updates documentation for all geographies and modelled outcomes years 2022-2050

nswartwo · nswartwo · commit f93fa859c700 · 2022-01-10T23:48:25.000-05:00
diff --git a/inst/md/about.md b/inst/md/about.md
@@ -4,9 +4,7 @@ The estimates shown by Tabby2 are based on a mathematical model of TB epidemiolo
 
 **The model has been fit to TB data through 2019. Preliminary data suggests that during the COVID-19 pandemic, reported cases of TB in the United States declined by 20% compared with 2019; this decline is not reflected in modeling estimates at this time. (https://www.cdc.gov/mmwr/volumes/70/wr/mm7012a1.htm) We are in the process of incorporating these data into our estimates and will update the site once revised estimates are complete.**
  
-This model has been fit to local data from each of the following states: 
-
-Alabama, Alaska, Arizona, Arkansas, California, Colorado, Connecticut, Delaware, District of Columbia, Florida, Georgia, Hawaii, Idaho, Illinois, Indiana, Iowa, Kansas, Kentucky, Louisiana, Maine, Maryland, Massachusetts, Michigan, Minnesota, Mississippi, Missouri, Montana, Nebraska, Nevada, New Hampshire, New Jersey, New Mexico, New York, North Carolina, Ohio, Oklahoma, Oregon, Pennsylvania, Rhode Island, South Carolina, South Dakota, Tennessee, Texas, Utah, Vermont, Virginia, Washington, West Virginia, Wisconsin, Wyoming. 
+This model has been fit to local data from all fifty states and District of Columbia. 
 
 The model has also been fit to aggregate data for the United States to allow national-level analyses. These analyses expand on an earlier study on future TB epidemiology in the United States (Menzies et al 2018. “Prospects for tuberculosis elimination in the United States: results of a transmission dynamic model” Am J Epid 187(9):2011-2020) (https://academic.oup.com/aje/article/187/9/2011/4995883)).  
 
