From 9fd931aeeba4ab7bdede1a625f64e7024c2b55aa Mon Sep 17 00:00:00 2001 From: Naeem Model Date: Sun, 9 Jun 2024 16:01:51 +0000 Subject: Update Shiny app - Remove template/logic for single data entry - Change 'Add estimators' to 'About estimators'; adding estimators and viewing estimates are now done in the same tab - Swap rows and columns in estimates table (estimators as row names, datasets as column names) - Add a separate column for the serial interval to the estimates table - Add plots for daily and weekly data using the Plotly library - Remove italics from the subscript in all occurences of 'R_0' - Fix code/text formatting --- .../estimators/add-estimators/components/mu.html | 20 ----------- .../add-estimators/components/panel.html | 21 ------------ .../estimators/add-estimators/descriptions/id.html | 1 - .../add-estimators/descriptions/idea.html | 1 - .../estimators/add-estimators/descriptions/mu.html | 7 ---- .../add-estimators/descriptions/seq_bayes.html | 1 - .../estimators/add-estimators/descriptions/wp.html | 1 - .../estimators/add-estimators/parameters/id.html | 1 - .../estimators/add-estimators/parameters/idea.html | 1 - .../estimators/add-estimators/parameters/mu.html | 1 - .../add-estimators/parameters/seq_bayes.html | 22 ------------ .../estimators/add-estimators/parameters/wp.html | 39 ---------------------- 12 files changed, 116 deletions(-) delete mode 100644 inst/app/templates/content/estimators/add-estimators/components/mu.html delete mode 100644 inst/app/templates/content/estimators/add-estimators/components/panel.html delete mode 100644 inst/app/templates/content/estimators/add-estimators/descriptions/id.html delete mode 100644 inst/app/templates/content/estimators/add-estimators/descriptions/idea.html delete mode 100644 inst/app/templates/content/estimators/add-estimators/descriptions/mu.html delete mode 100644 inst/app/templates/content/estimators/add-estimators/descriptions/seq_bayes.html delete mode 100644 inst/app/templates/content/estimators/add-estimators/descriptions/wp.html delete mode 100644 inst/app/templates/content/estimators/add-estimators/parameters/id.html delete mode 100644 inst/app/templates/content/estimators/add-estimators/parameters/idea.html delete mode 100644 inst/app/templates/content/estimators/add-estimators/parameters/mu.html delete mode 100644 inst/app/templates/content/estimators/add-estimators/parameters/seq_bayes.html delete mode 100644 inst/app/templates/content/estimators/add-estimators/parameters/wp.html (limited to 'inst/app/templates/content/estimators/add-estimators') diff --git a/inst/app/templates/content/estimators/add-estimators/components/mu.html b/inst/app/templates/content/estimators/add-estimators/components/mu.html deleted file mode 100644 index f25a1c8..0000000 --- a/inst/app/templates/content/estimators/add-estimators/components/mu.html +++ /dev/null @@ -1,20 +0,0 @@ - - -
- - - - -
- - diff --git a/inst/app/templates/content/estimators/add-estimators/components/panel.html b/inst/app/templates/content/estimators/add-estimators/components/panel.html deleted file mode 100644 index b1e0378..0000000 --- a/inst/app/templates/content/estimators/add-estimators/components/panel.html +++ /dev/null @@ -1,21 +0,0 @@ -
-

- -

-
-
-

Reference: {{ reference_label }}

-

{{ htmlTemplate(paste0("templates/content/estimators/add-estimators/descriptions/", id, ".html")) }}

