fix check warnings

NAMESPACE

@@ -28,9 +28,7 @@ export(recovery.FUN)
 export(seiqhrf)
 export(simulate_seiqhrf)
 export(vary_param)
-import(dplyr)
 import(ggplot2)
-import(lubridate)
 importFrom(EpiModel,get_prev.icm)
 importFrom(EpiModel,ssample)
 importFrom(EpiModel,verbose.icm)
@@ -39,11 +37,13 @@ importFrom(dplyr,"%>%")
 importFrom(dplyr,between)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,filter)
+importFrom(dplyr,full_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
 importFrom(future,availableCores)
+importFrom(lubridate,ymd)
 importFrom(stats,pweibull)
 importFrom(stats,rbinom)
 importFrom(stats,rgeom)

R/FIN_plot.R

@@ -32,7 +32,7 @@
 #' @importFrom dplyr bind_rows
 #' @importFrom dplyr select
 #' @importFrom dplyr filter
-#' @import lubridate
+#' @importFrom lubridate ymd
 #' @import ggplot2
 #' @export
 plot.seiqhrf <- function(x, method = NULL, 
@@ -104,7 +104,7 @@ plot.seiqhrf <- function(x, method = NULL,
 #' @importFrom dplyr bind_rows
 #' @importFrom dplyr select
 #' @importFrom dplyr filter
-#' @import lubridate
+#' @importFrom lubridate ymd
 #' @import ggplot2
 #' @export
 plot.list <- function(x, comp_remove = "none",
@@ -165,15 +165,15 @@ plot.list <- function(x, comp_remove = "none",
 #' @importFrom dplyr filter
 #' @import ggplot2
 #' @export
-plot_sirplus <- function(x, comp_remove = comp_remove,
-                         time_lim = time_lim,
-                         ci = ci,
-                         sep_compartments = sep_compartments,
-                         trans = trans,
-                         known = known,
-                         start_date = start_date,
-                         x_axis = x_axis,
-                         plot_title = plot_title, ...){
+plot_sirplus <- function(x, comp_remove,
+                         time_lim,
+                         ci,
+                         sep_compartments,
+                         trans,
+                         known,
+                         start_date,
+                         x_axis,
+                         plot_title, ...){
     
     # Convert from seiqhrf object to dataframe
     plot_df <- format_sims(x, time_lim = time_lim, start_date = start_date)
@@ -306,7 +306,7 @@ plot_times <- function(sim) {
 #' @return dataframe
 #' 
 #' @export
-format_sims <- function(x, time_lim = time_lim, start_date = start_date){
+format_sims <- function(x, time_lim, start_date){
     
     # Merge models to plot together
     if(class(x) == "seiqhrf"){
@@ -343,11 +343,12 @@ format_sims <- function(x, time_lim = time_lim, start_date = start_date){
 #' Get 95\% confidence intervals
 #'
 #' @param x An seiqhrf object returned from function \code{\link{seiqhrf}}.
-#' @param known Dataframe with known compartment numbers to plot alongside
+#' @param plot_df Dataframe with known compartment numbers to plot alongside
 #'        projections
 #' 
 #' @return dataframe with CIs and sd added
 #' @importFrom tidyr separate
+#' @importFrom dplyr full_join
 #' 
 #' @export
 #' 
@@ -404,22 +405,23 @@ get_ci <- function(x, plot_df){
     ci_info[is.na(ci_info)] <- 0
         
     plot_df <- plot_df %>% 
-        full_join(ci_info, by = c('time', 'compartment', 'experiment', 'sim'))
+      dplyr::full_join(ci_info, by = c('time', 'compartment', 'experiment', 'sim'))
     
     return(plot_df)
 }
 
 #' Add known counts to sims dataframe for ggplot
 #'
-#' @param x An seiqhrf object returned from function \code{\link{seiqhrf}}.
+#' @param plot_df An seiqhrf object returned from function \code{\link{seiqhrf}}.
 #' @param known Dataframe with known compartment numbers to plot alongside
 #'        projections
+#' @param start_date Date for day 0. 
 #' 
 #' @return dataframe with known data added
 #' 
 #' @export
 #' 
-add_known <- function(plot_df, known = known, start_date = start_date){
+add_known <- function(plot_df, known, start_date){
     
     # Add Date to known data
     missing_cols <- setdiff(names(plot_df), names(known))

R/original_plot_models.R

@@ -15,7 +15,6 @@
 #'
 #' @return ggplot2 object
 #' 
-#' @import dplyr
 #' @importFrom tidyr pivot_longer
 
 plot_models <- function(sims = baseline_sim,

man/add_known.Rd

@@ -4,13 +4,15 @@
 \alias{add_known}
 \title{Add known counts to sims dataframe for ggplot}
 \usage{
-add_known(plot_df, known = known, start_date = start_date)
+add_known(plot_df, known, start_date)
 }
 \arguments{
+\item{plot_df}{An seiqhrf object returned from function \code{\link{seiqhrf}}.}
+
 \item{known}{Dataframe with known compartment numbers to plot alongside
 projections}
 
-\item{x}{An seiqhrf object returned from function \code{\link{seiqhrf}}.}
+\item{start_date}{Date for day 0.}
 }
 \value{
 dataframe with known data added

man/format_sims.Rd

@@ -4,7 +4,7 @@
 \alias{format_sims}
 \title{Format seiqhrf objects into dataframe for ggplot}
 \usage{
-format_sims(x, time_lim = time_lim, start_date = start_date)
+format_sims(x, time_lim, start_date)
 }
 \arguments{
 \item{x}{An seiqhrf object returned from function \code{\link{seiqhrf}}.}

man/get_ci.Rd

@@ -9,7 +9,7 @@ get_ci(x, plot_df)
 \arguments{
 \item{x}{An seiqhrf object returned from function \code{\link{seiqhrf}}.}
 
-\item{known}{Dataframe with known compartment numbers to plot alongside
+\item{plot_df}{Dataframe with known compartment numbers to plot alongside
 projections}
 }
 \value{

man/plot_sirplus.Rd

@@ -6,15 +6,15 @@
 \usage{
 plot_sirplus(
   x,
-  comp_remove = comp_remove,
-  time_lim = time_lim,
-  ci = ci,
-  sep_compartments = sep_compartments,
-  trans = trans,
-  known = known,
-  start_date = start_date,
-  x_axis = x_axis,
-  plot_title = plot_title,
+  comp_remove,
+  time_lim,
+  ci,
+  sep_compartments,
+  trans,
+  known,
+  start_date,
+  x_axis,
+  plot_title,
   ...
 )
 }