epiforecasts · seabbs · May 15, 2020 · May 15, 2020
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -44,7 +44,7 @@ Authors@R: c(
     person("Sebastian", "Funk", 
             email = "[email protected]", 
             role = c("aut")))
-Description: To forecast the time-varying reproduction number and using this to forecast reported case counts. Includes
+Description: To forecast the time-varying reproduction number and use this to forecast reported case counts. Includes
              tools to evaluate a range of models across samples and time series using proper scoring rules.
 License: MIT + file LICENSE
 Encoding: UTF-8

diff --git a/README.Rmd b/README.Rmd
@@ -16,10 +16,7 @@ knitr::opts_chunk$set(
 [![R build status](https://github.com/epiforecasts/EpiSoon/workflows/R-CMD-check/badge.svg)](https://github.com/epiforecasts/EpiSoon)
 [![Build Status](https://travis-ci.com/epiforecasts/EpiSoon.svg?branch=master)](https://travis-ci.com/epiforecasts/EpiSoon)
 
-
-*Warning: This package is a work in progress and is currently developed solely with the COVID-19 outbreak in mind. Breaking changes may occur and the authors cannot guarantee support.*
-
-**Aim:** To forecast the time-varying reproduction number and using this to forecast reported case counts. 
+**Aim:** To forecast the time-varying reproduction number and use this to forecast reported case counts. 
 
 ## Installation
 

diff --git a/README.md b/README.md
@@ -2,14 +2,12 @@
 # EpiSoon
 
 [![DOI](https://zenodo.org/badge/248311916.svg)](https://zenodo.org/badge/latestdoi/248311916)
+[![R build
+status](https://github.com/epiforecasts/EpiSoon/workflows/R-CMD-check/badge.svg)](https://github.com/epiforecasts/EpiSoon)
 [![Build
 Status](https://travis-ci.com/epiforecasts/EpiSoon.svg?branch=master)](https://travis-ci.com/epiforecasts/EpiSoon)
 
-*Warning: This package is a work in progress and is currently developed
-solely with the COVID-19 outbreak in mind. Breaking changes may occur
-and the authors cannot guarantee support.*
-
-**Aim:** To forecast the time-varying reproduction number and using this
+**Aim:** To forecast the time-varying reproduction number and use this
 to forecast reported case counts.
 
