Merge branch 'master' of https://github.com/fhoces/opa-deworming

all_analysis.R

@@ -24,8 +24,9 @@ if (FALSE) {
 
 setwd(here())
 
-# get links
-links <- read.csv("links.csv")
+# change to the following when deploying:
+# links <- read.csv("links.csv")
+links <- read.csv("code/shiny_app/links.csv")
 rownames(links) <- links$name
 
 knitr::opts_knit$set(root.dir = here())

code/01_final_opa.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "<center><div class= 'mytitle'>Open Policy Analysis for Deworming</div></center>"
-date: "<center><div class='mysubtitle'>`r format(Sys.time(), '%d %B, %Y')` <br><img height = '60px' src = './shiny_app/www/BITSS_logo_horizontal.png'><img height='60px' src='./shiny_app/www/CEGA_logo.png'><img height = '60px' src = './shiny_app/www/OPA_layers.png'></div></center>"
+date: "<center><div class='mysubtitle'>`r format(Sys.time(), '%d %B, %Y')` <br><img height = '60px' src = './shiny_app/www/BITSS_logo_horizontal.png'><img height='60px' src='./shiny_app/www/CEGA_logo.png'><a href = 'http://www.bitss.org/opa/projects/deworming/'><img height = '60px' src = './shiny_app/www/OPA_layers.png'></a></div></center>"
 author: "<center><div class = 'contributors'>BITSS Team. Full list of contributors [here](https://github.com/BITSS-OPA/opa-deworming#list-of-contributors)</div></center>"
 editor_options:
   chunk_output_type: console
@@ -209,7 +209,7 @@ chunk_sources <- function(){
     df_prevalence_so <- read_excel("data/prevalence_data.xlsx",
                            sheet = "Sheet1")
     # prevalence_0_so <- c("hookworm" = 0.77, "roundworm" = 0.42, "whipworm" =0.55, "Schisto mansoni" = 0.22) # from Draft Cost-Effectiveness Model.xlsx ADD ORIGINAL SOURCE
-    prevalence_r_so <- c("india" = 0.5665, "kenya" = 0.345, 
+    prevalence_r_so <- c("india" = 0.5665, "kenya" = 0.345,
                          "nigeria" = 0.27, "vietnam" = 0.145)  #0.5665   0.5013121
     # based on https://docs.google.com/spreadsheets/d/1drKdU-kRjlRtwXq6nCqFC6gcoQ-eOaLfT9MWHSMZ0MA/edit?usp=sharing
     years_of_treat_t_so <- 2.41      #Years of Treatment in new setting
@@ -913,7 +913,7 @@ pv_benef_yes_ext_in <- pv_benef_f(
 
 </details>
 
- 
+
 
 #### Assessing computational reproducibility of original results
 
@@ -1093,7 +1093,7 @@ s2_in <- s2_f()
 
 </details>
 
- 
+
 
 #### Indirect costs: additional years of education and its costs for government
 
@@ -1270,7 +1270,7 @@ earnings_no_ext_new_in <- earnings_app2_f(t_var = 0:50,
 
 </details>
 
- 
+
 
 ```{r sum-tables17, purl=FALSE, echo=FALSE, eval=show_summary_tables}
 
@@ -1456,7 +1456,7 @@ irr_in <- (multiroot(function(x) get_irr(rate_var = x), .1, maxiter=10000000, po
 
 </details>
 
- 
+
 
 Over this nine-year period, treated students attended school for an additional `r round(sum(delta_ed_so[,1]),2)` years on average. Thus the average cost of additional schooling per child over the nine-year period is \$`r format(round((cost_per_student_new_in*sum( (1/(1+interest_new_in))^(0:8) * delta_ed_in )),2), nsmall = 2)`.
 
@@ -2872,7 +2872,7 @@ write.csv(ea3_pe, file = ea3_save_path)
 | 3.2      | 1.2 + prevalence + length              | Treatment (EA)                          | `r round(ea2_pe, 1)`      | \-                        |
 | **3.3**  | **2.1 + prevalence + length**          | **Treatment (EA)**                      | **`r round(ea3_pe, 1)`**  | **-**                     |
 
- 
+
 
 ```{r generate-plot-function, purl = TRUE, echo = FALSE}
 # generate_plot_f: function to generate plots for both Dynamic Document and

code/shiny_app/all_analysis.R

@@ -24,7 +24,7 @@ if (TRUE) {
 
 
 # get links
-links <- read.csv(here("links.csv"))
+links <- read.csv(here("code/shiny_app/links.csv"))
 rownames(links) <- links$name
 
 knitr::opts_knit$set(root.dir = here())

code/shiny_app/ui.R

@@ -12,7 +12,9 @@ library(ggplot2)
 
