diff --git a/.Rbuildignore b/.Rbuildignore
index 89aa541..045954b 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -12,5 +12,5 @@
^figure*
^docs*
.*tar.gz$
-
+^README.html$
^\.github$
diff --git a/DESCRIPTION b/DESCRIPTION
index 2d3616a..2671b10 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: projections
Title: Project Future Case Incidence
-Version: 0.6.0
+Version: 0.6.1
Authors@R:
c(person(given = "Thibaut",
family = "Jombart",
@@ -46,7 +46,7 @@ Imports:
incidence (>= 1.4.1),
ggplot2,
methods
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
URL: https://www.repidemicsconsortium.org/projections/
BugReports: https://github.com/reconhub/projections/issues
diff --git a/NEWS.md b/NEWS.md
index c7e4536..88c626d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,12 @@
+# projections 0.6.1
+
+## Fixes and improvements
+
+- fixed tests of dates due failing due to changes in `as.Date()`
+- fixed example in the manpage of `summary.projection`
+
+
+
# projections 0.6.0
## Fixes and improvements
diff --git a/R/summary.R b/R/summary.R
index 8e0f79e..a48aa87 100644
--- a/R/summary.R
+++ b/R/summary.R
@@ -26,6 +26,7 @@
#'
#' @param ... only preesnt for compatibility with the generic
#'
+#' @examples
#' if (require(incidence)) {
#' i <- incidence::incidence(as.Date('2020-01-23'))
#' si <- c(0.2, 0.5, 0.2, 0.1)
diff --git a/man/summary.projections.Rd b/man/summary.projections.Rd
index 2bef359..5dbd0e0 100644
--- a/man/summary.projections.Rd
+++ b/man/summary.projections.Rd
@@ -28,30 +28,31 @@ computed; ignored if \code{FALSE} or of length 0}
\item{max}{a \code{logical} indicating of the maximum should be computed}
-\item{...}{only preesnt for compatibility with the generic
-
-if (require(incidence)) {
-i <- incidence::incidence(as.Date('2020-01-23'))
-si <- c(0.2, 0.5, 0.2, 0.1)
-R0 <- 2
-
-p <- project(x = i,
-si = si,
-R = R0,
-n_sim = 2,
-R_fix_within = TRUE,
-n_days = 10,
-model = "poisson"
-)
-summary(p)
-
-}}
+\item{...}{only preesnt for compatibility with the generic}
}
\description{
This method summarises predicted epidemic trajectories contained in a
\code{projections} object by days, deriving the mean, standard deviation, and
user-specified quantiles for each day.
}
+\examples{
+if (require(incidence)) {
+ i <- incidence::incidence(as.Date('2020-01-23'))
+ si <- c(0.2, 0.5, 0.2, 0.1)
+ R0 <- 2
+
+ p <- project(x = i,
+ si = si,
+ R = R0,
+ n_sim = 2,
+ R_fix_within = TRUE,
+ n_days = 10,
+ model = "poisson"
+ )
+ summary(p)
+
+}
+}
\author{
Thibaut Jombart
}
diff --git a/tests/testthat/_snaps/plots/basic-example-plot.svg b/tests/testthat/_snaps/plots/basic-example-plot.svg
index 600cf92..baa9fd8 100644
--- a/tests/testthat/_snaps/plots/basic-example-plot.svg
+++ b/tests/testthat/_snaps/plots/basic-example-plot.svg
@@ -72,19 +72,19 @@
Predicted incidence
quantile
-
+
-
+
-
+
-
+
-
+
-
+
-
+
1%
5%
diff --git a/tests/testthat/_snaps/plots/evd-proj-box-no-outliers.svg b/tests/testthat/_snaps/plots/evd-proj-box-no-outliers.svg
index afb8987..2ac1f5f 100644
--- a/tests/testthat/_snaps/plots/evd-proj-box-no-outliers.svg
+++ b/tests/testthat/_snaps/plots/evd-proj-box-no-outliers.svg
@@ -406,19 +406,19 @@
Predicted incidence
quantile
-
+
-
+
-
+
-
+
-
+
-
+
-
+
1%
5%
diff --git a/tests/testthat/_snaps/plots/evd-proj-no-box-custom-lines.svg b/tests/testthat/_snaps/plots/evd-proj-no-box-custom-lines.svg
index 755e147..8f80ccd 100644
