | | Quantile | Add option for parallelism. Supported only where C++ execution policy is supported. |
LinkingTo
(by speed, correctness or options)| Function/Structure | What's new! | |:------------------:|:--------------------:| | Quantile | Exported for linking | | rowQuantile | Exported for linking | | colQuantile | Exported for linking | | TrimMean | Exported for linking | | rowTrimMean | Exported for linking | | colTrimMean | Exported for linking | | colTrimMean | Exported for linking |
Comments
- All the exported functions for linking to mechanism are in namespace
Rfast.- We have added the header file
parallel.hwhich automatically includes the new parallelism policy rules of C++17. If not supported by your system, non-parallel algorithms are automatically used.
Version 0.1.4 - Heracles
New
| Function | What's new! | |:---------:|:-----------------------------------------------:| | covrob.lm | Linear regression with robust covariance matrix |
Version 0.1.3
New
| Function | What's new! | |:-----------:|:-------------------------------------------------------------------------------:| | Runif | Like R's runif but faster. | | Sample | Like R's Sample but faster. | | Sample.int | Like R's Sample.int but faster. | | colaccs | Column-wise accuracies | | colsens | Column-wise sensitivities | | colspecs | Column-wise specificities | | colprecs | Column-wise precisions | | colfscores | Column-wise F-scores | | colfbscores | Column-wise F-beta-scores | | colfmis | Column-wise Fowlkes--Mallows index | | colfmses | Column-wise MSEs | | colmaes | Column-wise MAEs | | colpkl | Column-wise Kullback-Leibler divergence for percentages | | colukl | Column-wise Kullback-Leibler divergence for non-negative or non-negative values | | pinar1 | Poisson INAR(1) model estimation | | colpinar1 | Column-wise Poisson INAR(1) model estimation |
Improved
(by speed, correctness or options)| Function | What's new! | |:---------------------:|:-------------------------------------------------:| | Quantile, rowQuantile | Optimize algorithm | | colQuantile | Optimize algorithm and new method for data.frames | | colTrimMean | Optimize algorithm and new method for data.frames |
Version 0.1.1
New
| Function | What's new! | |:----------:|:-----------------------------------------------------:| | mmhc.skel | Skeleton of MMHC Bayesian network learning algorithm | | fedhc.skel | Skeleton of FEDHC Bayesian network learning algorithm | | fe.lmfit | Fixed effects linear regression for panel data |
Version 0.0.8
New
| Function | What's new! | |:--------------:|:--------------------------------------------------:| | gammareg | Gamma regression | | gammaregs | Many gamma regressions | | cor_test | Hypothesis testing for the correlation coefficient | | cor_test | Hypothesis testing for the correlation coefficient | | hcf.circaov | ANOVA for circular data | | het.circaov | ANOVA for circular data | | lr.circaov | ANOVA for circular data | | multivm.mle | Fitting many von Mises distributions | | multispml.mle | Fitting many von SPML distributions | | depth.mahala | Mahalanobis depth | | perm.ttest2 | Permutation based 2 sample t-test | | lm.parboot | Parametric bootstrap for linear models | | weibull.nb | Weibull Naive Bayes (NB) classifier | | weibullnb.pred | Prediction using Weibull NB classifier | | normlog.nb | Gaussian(log-link) NB classifier | | normlognb.pred | Prediction using Gaussian(log-link) NB classifier | | laplace.nb | Laplace NB classifier | | laplacenb.pred | Prediction using Laplace NB classifier | | vm.nb | von Mises NB classifier | | vmnb.pred | Prediction using von Mises NB classifier | | spml.nb | SPML NB classifier | | spml.pred | Prediction using SPML NB classifier |
Version 0.0.4
Improved
(by speed, correctness or options)| Function | What's new! | |:-----------:|:------------------------------------:| | bic.regs | Addition SPML and Weibull regression | | pc.sel | Time improvement | | welch.tests | Time improevement |
New