diff --git a/tabby1/tabby1utilities/inst/configs/config-addoutputs.yaml b/tabby1/tabby1utilities/inst/configs/config-addoutputs.yaml
@@ -28,11 +28,11 @@ comparators:
   labels:
     absolute_value: Absolute values
     pct_basecase_same_year: Percentage of base case value in the same year
-    pct_basecase_2018: Percentage of base case value in 2020
+    pct_basecase_2018: Percentage of base case value in 2022
   formatted:
     absolute_value: ''
     pct_basecase_same_year: Percentage of base case value in the same year
-    pct_basecase_2018: Percentage of base case value in 2020
+    pct_basecase_2018: Percentage of base case value in 2022
   selected:
   - yes
   - no
@@ -158,19 +158,19 @@ analyses:
   - scenario_6
   - scenario_7
   labels:
-    scenario_1: No Transmission Within the US After 2020
-    scenario_2: No TB or LTBI in New Migrants After 2020
+    scenario_1: No Transmission Within the US After 2022
+    scenario_2: No TB or LTBI in New Migrants After 2022
     scenario_3: Reduced TB Prevention Effort
-    scenario_5: Future Immigration at 2020 Levels
+    scenario_5: Future Immigration at 2022 Levels
     scenario_6: Improving Global TB Control
     scenario_7: Rising Reactivation Risks
   formatted: # the |- allows newlines
     scenario_1: |-
       No transmission within
-      the US after 2020
+      the US after 2022
     scenario_2: |-
       No TB or LTBI in new
-      migrants after 2020
+      migrants after 2022
     scenario_3: |-
       Reduced TB prevention
       effort
@@ -179,18 +179,18 @@ analyses:
       new migrants
     scenario_5: |-
       Future immigration at
-      2020 levels
+      2022 levels
     scenario_6: |-
       Improving global TB
       control
     scenario_7: |-
       Rising reactivation
       risk
   descriptions:
-    scenario_1: From 2020 onwards, no individuals acquire M. TB infection from transmission within
+    scenario_1: From 2022 onwards, no individuals acquire M. TB infection from transmission within
       the United States. In this scenario the only source of new LTBI cases is from
       existing infection in new immigrants.
-    scenario_2: From 2020 onwards, all individuals immigrating to the United States are free of
+    scenario_2: From 2022 onwards, all individuals immigrating to the United States are free of
       M. TB infection, while maintaining the same total volume of immigration.
 downloads:
   heading: Download
diff --git a/tabby1/tabby1utilities/inst/configs/config-agegroups.yaml b/tabby1/tabby1utilities/inst/configs/config-agegroups.yaml
@@ -28,11 +28,11 @@ comparators:
   labels:
     absolute_value: Absolute values
     pct_basecase_same_year: Percentage of base case value in the same year
-    pct_basecase_2018: Percentage of base case value in 2020
+    pct_basecase_2018: Percentage of base case value in 2022
   formatted:
     absolute_value: ''
     pct_basecase_same_year: Percentage of base case value in the same year
-    pct_basecase_2018: Percentage of base case value in 2020
+    pct_basecase_2018: Percentage of base case value in 2022
   selected:
   - yes
   - no
@@ -156,25 +156,25 @@ analyses:
   - scenario_6
   - scenario_7
   labels:
-    scenario_1: No Transmission Within the US After 2020
-    scenario_2: No TB or LTBI in New Migrants After 2020
+    scenario_1: No Transmission Within the US After 2022
+    scenario_2: No TB or LTBI in New Migrants After 2022
     scenario_3: Reduced TB Prevention Effort
-    scenario_5: Future Immigration at 2020 Levels
+    scenario_5: Future Immigration at 2022 Levels
     scenario_6: Improving Global TB Control
     scenario_7: Rising Reactivation Risks
   formatted: # use |- to include newline characters
     scenario_1: |-
       No transmission within
-      the US after 2020
+      the US after 2022
     scenario_2: |-
       No TB or LTBI in new
-      migrants after 2020
+      migrants after 2022
     scenario_3: |-
       Reduced TB prevention
       effort
     scenario_5: |-
       Future immigration
-      at 2020 levels
+      at 2022 levels
     scenario_6: |-
       Improving global TB
       control
diff --git a/tabby1/tabby1utilities/inst/configs/config-estimates.yaml b/tabby1/tabby1utilities/inst/configs/config-estimates.yaml
@@ -32,11 +32,11 @@ comparators:
   labels:
     absolute_value: Absolute values
     pct_basecase_same_year: Percentage of base case value in the same year
-    pct_basecase_2018: Percentage of base case value in 2020
+    pct_basecase_2018: Percentage of base case value in 2022
   formatted:
     absolute_value: ''
     pct_basecase_same_year: Percentage of base case value in the same year
-    pct_basecase_2018: Percentage of base case value in 2020
+    pct_basecase_2018: Percentage of base case value in 2022
