Fixing description and docs

DESCRIPTION

@@ -2,7 +2,7 @@ Package: sirplus
 Type: Package
 Title: Using stochastic individual compartment models (ICMs) to simulate COVID-19 spread
 Version: 0.1
-Date: 2020-03-26
+Date: 2020-03-29
 Authors@R:
     c(person("Christina", "Azodi", role = c("aut"),
       email = "cazodi@svi.edu.au",
@@ -28,7 +28,7 @@ Imports:
     dplyr,
     tidyr, 
     stats, 
-    future
+    future,
     EpiModel, 
     ggplot2,
     foreach
@@ -39,12 +39,7 @@ Suggests:
     magick,
     rmarkdown,
     spelling, 
-<<<<<<< HEAD
-    earlyR, 
-    knitr
-=======
     testthat
->>>>>>> 382b87aca1de22f5aeea1065b2d6138cc69bc13a
 biocViews: Epidemiology, Software
 RoxygenNote: 7.1.0
 VignetteBuilder: knitr

R/get_weekly_local.R

@@ -31,7 +31,7 @@ get_weekly_local <- function(sim,
                              market.share = .04,
                              icu_percent = .1, 
                              start_date = 'na',
-                             time_lim = 90,
+                             time_limit = 90,
                              total_population = NULL){
   
   hosp <- sim$df$h.num
@@ -49,7 +49,7 @@ get_weekly_local <- function(sim,
                                               0 and 1")
   
   hosp[is.na(hosp)] <- 0
-  hosp <- hosp[1: time_lim]
+  hosp <- hosp[1: time_limit]
   
   hosp_week <- split(hosp, ceiling(seq_along(hosp)/7))
   hosp_sum_week <- unlist(lapply(hosp_week, sum))

README.md

@@ -2,10 +2,12 @@
 
 sirplus is a package for the modeling of COVID-19 spread using stochastic individual compartment models (ICMs). The model implemented extends the classical Susceptible-Infectious-Recovered (SIR) model by adding compartments for Exposed, Quarantined, Hospitalised and Case Fatality individuals. The package provides a simple interface for creating experiments to demonstrate how factors like social-distancing and epidemiological parameters will change the curve.
 
+## Installation and vignette
+
 To view the vignette install the package then: 
 
 ```
 devtools::install(build_vignettes=TRUE)
 library(sirplus)
 browseVignettes("sirplus")  
-```
\ No newline at end of file
+```

man/get_weekly_local.Rd

@@ -9,7 +9,7 @@ get_weekly_local(
   market.share = 0.04,
   icu_percent = 0.1,
   start_date = "na",
-  time_lim = 90,
+  time_limit = 90,
   total_population = NULL
 )
 }
@@ -26,11 +26,11 @@ ICU among the ones that need hospitalization}
 plot week numbers, if provided will plot the first day (Sunday) of the
 week.}
 
+\item{time_limit}{Number of days to include. Default = 90.}
+
 \item{total_population}{True population size, needed only if simulation size 
 is smaller than the true population size due to computational cost 
 etc.}
-
-\item{time_limit}{Number of days to include. Default = 90.}
 }
 \value{
 \itemize{