Merge branch 'master' of https://github.com/fwhigh/MedicMobileImpact

.gitignore

@@ -1,2 +1,2 @@
-*.html
-*.md
+*.md
+.Rhistory

DESCRIPTION

@@ -0,0 +1,13 @@
+Package: MedicMobileImpact
+Type: OpenCPU Application
+Title: Markdown Application for OpenCPU
+Version: 0.1
+Date: 2014-03-08
+Author: F. William High
+Maintainer: F. William High <[email protected]>
+Description: OpenCPU App for markdown package
+License: Apache2
+Depends:
+    knitr
+Suggests:
+    opencpu (>= 1.0.1)

MedicMobileImpact.Rproj

@@ -0,0 +1,16 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageInstallArgs: --no-multiarch --with-keep.source

Medic_Mobile_ANC_worksheet/Medic_Mobile_ANC_worksheet.Rmd

@@ -26,13 +26,13 @@ CBR:  Crude birth rate
 **What is the name of the country?**
 
 ```{r}
-country.name <- "Kenya"
+country.name <- "Nigeria"
 ```
 
 **Provide a recent estimate of the population of `r country.name`.**
 
 ```{r}
-country.population <- 43200000
+country.population <- 168.8e6
 ```
 
 **What is the year of this estimate?  It's okay if the year is approximate.**
@@ -44,13 +44,13 @@ country.population.year <- 2012
 **What is the name of the catchment?**
 
 ```{r}
-catchment.name <- "Kilifi county"
+catchment.name <- "Lagos"
 ```
 
 **What is the population of `r catchment.name`?**
 
 ```{r}
-catchment.population <- 1109735
+catchment.population <- 5.195e6
 ```
 
 **What is the year of this estimate?  It's okay if it is approximate, but it should at least be roughly around `r country.population.year`.**
@@ -68,7 +68,7 @@ first.anc.year <- 2014
 **How many women will your program serve in `r first.anc.year`?**
 
 ```{r}
-n.women.covered <- 91600
+n.women.covered <- 100000
 ```
 
 You are embarking on an ANC projection for `r catchment.name`, `r country.name`.  The population of `r catchment.name` is `r sprintf("%i",catchment.population)`, which is `r sprintf("%.2f",catchment.population/country.population*100)`% of `r country.name`'s population.  Your baseline year for demographic projections is `r country.population.year`, and the year you want to model an increase in coverage is `r first.anc.year`.
@@ -119,13 +119,13 @@ Click the _Multiply_ button.  Enter the following number in Spectrum.
 Click _Ok_.  You will see all the numbers in the population table reduced by this fraction.  Double check that the total population is now roughly equal to your catchment area as follows.  **What is the total male population listed in the table?**
 
 ```{r}
-spectrum.catchment.male.population <- 544933
+spectrum.catchment.male.population <- 2.547e6
 ```
 
 **And what is the total female population?**
 
 ```{r}
-spectrum.catchment.female.population <- 550576
+spectrum.catchment.female.population <- 2.495e6
 ```
 
 ```{r echo=FALSE}
@@ -143,7 +143,7 @@ Click on _Results &rarr; Total Population_.  The defaults in the dialog you are
 **What, in whole numbers (not in millions), is the total projected population size in `r first.anc.year`?**
 
 ```{r}
-spectrum.catchment.population.first.anc.year <- 1.17e6
+spectrum.catchment.population.first.anc.year <- 5.09e6
 ```
 
 The projection population for your first year of increased ANC coverage (`r first.anc.year`) is `r sprintf("%.2f",(spectrum.catchment.population.first.anc.year/catchment.population-1)*100)`% bigger than the population in `r catchment.population.year`, which was `r sprintf("%i",catchment.population)`.
@@ -155,7 +155,7 @@ Click on _Results &rarr; Vital Events &rarr; Crude Birth Rate_.  The defaults in
 This is the number of births per 1000 people.  **What is the CBR for `r first.anc.year`?**
 
 ```{r}
-spectrum.cbr.first.anc.year <- 34.41
+spectrum.cbr.first.anc.year <- 38.15
 ```
 
 ```{r echo=FALSE}
@@ -171,7 +171,7 @@ Make sure you’re in the _Modules_ tab.  Select the _LiST_ module.
 Select _Coverage_.  In the dialog, select the _Pregnancy_ tab.  You’ll see nationally averaged coverage rates already populated in the table.  Look at the "Antenatal care" row of the table.  **What is the coverage rate shown for `r first.anc.year`?**
 
 ```{r}
-baseline.anc.coverage.rate <- 45.7
+baseline.anc.coverage.rate <- 44.8
 ```
 
 By default, LiST is assuming that `r sprintf("%.f",baseline.anc.coverage.rate/100*n.pregnant.women.first.anc.year)` out of `r sprintf("%.f",n.pregnant.women.first.anc.year)`  pregant women are being treated with antenatal care.  This coverage rate is equal to the national coverage rate by default, and we've just scaled it down to the catchment size.

NAMESPACE

@@ -0,0 +1 @@
+export(rmdtext)

R/rmdtext.R

@@ -0,0 +1,10 @@
+## This app requires OpenCPU 1.0.1 or higher !!!! 
+##
+
+#' @export
+rmdtext <- function(text){
+  writeLines(text, con="input.Rmd");
+  knit2html("input.Rmd", output="output.html");
+  invisible();
+}
+

README.md

@@ -5,11 +5,15 @@ MedicMobileImpact
 
  Step 1.  Download this repository.  On the GitHub site, you can download a zipped version of this repo, or if you are a savvy git user, you can clone it to your desktop.
 
- Step 2.  Download and install RStudio.
+ Step 2.  Download and install R.
+
+ http://cran.r-project.org/
+
+ And RStudio.
 
 https://www.rstudio.com/
 
- Step 3.  Open RStudio, and install the knitr package.  Do this by clicking _Packages_ tab, then click the _Install Packages_ button.  Search for "knitr", make sure _Install dependencies_ is checked, and click _Install_.
+ Step 3.  Open RStudio, and install the knitr package.  Do this by clicking _Packages_ tab, then click the _Install Packages_ button.  Search for "knitr", make sure _Install dependencies_ is checked, and click _Install_.  This procedure has been tested using knitr 1.5.  To make sure you have the latest knitr update, in RStudio in the _Packages_ tab click _Check for Updates_ and follow the instructions.
 
  Step 4.  Enable knitr in RStudio.  Do this by clicking _Preferences_, then clicking the _Sweave_ tab.  Next to "Weave Rnw files using", select knitr from the drop-down menu.  Click _Apply_ and _Ok_.