 ## Installation
@@ -85,72 +83,72 @@ forecasts <- EpiSoon::compare_timeseries(obs_rts, obs_cases, models,
 
 forecasts
 #> $forecast_rts
-#> # A tibble: 784 x 12
-#>    timeseries model forecast_date date       horizon median  mean     sd
-#>    <chr>      <chr> <chr>         <date>       <int>  <dbl> <dbl>  <dbl>
-#>  1 Region 1   AR 3  2020-03-05    2020-03-06       1   2.20  2.20 0.0422
-#>  2 Region 1   AR 3  2020-03-05    2020-03-07       2   2.15  2.15 0.0382
-#>  3 Region 1   AR 3  2020-03-05    2020-03-08       3   2.09  2.08 0.0611
-#>  4 Region 1   AR 3  2020-03-05    2020-03-09       4   2.01  2.01 0.0541
-#>  5 Region 1   AR 3  2020-03-05    2020-03-10       5   1.95  1.95 0.0331
-#>  6 Region 1   AR 3  2020-03-05    2020-03-11       6   1.91  1.91 0.0444
-#>  7 Region 1   AR 3  2020-03-05    2020-03-12       7   1.85  1.85 0.0375
-#>  8 Region 1   AR 3  2020-03-06    2020-03-07       1   2.09  2.10 0.0364
-#>  9 Region 1   AR 3  2020-03-06    2020-03-08       2   2.02  2.02 0.0158
-#> 10 Region 1   AR 3  2020-03-06    2020-03-09       3   1.94  1.94 0.0261
-#> # … with 774 more rows, and 4 more variables: bottom <dbl>, lower <dbl>,
-#> #   upper <dbl>, top <dbl>
+#> # A tibble: 798 x 12
+#>    timeseries model forecast_date date       horizon median  mean    sd bottom
+#>    <chr>      <chr> <chr>         <date>       <int>  <dbl> <dbl> <dbl>  <dbl>
+#>  1 Region 1   AR 3  2020-03-04    2020-03-05       1  0     1.08  2.15       0
+#>  2 Region 1   AR 3  2020-03-04    2020-03-06       2  0.203 0.955 1.59       0
+#>  3 Region 1   AR 3  2020-03-04    2020-03-07       3  0.232 0.790 1.26       0
+#>  4 Region 1   AR 3  2020-03-04    2020-03-08       4  0.259 1.70  2.69       0
+#>  5 Region 1   AR 3  2020-03-04    2020-03-09       5  0.238 1.40  2.35       0
+#>  6 Region 1   AR 3  2020-03-04    2020-03-10       6  0.862 0.830 0.880      0
+#>  7 Region 1   AR 3  2020-03-04    2020-03-11       7  1.22  1.92  2.95       0
+#>  8 Region 1   AR 3  2020-03-05    2020-03-06       1  0.378 1.18  1.88       0
+#>  9 Region 1   AR 3  2020-03-05    2020-03-07       2  0.536 1.87  3.64       0
+#> 10 Region 1   AR 3  2020-03-05    2020-03-08       3  0.758 1.87  3.44       0
+#> # … with 788 more rows, and 3 more variables: lower <dbl>, upper <dbl>,
+#> #   top <dbl>
 #> 
 #> $rt_scores
-#> # A tibble: 616 x 14
-#>    timeseries model forecast_date date       horizon    dss    crps   logs
-#>    <chr>      <chr> <chr>         <date>       <int>  <dbl>   <dbl>  <dbl>
-#>  1 Region 1   AR 3  2020-03-05    2020-03-06       1 -6.43  0.00837 -2.50 
-#>  2 Region 1   AR 3  2020-03-05    2020-03-07       2 -6.61  0.00733 -2.74 
-#>  3 Region 1   AR 3  2020-03-05    2020-03-08       3 -5.44  0.0117  -2.43 
-#>  4 Region 1   AR 3  2020-03-05    2020-03-09       4 -5.16  0.0337   1.22 
-#>  5 Region 1   AR 3  2020-03-05    2020-03-10       5 -0.766 0.0601  -0.295
-#>  6 Region 1   AR 3  2020-03-05    2020-03-11       6  0.361 0.0853   0.418
-#>  7 Region 1   AR 3  2020-03-05    2020-03-12       7 10.5   0.128   15.8  
-#>  8 Region 1   AR 3  2020-03-06    2020-03-07       1 -4.82  0.0378   0.634
-#>  9 Region 1   AR 3  2020-03-06    2020-03-08       2 23.8   0.0774  25.4  
-#> 10 Region 1   AR 3  2020-03-06    2020-03-09       3 14.5   0.102    7.65 
-#> # … with 606 more rows, and 6 more variables: bias <dbl>, sharpness <dbl>,
+#> # A tibble: 630 x 14
+#>    timeseries model forecast_date date       horizon   dss  crps  logs   bias
+#>    <chr>      <chr> <chr>         <date>       <int> <dbl> <dbl> <dbl>  <dbl>
+#>  1 Region 1   AR 3  2020-03-04    2020-03-05       1  1.76 1.42  13.8  -0.6  
+#>  2 Region 1   AR 3  2020-03-04    2020-03-06       2  1.49 1.14   2.48 -0.8  
+#>  3 Region 1   AR 3  2020-03-04    2020-03-07       3  1.65 1.15   2.49 -0.8  
+#>  4 Region 1   AR 3  2020-03-04    2020-03-08       4  1.90 0.914  2.04 -0.400