   selected:
   - yes
   - no
@@ -190,19 +190,19 @@ analyses:
   - scenario_6
   - scenario_7
   labels:
-    scenario_1: No Transmission Within the US After 2020
-    scenario_2: No TB or LTBI in New Migrants After 2020
+    scenario_1: No Transmission Within the US After 2022
+    scenario_2: No TB or LTBI in New Migrants After 2022
     scenario_3: Reduced TB Prevention Effort
-    scenario_5: Future Immigration at 2020 Levels
+    scenario_5: Future Immigration at 2022 Levels
     scenario_6: Improving Global TB Control
     scenario_7: Rising Reactivation Risks
   formatted:
     scenario_1: |-
       No transmission within
-      the US after 2020
+      the US after 2022
     scenario_2: |-
       No TB or LTBI in new
-      migrants after 2020
+      migrants after 2022
     scenario_3: |-
       Reduced TB prevention
       effort
@@ -216,10 +216,10 @@ analyses:
       Rising reactivation
       risks
   descriptions:
-    scenario_1: From 2020 onwards, no individuals acquire M. TB infection from transmission within
+    scenario_1: From 2022 onwards, no individuals acquire M. TB infection from transmission within
       the United States. In this scenario the only source of new LTBI cases is from
       existing infection in new immigrants.
-    scenario_2: From 2020 onwards, all individuals immigrating to the United States are free of
+    scenario_2: From 2022 onwards, all individuals immigrating to the United States are free of
       M. TB infection, while maintaining the same total volume of immigration.
 labels:
   heading: Labels
diff --git a/tabby1/tabby1utilities/inst/configs/config-trends.yaml b/tabby1/tabby1utilities/inst/configs/config-trends.yaml
@@ -28,11 +28,11 @@ comparators:
   labels:
     absolute_value: Absolute values
     pct_basecase_same_year: Percentage of base case value in the same year
-    pct_basecase_2018: Percentage of base case value in 2020
+    pct_basecase_2018: Percentage of base case value in 2022
   formatted:
     absolute_value: ''
     pct_basecase_same_year: Percentage of base case value in the same year
-    pct_basecase_2018: Percentage of base case value in 2020
+    pct_basecase_2018: Percentage of base case value in 2022
   selected:
   - yes
   - no
@@ -178,19 +178,19 @@ analyses:
   - scenario_6
   - scenario_7
   labels:
-    scenario_1: No Transmission Within the US After 2020
-    scenario_2: No TB or LTBI in New Migrants After 2020
+    scenario_1: No Transmission Within the US After 2022
+    scenario_2: No TB or LTBI in New Migrants After 2022
     scenario_3: Reduced TB Prevention Effort
-    scenario_5: Future Immigration at 2020 Levels
+    scenario_5: Future Immigration at 2022 Levels
     scenario_6: Improving Global TB Control
     scenario_7: Rising Reactivation Risks
   formatted: # the |- allows newlines
     scenario_1: |-
       No transmission within
-      the US after 2020
+      the US after 2022
     scenario_2: |-
       No TB or LTBI in new
-      migrants after 2020
+      migrants after 2022
     scenario_3: |-
       Reduced TB prevention
       effort
@@ -199,18 +199,18 @@ analyses:
       new migrants
     scenario_5: |-
       Future immigration at
-      2020 levels
+      2022 levels
     scenario_6: |-
       Improving global TB
       control
     scenario_7: |-
       Rising reactivation
       risk
   descriptions:
-    scenario_1: From 2020 onwards, no individuals acquire M. TB infection from transmission within
+    scenario_1: From 2022 onwards, no individuals acquire M. TB infection from transmission within
       the United States. In this scenario the only source of new LTBI cases is from
       existing infection in new immigrants.
-    scenario_2: From 2020 onwards, all individuals immigrating to the United States are free of
+    scenario_2: From 2022 onwards, all individuals immigrating to the United States are free of
       M. TB infection, while maintaining the same total volume of immigration.
 downloads:
   heading: Download
diff --git a/utilities/inst/md/changelog.md b/utilities/inst/md/changelog.md
@@ -1,4 +1,5 @@
-  - Version 3.1.0 (2021-12-10) updates the basecase year of Tabby2 to 2022 from 2020.
+  - Version 3.1.0 (2022-01-10) represents the first version of Tabby2 to contain all fifty states and the District of Columbia. 
+  - Version 3.0.1 (2021-12-10) updates the interval of years shown in modelled outcomes to 2022-2050.
   - Version 3.0.0 (2021-08-27) represents the second version of Tabby2 which has passed the CDC Scientific Web Tool Clearance process; first release with Economic Analysis functionality.
   - Version 2.0.3 (2020-03-13) adds TB outcomes formatted in counts of individuals.
   - Version 2.0.2 (2020-02-20) updates the interval of years shown in modelled outcomes to 2020-2050.