| Function | What's new! | |:-----------------:|:---------------------------------------------------:| | cls | Constrained least squares regression | | cluster.lm | Linear regression with clustered data | | colborel.mle | Column-wise MLE of the Borel distribution | | collogitnorm.mle | Column-wise MLE of the logistic normal distribution | | collognorm.mle | Column-wise MLE of the log-normal distribution | | cospml.mle | Column-wise MLE of the SPML distribution | | empirical.entropy | Empirical entropy estimation with continuous data | | fbed.reg | FBED variable selection algorithm | | gumbel.reg | Gumbel regression | | moranI | Moran's I measure of spatial autocorrelation | | multinom.reg | Multinomial regression | | negbin.reg | Negative binomial regression | | pca | Principal component analysis | | refmeta | Random effects meta-analysis estimation | | simplex.mle | MLE of the simplex distribution | | weib.regs | Many simple weibull regressions | | ztp.reg | zero truncated Poisson regression | | mmpc2 | MMPC variable selection algorithm | | is.skew.symmetric | Checking if the given matrix is skew-symmetric. |
Version 0.0.3
Improved
(by speed, correctness or options)| Function | What's new! | |:---------:|:----------------------------:| | benchmark | fix a bug in printing names. |
Version 0.0.2
New
| Function | What's new! | |:--------------:|:---------------------------------------------------------------:| | gee.reg | Gereneralised estimating equations Gaussian regression | | halfcauchy.mle | MLE of the half Cauchy distribution | | kumar.mle | MLE of the Kumaraswamy distribution | | powerlaw.mle | MLE of the power law distribution | | reg.mle.lda | Regularised maximum likleihood linear discriminant analysis | | walter.ci | Confidence interval for the relative risk using Walter's method | | welch.tests | Many Welch t-tests |
Version 0.0.1
New
| Function | What's new! | |:---------------:|:----------------------------------------------------------------------------:| | add.term | Add many single terms to a model. | | bic.regs | BIC of many univariate regressions. | | censpois.mle | MLE of the left censored Poisson distribution. | | cesweibull.mle | MLE of the censored Weibull distribution. | | circ.cor1 | Circurlar correlations between two circular variables. | | circ.cors1 | Circurlar correlations between a circular and many circular variables. | | colmeansvars | Column-wise means and variances of a matrix. | | covar | Covariance betweeen a vector and a matrix. | | diffic | Difficulty of items (psychometric theory). | | discrim | Discrimination of items (psychometric theory). | | gammapois.mle | MLE of the gamma-Poisson distribution. | | km | Kaplan-Meier estimate of a survival function. | | logiquant.regs | Many simple quantile regressions using logistic regressions. | | mle.lda | Maximum likelihood linear discriminant analysis. | | pc.sel | Variable selection using the PC-simple algorithm. | | pooled.colVars | Column-wise pooled variances across groups. | | purka.mle | MLE of the Purkayastha distribution. | | sp.logiregs | Many approximate simple logistic regressionss. | | trunccauchy.mle | MLE of the truncated Cauchy distribution. | | truncexpmle | MLE of the truncated exponential distribution. | | wald.poisrat | Wald confidence interval for the ratio of two Poisson variables. | | col.waldpoisrat | Column-wise Wald confidence interval for the ratio of two Poisson variables. | | welch.tests | Many Welch tests. | | zigamma.mle | MLE of the zero inflated Gamma distribution. | | ziweibull.mle | MLE of the zero inflated Weibull distribution. | | zil.mle | MLE of the zero inflated logistic normal distribution. | | Intersect | Intersect as R's. | | is.lower.tri | Check if a matrix is lower triangular. | | is.upper.tri | Check if a matrix is upper triangular. | | lud | Split a matrix to a lower,upper matrix and diagonal vector. | | Merge | Merge 2 sorted vectors to a sorted vector. | | benchmark | Measure code's execution time. | | colGroup | Apply Rfast's gorup function to each column with some restrictions. | | Quantile | Quantile(s) of a vector. | | colQuantile | Column-wise quantile(s) of a matrix. | | rowQuantile | Row-wise quantile(s) of a matrix. | | trim.mean | Trimmed mean of a vector. | | colTrimMean | Column-wise trimmed mean of a matrix. | | rowTrimMean | Row-wise trimmed mean of a matrix. |
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