+#>  5 Region 1   AR 3  2020-03-04    2020-03-09       5  1.70 0.999  2.45 -0.400
+#>  6 Region 1   AR 3  2020-03-04    2020-03-10       6  1.70 0.851  1.80 -0.8  
+#>  7 Region 1   AR 3  2020-03-04    2020-03-11       7  2.06 0.564  1.62 -0.400
+#>  8 Region 1   AR 3  2020-03-05    2020-03-06       1  1.48 1.18   6.29 -0.6  
+#>  9 Region 1   AR 3  2020-03-05    2020-03-07       2  2.48 1.00   2.29 -0.6  
+#> 10 Region 1   AR 3  2020-03-05    2020-03-08       3  2.37 0.779  1.75 -0.6  
+#> # … with 620 more rows, and 5 more variables: sharpness <dbl>,
 #> #   calibration <dbl>, median <dbl>, iqr <dbl>, ci <dbl>
 #> 
 #> $forecast_cases
-#> # A tibble: 616 x 12
-#>    timeseries model forecast_date date       horizon median  mean    sd
-#>    <chr>      <chr> <chr>         <date>       <int>  <dbl> <dbl> <dbl>
-#>  1 Region 1   AR 3  2020-03-05    2020-03-06       1   84    81.7 12.0 
-#>  2 Region 1   AR 3  2020-03-05    2020-03-07       2  101   101.   7.16
-#>  3 Region 1   AR 3  2020-03-05    2020-03-08       3  114.  114.  13.8 
-#>  4 Region 1   AR 3  2020-03-05    2020-03-09       4  130.  133.  17.5 
-#>  5 Region 1   AR 3  2020-03-05    2020-03-10       5  152   156.  18.0 
-#>  6 Region 1   AR 3  2020-03-05    2020-03-11       6  187   184   24.0 
-#>  7 Region 1   AR 3  2020-03-05    2020-03-12       7  202.  212.  33.1 
-#>  8 Region 1   AR 3  2020-03-06    2020-03-07       1   93    91.2  8.98
-#>  9 Region 1   AR 3  2020-03-06    2020-03-08       2   94.5  97.3  8.71
-#> 10 Region 1   AR 3  2020-03-06    2020-03-09       3  118   116.  10.7 
-#> # … with 606 more rows, and 4 more variables: bottom <dbl>, lower <dbl>,
-#> #   upper <dbl>, top <dbl>
+#> # A tibble: 630 x 12
+#>    timeseries model forecast_date date       horizon median  mean    sd bottom
+#>    <chr>      <chr> <chr>         <date>       <int>  <dbl> <dbl> <dbl>  <dbl>
+#>  1 Region 1   AR 3  2020-03-04    2020-03-05       1    0    32.3  66.2      0
+#>  2 Region 1   AR 3  2020-03-04    2020-03-06       2    7.5  36.3  62.3      0
+#>  3 Region 1   AR 3  2020-03-04    2020-03-07       3    6    33.9  70.3      0
+#>  4 Region 1   AR 3  2020-03-04    2020-03-08       4    6.5  60.3 129.       0
+#>  5 Region 1   AR 3  2020-03-04    2020-03-09       5    4.5  67.7 170.       0
+#>  6 Region 1   AR 3  2020-03-04    2020-03-10       6   16    38.7  50.0      0
+#>  7 Region 1   AR 3  2020-03-04    2020-03-11       7   38.5  53.9  64.1      0
+#>  8 Region 1   AR 3  2020-03-05    2020-03-06       1   13    46.4  74.3      0
+#>  9 Region 1   AR 3  2020-03-05    2020-03-07       2   17.5  88.6 178.       0
+#> 10 Region 1   AR 3  2020-03-05    2020-03-08       3   30.5  67.7 107.       0
+#> # … with 620 more rows, and 3 more variables: lower <dbl>, upper <dbl>,
+#> #   top <dbl>
 #> 
 #> $case_scores
-#> # A tibble: 616 x 15
-#>    timeseries model sample forecast_date date       horizon   dss  crps
-#>    <chr>      <chr> <chr>  <chr>         <date>       <int> <dbl> <dbl>
-#>  1 Region 1   AR 3  1      2020-03-05    2020-03-06       1  5.45  6.13
-#>  2 Region 1   AR 3  1      2020-03-05    2020-03-07       2  7.38  8.96
-#>  3 Region 1   AR 3  1      2020-03-05    2020-03-08       3  5.96  7.5 
-#>  4 Region 1   AR 3  1      2020-03-05    2020-03-09       4  6.69  9.02
-#>  5 Region 1   AR 3  1      2020-03-05    2020-03-10       5  6.41  7.77
-#>  6 Region 1   AR 3  1      2020-03-05    2020-03-11       6  6.81 12.4 
-#>  7 Region 1   AR 3  1      2020-03-05    2020-03-12       7  7.21  7.99
-#>  8 Region 1   AR 3  1      2020-03-06    2020-03-07       1  4.43  2.98
-#>  9 Region 1   AR 3  1      2020-03-06    2020-03-08       2  4.55  3.51
-#> 10 Region 1   AR 3  1      2020-03-06    2020-03-09       3  4.64  2.86
-#> # … with 606 more rows, and 7 more variables: logs <dbl>, bias <dbl>,
-#> #   sharpness <dbl>, calibration <dbl>, median <dbl>, iqr <dbl>, ci <dbl>
