swash 3.0.3

Bugfixes

• breaks_growth() and plot(breaksgrowth) now treat results with less than two segments (which are rare) correctly
• calculate_rollmean(infpan) and calculate_rollsum(infpan): Check of the specified rolling window k with respect to the number of time points in the infpan object
• Check for NA values in observed and expected vectors in binary_metrics()
• Check for regions without any infection cases when using the Swash-Backwash Model with swash_backwash() or swash(infpan)
• Corrections in RD documentations

Other

• Comprehensive and consistent validation of user-supplied time-series and panel data across all functions and methods that utilize time series; included impute_missing_values option
• exponential growth(): Doubling time is set to NA if the estimated growth rate r is non-positive
• If no start values for NLS estimation is specified in exponential_growth(), coefficients from the OLS estimation are used as start values (as in logistic_growth())

swash 3.0.2

Bugfixes

• Fixed bugs in balancing datasets procedure in load_infections_paneldata(), is_balanced(), and as_balanced()
• Checking of correct time format of ‘col_date’ in load_infections_paneldata() and swash_backwash()
• Fixed bug in bootstrap sampling in confint(sbm)
• A potential error in plot_coef_ci() involving exclusively positive or exclusively negative significant estimates has been fixed
• Fixed bug in dealing with NA values in logistic_growth(), exponential_growth(), and breaks_growth()
• Fixed bug in bisection mode in logistic_growth()
• Checking of specified parameters in confint(sbm)
• Checking ‘infections’ vector length and type of parameter ‘GP’ in R_t()
• Restored erroneously removed NEWS.md

swash 3.0.1

Bugfixes

• Corrections in NAMESPACE (required for correct package installation)
• exponential growth(): R0 is set to NA (instead of 0) if the estimated growth rate is negative
• metrics(): Correcting R-squared for zero variance, added na.rm parameter (default: TRUE)

Other

• Implemented testthat testing in tests/ folder, keeping former swash_test.R in examples/ folder
• Extensions of documentation

swash 3.0.0

Breaking changes (Non-backwards compatible)

• Complete change to the nbmatrix() function: creation of an instance of the new nbmatrix class
• Replacement of the old nbstat() function with the nbstat() method of the nbmatrix class
• Rearrangement of the code in modules for better readability and easier maintaining

New features

• Spatial statistics based on neighborhood matrix: Global Getis-Ord, Global Moran’s I,
• Local Getis-Ord Gi*, with all of them being methods of class nbmatrix
• Plotting a map from an nbmatrix object
• Importing geodata (sf) in infpan objects
• Plotting maps of attributes in an infpan object with method plot_map()

Bugfixes

• Corrections in RD documentations

swash 2.0.2

General

• Deprecation warnings with respect to version >=3.0.0

Bugfixes

• Updating URLs in help texts that are no longer valid

swash 2.0.1

Bugfixes

• Extensions and corrections of documentation files

swash 2.0.0

Breaking changes (Non-backwards compatible)

• Analyses are conducted via infpan objects rather than sbm objects
• Former method plot_regions() for class sbm is replaced by generic method plot() for infpan objects
• Former methods growth() and growth_initial() for sbm objects are are now methods for the infpan class
• Former function plot_breakpoints() is replaced by function breaks_growth() and the corresponding plot() method

New features

• Importing infections panel data via load_infections_paneldata(), which creates and instance of the new class infpan
• Calculation of spread indicators for infpan objects such as incidence and effective reproduction number \(R_t\)
• Function hawkes_growth() for parametrization of a Hawkes process equation for infections
• Method growth_hawkes() for parametrization of Hawkes process equations based on infpan objects
• Additional NLS estimation in function exponential_growth()
• Option to add a constant (if values of y equal to zero occur) in functions logistic_growth() and exponential_growth(), as well as in methods growth(infpan) and growth_initial(infpan)

Bugfixes

• Functions metrics(), binary_metrics() and binary_metrics_glm() now return results invisible
• Check for equal length of input vectors in logistic_growth()

swash 1.3.3

New features

• Fit metrics for logistic and exponential growth models

Bugfixes

• Bug in calculation in metrics() fixed
• Check for vectors lengths in logistic_growth() and exponential_growth()
• Deprecation warnings with respect to version >=2.0.0

swash 1.3.2

New features

• New option verbose in time-consuming calculation functions.

Bugfixes

• Deprecation warnings with respect to version >=2.0.0.