metrica 2.0.1

• July 23th, 2022.
  

This new version fixes minor bugs found in v2.0.0:

1. regression lines with “OP” orientation in scatter_plot(), density_plot(), and tiles_plot(), which were producing the “PO” oriented regression lines instead.

2. estimation of “d1r” index for regression, which produced misleading values due to a typo in the denominator.

3. printing metrics on confusion matrix, which produced a NaN when printing 9 metrics.

• PREVIOUS VERSIONS

metrica 2.0.0

• July 4th, 2022.
  

This new version of metrica includes:

1. Twenty-seven (27) additional functions to evaluate quality of predictions for classification problems:

• confusion_matrix(): Confusion matrix (as data.frame or plot).
• accuracy(): Accuracy.
• error_rate(): Error Rate, misclassification rate.
• precision(): Precision.
• recall(): Recall, sensitivity, true positive rate.
• specificity(): Specificity, selectivity, true negative rate.
• fscore(): F-score.
• agf(): Adjusted F-score.
• gmean(): G-mean.
• khat(): Cohen’s Kappa Coefficient.
• baccu(): Balanced Accuracy.
• mcc(): Matthews Correlation Coefficient.
• fmi(): Fowlkes-Mallows Index.
• bmi(): Informedness, Bookmaker Index.
• csi(): Critical Success Index, Threat Score, Jaccard Index.
• deltap(): Markedness or deltaP.
• posLr(): Positive Likelihood Ratio.
• negLr(): Negative Likelihood Ratio.
• dor(): Diagnostic Odds Ratio.
• npv(): Negative Predictive Value.
• FPR(): False Positive Rate, false alarm, fall-out.
• FNR(): False Negative Rate, miss rate.
• FDR(): False Detection Rate, False Discovery Rate.
• FOR(): False Omission Rate.
• preval(): Prevalence.
• preval_t(): Prevalence threshold.
• AUC_roc(): Area Under the ROC Curve (trapezoid approach).

2. Three (3) additional functions to the family of regression performance metrics:

• MASE() (Mean Absolute Scaled Error) for Time Series Analysis.
• dcorr() (Distance correlation) as wrapper of dcor() from energy package (https://CRAN.R-project.org/package=energy), and
• MIC() (Maximal Information Coefficient) as wrapper of mine_stat() from minerva package (https://CRAN.R-project.org/package=minerva).
• RMLA() (Root Mean Lack of Accuracy)
• RMLP() (Root Mean Lack of Precision)

3. Update of the metrics_summary() function including:

• run performance metrics summary either for “regression” or “classification” using the new type argument, ‘required’ to specify the type of prediction task.
• pos_level argument, for binomial classification, to allow the user to specify the alphanumeric order of the “positive” level.

4. One (1) additional plotting function for regression:

• density_plot(), to create a plot that paints density areas of predicted and observed coordinates.

5. Fixing issue with the tiles_plot() not plotting hexagons. Changed ggplot2::geom_hex() by ggplot2::stat_bin2d

6. Seventeen (17) additional arguments to customize scatter_plot, tiles_plot, and density_plot:

• print_eq (to print equation or not)
• position_metrics (to customize position of metrics_table when print_metrics = TRUE)
• position_eq (to customize position of equation when print_eq = TRUE)
• eq_color (to customize color of the equation when print_eq = TRUE)
• colors (for tile_plot and density_plot, to paint gradient from “low” to “high” density of points)
• shape_type (to customize shape of the scatter_plot() and bland_altman_plot())
• shape_size (to customize shape of the scatter_plot() and bland_altman_plot())
• shape_color (to customize shape of the scatter_plot() and bland_altman_plot())
• regline_type (to customize regression line of the scatter_plot(), tiles_plot, and density_plot())
• regline_size (to customize regression line of the scatter_plot(), tiles_plot, and density_plot())
• regline_color (to customize regression line of the scatter_plot(), tiles_plot, and density_plot())
• zeroline_type (to customize lines of the bland_altman_plot())
• zeroline_size (to customize lines of the bland_altman_plot())
• zeroline_color (to customize lines of the bland_altman_plot())
• limitsline_type (to customize lines of the bland_altman_plot())
• limitsline_size (to customize lines of the bland_altman_plot())
• limitsline_color (to customize lines of the bland_altman_plot())

7. Adding the argument tidy to all metrics functions, which allows to control the user the type of return (tidy=TRUE returns a data.frame, tidy = FALSE returns a list)

8. Fixing a minor a bug on the NSE() function to estimate the Nash-Sutcliffe model efficiency that produced only values of NSE=1.00 on v1.2.3.

9. Improved coverage of the code testing.

10. README update with new features descriptions and links to vignettes.

11. Updated vignettes creating independent versions for classification and regression models, and for importing APSIM files.

metrica 1.2.3

• May, 10, 2022.
  

Maintenance update fixing minor errors after feedback from CRAN submission of v1.2.2 (e.g. use ‘donttest’ instead of ‘dontrun’ in functions’ examples, adding references into functions). Also, the available metrics vignette was updated adding the corresponding citations of formulae used into functions.

metrica 1.2.2

• May, 05, 2022.
  

Maintenance update fixing minor bugs related to checks before CRAN submission (e.g. spelling check, URLs, DOIs, etc.)

metrica 1.2.1

Minor updates (1.2.1):

Update of function and arguments’ names replacing “.” by “_“:

Old | New import.apsim.out | import_apsim_out import.apsim.db | import_apsim_db metrics.summary | metrics_summary scatter.plot | scatter_plot tiles.plot | tiles_plot bland.altman.plot | bland_altman_plot B0.sma | B0_sma B1.sma | B1_sma metrics.list | metrics_list print.metrics | print_metrics

New features (1.2.0)

Data: a new (Optional) arg. called “data” is included for all functions, which serves to call an existing data frame containing the predicted-observed data. This facilitates passing the functions to multiple and nested data frames at once using mapping functions.

APSIM: includes two new functions to read APSIM output files from APSIM Classic [“*.out”, import.apsim.out()] and APSIM NextGen [“*.db”, import.apsim.db()].