+#> # A tibble: 630 x 15
+#>    timeseries model sample forecast_date date       horizon   dss  crps  logs
+#>    <chr>      <chr> <chr>  <chr>         <date>       <int> <dbl> <dbl> <dbl>
+#>  1 Region 1   AR 3  1      2020-03-04    2020-03-05       1  8.52  40.8 35.8 
+#>  2 Region 1   AR 3  1      2020-03-04    2020-03-06       2  8.54  36.3  5.79
+#>  3 Region 1   AR 3  1      2020-03-04    2020-03-07       3  9.06  55.9  8.89
+#>  4 Region 1   AR 3  1      2020-03-04    2020-03-08       4  9.74  58.9  6.74
+#>  5 Region 1   AR 3  1      2020-03-04    2020-03-09       5 10.3   77.9 10.3 
+#>  6 Region 1   AR 3  1      2020-03-04    2020-03-10       6 12.4   78.2  6.29
+#>  7 Region 1   AR 3  1      2020-03-04    2020-03-11       7 11.7   91.1  7.27
+#>  8 Region 1   AR 3  1      2020-03-05    2020-03-06       1  8.65  38.1  7.27
+#>  9 Region 1   AR 3  1      2020-03-05    2020-03-07       2 10.3   43.1  6.13
+#> 10 Region 1   AR 3  1      2020-03-05    2020-03-08       3  9.36  38.6  5.66
+#> # … with 620 more rows, and 6 more variables: bias <dbl>, sharpness <dbl>,
+#> #   calibration <dbl>, median <dbl>, iqr <dbl>, ci <dbl>
 ```
 
   - Plot an evaluation of Rt forecasts using iterative
@@ -186,18 +184,18 @@ EpiSoon::plot_forecast_evaluation(forecasts$forecast_cases, obs_cases, c(7)) +
 ``` r
 EpiSoon::summarise_scores(forecasts$case_scores)
 #> # A tibble: 27 x 9
-#>    score  model      bottom   lower  median    mean   upper     top      sd
-#>    <chr>  <chr>       <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
-#>  1 bias   AR 3     -1.00e+0 1.00e-1 7.00e-1 4.81e-1 1.00e+0 1.00e+0 6.01e-1
-#>  2 bias   ARIMA    -1.00e+0 2.00e-1 8.00e-1 5.37e-1 1.00e+0 1.00e+0 5.79e-1
-#>  3 bias   Semi-l…  -1.00e+0 2.00e-1 6.00e-1 4.87e-1 1.00e+0 1.00e+0 5.79e-1
-#>  4 calib… AR 3      8.57e-5 8.57e-5 8.57e-5 2.83e-2 1.20e-4 3.16e-1 8.06e-2
-#>  5 calib… ARIMA     8.57e-5 8.57e-5 8.57e-5 3.80e-2 2.00e-4 4.12e-1 9.34e-2
-#>  6 calib… Semi-l…   8.57e-5 8.57e-5 9.29e-5 7.22e-2 6.04e-3 9.11e-1 2.01e-1
-#>  7 ci     AR 3      2.64e+1 5.07e+1 9.99e+1 1.18e+3 2.05e+3 6.79e+3 1.94e+3
-#>  8 ci     ARIMA     2.25e+1 4.55e+1 9.51e+1 1.09e+3 2.02e+3 6.14e+3 1.77e+3
-#>  9 ci     Semi-l…   2.61e+1 5.30e+1 9.60e+1 1.07e+3 1.76e+3 5.29e+3 1.71e+3
-#> 10 crps   AR 3      2.84e+0 6.37e+0 1.66e+1 4.55e+1 7.54e+1 2.03e+2 5.76e+1
+#>    score  model      bottom    lower   median     mean    upper      top      sd
+#>    <chr>  <chr>       <dbl>    <dbl>    <dbl>    <dbl>    <dbl>    <dbl>   <dbl>
+#>  1 bias   AR 3     -1.00e+0 -8.75e-1 -8.00e-1 -6.94e-1 -6.00e-1   -0.200 2.65e-1
+#>  2 bias   ARIMA    -1.00e+0  2.00e-1  8.00e-1  5.33e-1  1.00e+0    1     5.70e-1
+#>  3 bias   Semi-l…  -1.00e+0  3.00e-1  8.00e-1  5.37e-1  1.00e+0    1     5.63e-1
+#>  4 calib… AR 3      8.57e-5  8.57e-5  8.57e-5  2.83e-2  2.00e-3    0.504 1.26e-1
+#>  5 calib… ARIMA     8.57e-5  8.57e-5  8.57e-5  3.59e-2  1.50e-4    0.509 1.15e-1
+#>  6 calib… Semi-l…   8.57e-5  8.57e-5  8.57e-5  4.30e-2  1.50e-4    0.587 1.28e-1
+#>  7 ci     AR 3      1.41e+2  3.76e+2  6.91e+2  1.60e+3  1.63e+3 8488.    2.28e+3
+#>  8 ci     ARIMA     2.28e+1  4.62e+1  8.40e+1  1.04e+3  1.57e+3 6341.    1.72e+3
+#>  9 ci     Semi-l…   2.51e+1  5.67e+1  1.26e+2  1.05e+3  1.62e+3 5913.    1.75e+3
+#> 10 crps   AR 3      3.63e+1  9.19e+1  1.40e+2  1.58e+2  2.00e+2  429.    9.54e+1
 #> # … with 17 more rows
 ```
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -44,6 +44,7 @@ reference:
       - bsts_model
       - fable_model
       - brms_model
+      - forecastHybrid_model
   - title: Predicting cases from reproduction numbers
     desc: Functions to for mapping reproduction number estimates to forecast cases
     contents:

diff --git a/man/figures/unnamed-chunk-7-1.png b/man/figures/unnamed-chunk-7-1.png
diff --git a/man/figures/unnamed-chunk-8-1.png b/man/figures/unnamed-chunk-8-1.png