--- a/tests/testthat/_snaps/plots/evd-proj-no-box-custom-lines.svg
+++ b/tests/testthat/_snaps/plots/evd-proj-no-box-custom-lines.svg
@@ -21,7 +21,7 @@
-
+
@@ -83,19 +83,19 @@
Predicted incidence
quantile
-
+
-
+
-
+
-
+
-
+
-
+
-
+
1%
5%
diff --git a/tests/testthat/_snaps/plots/evd-proj-no-ribbon.svg b/tests/testthat/_snaps/plots/evd-proj-no-ribbon.svg
index 9a281f0..1e94472 100644
--- a/tests/testthat/_snaps/plots/evd-proj-no-ribbon.svg
+++ b/tests/testthat/_snaps/plots/evd-proj-no-ribbon.svg
@@ -21,7 +21,7 @@
-
+
@@ -80,19 +80,19 @@
Predicted incidence
quantile
-
+
-
+
-
+
-
+
-
+
-
+
-
+
1%
5%
diff --git a/tests/testthat/_snaps/plots/evd-proj-red-box.svg b/tests/testthat/_snaps/plots/evd-proj-red-box.svg
index a8fee77..f0d4c0f 100644
--- a/tests/testthat/_snaps/plots/evd-proj-red-box.svg
+++ b/tests/testthat/_snaps/plots/evd-proj-red-box.svg
@@ -406,19 +406,19 @@
Predicted incidence
quantile
-
+
-
+
-
+
-
+
-
+
-
+
-
+
1%
5%
diff --git a/tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-and-custom.svg b/tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-and-custom.svg
index 6adf373..fe1ae06 100644
--- a/tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-and-custom.svg
+++ b/tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-and-custom.svg
@@ -280,35 +280,35 @@
Daily incidence
quantile
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
0.1%
1%
diff --git a/tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-no-box.svg b/tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-no-box.svg
index 7d8ace8..00976db 100644
--- a/tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-no-box.svg
+++ b/tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-no-box.svg
@@ -796,19 +796,19 @@
Daily incidence
quantile
-
+
-
+
-
+
-
+
-
+
-
+
-
+
1%
5%
diff --git a/tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence.svg b/tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence.svg
index aaee8a1..959f9af 100644
--- a/tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence.svg
+++ b/tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence.svg
@@ -21,7 +21,7 @@
-
+
@@ -473,19 +473,19 @@
Daily incidence
quantile
-
+
-
+
-
+
-
+
-
+
-
+
-
+
1%
5%
diff --git a/tests/testthat/_snaps/plots/evd-proj.svg b/tests/testthat/_snaps/plots/evd-proj.svg
index 0a2f67f..1ddfd57 100644
--- a/tests/testthat/_snaps/plots/evd-proj.svg
+++ b/tests/testthat/_snaps/plots/evd-proj.svg
@@ -21,7 +21,7 @@
-
+
@@ -83,19 +83,19 @@
Predicted incidence
quantile
-
+
-
+
-
+
-
+
-
+
-
+
-
+
1%
5%
diff --git a/tests/testthat/test-project.R b/tests/testthat/test-project.R
index 230b97d..c8deed4 100644
--- a/tests/testthat/test-project.R
+++ b/tests/testthat/test-project.R
@@ -12,7 +12,7 @@ test_that("Projections can be performed for a single day", {
model = "poisson"
)
- expect_identical(get_dates(p), as.Date("2020-01-24"))
+ expect_equal(get_dates(p), as.Date("2020-01-24"))
})
@@ -33,7 +33,7 @@ test_that("Projections can be performed for a single day", {
model = "poisson"
)
- expect_identical(get_dates(p), as.Date("2020-01-24") + 0:1)
+ expect_equal(get_dates(p), as.Date("2020-01-24") + 0:1)
expect_identical(ncol(p), 1L)
})
@@ -55,7 +55,7 @@ test_that("Projections can be performed for a single day and single simulation",
model = "poisson"
)
- expect_identical(get_dates(p), as.Date("2020-01-24"))
+ expect_equal(get_dates(p), as.Date("2020-01-24"))
expect_identical(ncol(p), 1L)
})