Issue 48: Ebola vignette (#52)

* Template for second vignette * Add ebola data and figure * Add segments and reference for data * Better title and cleaning up of data into ptime and stime format * Working through the processing of data * Merge references * Use @ for reference * More clarity on what's going on in Ebola data preparation section * Start with model fitting section * Statement of intent about what the vignette might contain * Start getting shapefiles for plot / spatial analysis * Figure of SL spatial working * Further writing * Update introduction writing * Start to correct Ebola vignette * Trying to line up shapefile chiefdom names * Use districts over chiefdoms, start trying to fit district-sex level delay models * Move out things we don't need and start fitting stratified models with subsampling and Laplace for now * Trying out tidybayes * It works! * Better laying out the things wanted in this vignette * Move library to top, improve plot, add text * The small districts are worse, but I still think the priors are wrong * Add fitting with gamma * Add column descriptions * Testing prediction tidybayes functions * Replace epidist::epidist by epidist * Improvements to writing, looking at the linear predictors, attempting to do posterior predictions * Add sf dependency * Lint * Add modelr to suggests * Move fraction, add dplyr:: to select, and create PMF and PDF figures * Add SLE shapefiles * This question is now an issue * Remove warnings, make brms silent, filter to only data with >30 points, produce all epred and pred figures, add conclusion * Work through more writing in the vignette * Lint vignette and aim to make reproducible * Correct error that prevents render * Some wording fixes * Remove dplyr:: and put library(dplyr) * Use system.file * Remove modelr:: and tidybayes:: apart from in text * Put () after functions to get link in pkgdown * Add link to pkgdown header * Reproduce summary level of rounding inline * Moved to issue * All figures in own chunk * Move rvars to issue * Fix first x-axis * Remove complaining about KDE * Text update * Use "lognormal" not brms::lognormal() * Add figure captions to all figures * Remove parts about gamma and model comparison * Be specific about the dates * Improve intercept only text Co-authored-by: Katie Gostic (she/her) <kategostic@gmail.com> * Comment about lubridate Co-authored-by: Katie Gostic (she/her) <kategostic@gmail.com> * Add comment on ptime and stime Co-authored-by: Katie Gostic (she/her) <kategostic@gmail.com> * Comment on using all available data * Move column descriptions into function roxygen * Set all x-axis limits to 30, and set pwindow_upr and swindow_upr to 0 now that it's possible * More verbose on sex-stratified model Co-authored-by: Katie Gostic (she/her) <kategostic@gmail.com> * Note on interpreting the summary * Make introduction shorter * Lint package * Collapse plots into a 3 level patchwork (part 1) * Update documentation * More collapse 3 plots into patchwork * Correct figure chunk name * Range of improvements to Ebola vignette (sorry for squashed commit message) * Add head(obs_prep) Co-authored-by: Katie Gostic (she/her) <kategostic@gmail.com> * Add patchwork to suggests * Don't need sec: --------- Co-authored-by: Katie Gostic (she/her) <kategostic@gmail.com> Former-commit-id: 0b0032e Former-commit-id: 762cfc5305b1095350d0a4c965c0a100aba983bf Former-commit-id: b7cd78a5aa14e0dcaac942848a0a9f1c222057cb [formerly 5577850] Former-commit-id: 584b9616264ba79cde4198770095488d4c5564a5
epinowcast · Sep 9, 2024 · 189afca · 189afca
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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.REMOVED.git-id b/inst/gadm41_SLE_shp/gadm41_SLE_3.shp.REMOVED.git-id
@@ -0,0 +1 @@
+767ca43a6e31cb04ea37a21a807badd8a1632b41
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
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		@@ -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]]