 # get links
 setwd(here())
-links <- read.csv("links.csv")
+# change to the following when deploying:
+# links <- read.csv("links.csv")
+links <- read.csv("code/shiny_app/links.csv")
 rownames(links) <- links$name
 
 # not sure if this makes a difference
@@ -114,7 +116,7 @@ shinyUI(
                         width = "20%",
                         height = "auto"
                       ),
-                      href = links['bitss_opa','url']
+                      href = links['dw_info','url']
                     )                    
                   )),
                   fluidRow(
@@ -200,7 +202,7 @@ shinyUI(
                           align = "center",
                           tags$a(
                             img(
-                              src = "OPA_layers_assumptions.png",
+                              src = "OPA_layers_output.png",
                               width = "70%",
                               height = "auto"
                             )

code/style.css

@@ -111,7 +111,7 @@ img[alt = screenshot]{height: 20px}
   margin: 20px 5px 20px 15px ;
   background-image: url("./shiny_app/www/OPA_layers_details.png");
   background-size: contain;
-  background-position: right;
+  background-position: center;
   background-repeat: no-repeat;
 }
 

index.md

@@ -1,6 +1,6 @@
 ---
 title: "<center><div class= 'mytitle'>Open Policy Analysis for Deworming</div></center>"
-date: "<center><div class='mysubtitle'>01 April, 2021 <img height = '80px' src = './shiny_app/www/BITSS_logo_horizontal.png'><img height='80px' src='./shiny_app/www/CEGA_logo.png'></div></center>"
+date: "<center><div class='mysubtitle'>01 April, 2021 <br><img height = '60px' src = './shiny_app/www/BITSS_logo_horizontal.png'><img height='60px' src='./shiny_app/www/CEGA_logo.png'><a href = 'http://www.bitss.org/opa/projects/deworming/'><img height = '60px' src = './shiny_app/www/OPA_layers.png'></a></div></center>"
 author: "<center><div class = 'contributors'>BITSS Team. Full list of contributors [here](https://github.com/BITSS-OPA/opa-deworming#list-of-contributors)</div></center>"
 editor_options:
   chunk_output_type: console
@@ -258,7 +258,6 @@ invisible( list2env(chunk_sources(),.GlobalEnv) )
 # coverage_so: Overall Saturation (0.511) / 0.75 - not reported in table, average of T & C
 ```
 
-*Note: This is Version 1.0 of the OPA. Please kindly report any errors in the dynamic document [here](https://github.com/BITSS-OPA/opa-deworming/blob/master/issue_template.md).*
 
 <img src="C:/Users/thepe/Documents/GitHub/opa-deworming/code/images/main_pe.png" width="100%" style="display: block; margin: auto;" />
 
@@ -292,6 +291,9 @@ This OPA project contains three components, following the OPA principles laid ou
 
 This report provides a complete description of the analysis behind the results presented to inform a policy discussion on deworming interventions. It describes how to reproduce the analysis in its entirety, and includes all the methodological choices involved. In order to document all the steps without overwhelming the reader, the report is displayed in a layered fashion. The first layer consists of a narrative description of the analysis. The second layer, which appears after clicking in the ![screenshot](images/show_details.png?display%20=%20inline-block) contains equations that show how each piece of the analysis was carried out. The third and final layer displays the code used to operationalize each equation. This information is contained within this document using dynamic documentation [@xie2015dynamic], so interested readers can access the report's source file and easily reproduce the entire document in their own computing environments.
 
+> *Note: This is Version 1.0 of the OPA. Please kindly report any errors in the dynamic document [here](https://github.com/BITSS-OPA/opa-deworming/issues/new/choose).*
+
+
 # Introduction
 
 Parasitic worm infections, also known as soil-transmitted helminths (STH) and schistosomiasis, are endemic in many countries, and disproportionately affect the poor. These parasitic worms interfere with regular bodily processes by decreasing nutrient uptake. Thus, these worms can lead to serious consequences on human health, education outcomes, and long-term economic well being. In particular, evidence indicates that these worms contribute to malnourishment, impairment of mental and physical development, lower school attendance, and decreased wages [@croke2014long; @miguel2004worms; @baird2016worms].
@@ -1147,10 +1149,14 @@ chunk_unit_costs2_new <- function(){
       unit_cost <- ( unit_cost_local_var / ex_rate_var )
       periods_temp <- floor(year_of_treat_var)
       part_of_last_year_temp <- round(year_of_treat_var - periods_temp, 1)
+      if (periods_temp < 1) {
+        0
+      } else {
       sum(
         ( unit_cost * (1 + interest_var)^(-(0:periods_temp)) ) *
             c(rep(1,periods_temp), part_of_last_year_temp)
         )
+      }
     }
 
 ###############################################################################