epinowcast · seabbs · Sep 9, 2024 · May 21, 2024 · May 22, 2024 · May 23, 2024
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -49,7 +49,10 @@ Suggests:
     tidyr,
     posterior,
     fs,
-    tidybayes
+    sf,
+    tidybayes,
+    modelr,
+    patchwork
 Remotes:
     stan-dev/cmdstanr,
     Rdatatable/data.table,

diff --git a/R/observe.R b/R/observe.R
@@ -1,5 +1,19 @@
 #' Observation process for primary and secondary events
 #'
+#' This function adds columns to linelist data representing an observation
+#' process with daily primary and secondary censoring, as well as right
+#' truncation. The columns added are:
+#' * `ptime_daily`: The floor of `ptime`
+#' * `ptime_lwr`: The lower bound of `ptime`. Equal to `ptime_daily`
+#' * `ptime_upr`: The upper bound of `ptime`. Equal to `ptime_lwr + 1`
+#' * `stime_daily`: The floor of `stime`
+#' * `stime_lwr`: The lower bound of `stime`. Equal to `stime_daily`
+#' * `stime_upr`: The upper bound of `stime`. Equal to `stime_lwr + 1`
+#' * `delay_daily`: Given by `stime_daily - ptime_daily`
+#' * `delay_lwr`: Given by `delay_daily - 1` (or 0 if `delay_daily < 1`)
+#' * `delay_upr`: Given by `delay_daily + 1`
+#' * `obs_at`: The maximum value of `stime`
+#'
 #' @param linelist ...
 #' @family observe
 #' @autoglobal

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -16,6 +16,8 @@ navbar:
     articles:
       text: Articles
       menu:
+      - text: Advanced features with Ebola data
+        href: articles/ebola.html
       - text: Approximate Bayesian inference
         href: articles/approx-inference.html
 

diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_0.cpg b/inst/gadm41_SLE_shp/gadm41_SLE_0.cpg
@@ -0,0 +1 @@
+UTF-8
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_0.dbf b/inst/gadm41_SLE_shp/gadm41_SLE_0.dbf
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_0.prj b/inst/gadm41_SLE_shp/gadm41_SLE_0.prj
@@ -0,0 +1 @@
+GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_0.shp b/inst/gadm41_SLE_shp/gadm41_SLE_0.shp
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_0.shx b/inst/gadm41_SLE_shp/gadm41_SLE_0.shx
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_1.cpg b/inst/gadm41_SLE_shp/gadm41_SLE_1.cpg
@@ -0,0 +1 @@
+UTF-8
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_1.dbf b/inst/gadm41_SLE_shp/gadm41_SLE_1.dbf
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_1.prj b/inst/gadm41_SLE_shp/gadm41_SLE_1.prj
@@ -0,0 +1 @@
+GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_1.shp b/inst/gadm41_SLE_shp/gadm41_SLE_1.shp
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_1.shx b/inst/gadm41_SLE_shp/gadm41_SLE_1.shx
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_2.cpg b/inst/gadm41_SLE_shp/gadm41_SLE_2.cpg
@@ -0,0 +1 @@
+UTF-8
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_2.dbf b/inst/gadm41_SLE_shp/gadm41_SLE_2.dbf
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_2.prj b/inst/gadm41_SLE_shp/gadm41_SLE_2.prj
@@ -0,0 +1 @@
+GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_2.shp b/inst/gadm41_SLE_shp/gadm41_SLE_2.shp
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_2.shx b/inst/gadm41_SLE_shp/gadm41_SLE_2.shx
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_3.cpg b/inst/gadm41_SLE_shp/gadm41_SLE_3.cpg
@@ -0,0 +1 @@
+UTF-8
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_3.dbf b/inst/gadm41_SLE_shp/gadm41_SLE_3.dbf
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_3.prj b/inst/gadm41_SLE_shp/gadm41_SLE_3.prj
@@ -0,0 +1 @@
+GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_3.shp b/inst/gadm41_SLE_shp/gadm41_SLE_3.shp
diff --git a/inst/gadm41_SLE_shp/gadm41_SLE_3.shx b/inst/gadm41_SLE_shp/gadm41_SLE_3.shx
diff --git a/man/observe_process.Rd b/man/observe_process.Rd
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]