-
Parameters
-
- {{ htmlTemplate(paste0("templates/content/estimators/add-estimators/parameters/", id, ".html")) }} -
- -
-
-
diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/id.html b/inst/app/templates/content/estimators/add-estimators/descriptions/id.html deleted file mode 100644 index b47850f..0000000 --- a/inst/app/templates/content/estimators/add-estimators/descriptions/id.html +++ /dev/null @@ -1 +0,0 @@ -The incidence decay (ID) estimator assumes an exponential model and finds the parameters by minimizing the sum of the squared differences between the observed cases counts and the case counts expected based on the assumed model. The method assumes that the serial interval is known. This means that the user needs to input the value of the serial interval. The serial interval is the average time between the first infection and the time the first infected individual exhibits disease symptoms. diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/idea.html b/inst/app/templates/content/estimators/add-estimators/descriptions/idea.html deleted file mode 100644 index edfbb79..0000000 --- a/inst/app/templates/content/estimators/add-estimators/descriptions/idea.html +++ /dev/null @@ -1 +0,0 @@ -This is a short description of the IDEA method. diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/mu.html b/inst/app/templates/content/estimators/add-estimators/descriptions/mu.html deleted file mode 100644 index 6e7bfe9..0000000 --- a/inst/app/templates/content/estimators/add-estimators/descriptions/mu.html +++ /dev/null @@ -1,7 +0,0 @@ -The serial interval (SI) is NOT one of the estimators. - -

The SI is a parameter required by all of the estimators, and can also be estimated by the WP method.

- -

The SI is defined as the average time between successive infections in a chain of transmission i.e., the time between the infection of an infected and their subsequent transmissions.

- -

Make the tab a different shade (light gray) and then this won't have parameters. It will let us not have to explain SI every single time. We'll expand the description later.

diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/seq_bayes.html b/inst/app/templates/content/estimators/add-estimators/descriptions/seq_bayes.html deleted file mode 100644 index f6df3ee..0000000 --- a/inst/app/templates/content/estimators/add-estimators/descriptions/seq_bayes.html +++ /dev/null @@ -1 +0,0 @@ -This is a short description of the seqB method. diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/wp.html b/inst/app/templates/content/estimators/add-estimators/descriptions/wp.html deleted file mode 100644 index 640b44d..0000000 --- a/inst/app/templates/content/estimators/add-estimators/descriptions/wp.html +++ /dev/null @@ -1 +0,0 @@ -This is a short description of the WP method. diff --git a/inst/app/templates/content/estimators/add-estimators/parameters/id.html b/inst/app/templates/content/estimators/add-estimators/parameters/id.html deleted file mode 100644 index a3159ca..0000000 --- a/inst/app/templates/content/estimators/add-estimators/parameters/id.html +++ /dev/null @@ -1 +0,0 @@ -{{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "id") }} diff --git a/inst/app/templates/content/estimators/add-estimators/parameters/idea.html b/inst/app/templates/content/estimators/add-estimators/parameters/idea.html deleted file mode 100644 index 379be84..0000000 --- a/inst/app/templates/content/estimators/add-estimators/parameters/idea.html +++ /dev/null @@ -1 +0,0 @@ -{{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "idea") }} diff --git a/inst/app/templates/content/estimators/add-estimators/parameters/mu.html b/inst/app/templates/content/estimators/add-estimators/parameters/mu.html deleted file mode 100644 index a3159ca..0000000 --- a/inst/app/templates/content/estimators/add-estimators/parameters/mu.html +++ /dev/null @@ -1 +0,0 @@ -{{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "id") }} diff --git a/inst/app/templates/content/estimators/add-estimators/parameters/seq_bayes.html b/inst/app/templates/content/estimators/add-estimators/parameters/seq_bayes.html deleted file mode 100644 index bcc82b7..0000000 --- a/inst/app/templates/content/estimators/add-estimators/parameters/seq_bayes.html +++ /dev/null @@ -1,22 +0,0 @@ -
- -
- {{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "seq_bayes") }} -
- -
- - - - - - -
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diff --git a/inst/app/templates/content/estimators/add-estimators/parameters/wp.html b/inst/app/templates/content/estimators/add-estimators/parameters/wp.html deleted file mode 100644 index b789a23..0000000 --- a/inst/app/templates/content/estimators/add-estimators/parameters/wp.html +++ /dev/null @@ -1,39 +0,0 @@ - - -
-
- -
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- {{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "wp") }} -
- -
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- - - -
- -
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