From 0409143d94862d4e6b6b368cc98f769944e75566 Mon Sep 17 00:00:00 2001
From: pqiao29 <pqiao@student.unimelb.edu.au>
Date: Thu, 16 Apr 2020 18:32:37 +1000
Subject: [PATCH] fix check warnings
---
NAMESPACE | 4 ++--
R/FIN_plot.R | 34 ++++++++++++++++++----------------
R/original_plot_models.R | 1 -
man/add_known.Rd | 6 ++++--
man/format_sims.Rd | 2 +-
man/get_ci.Rd | 2 +-
man/plot_sirplus.Rd | 18 +++++++++---------
7 files changed, 35 insertions(+), 32 deletions(-)
diff --git a/NAMESPACE b/NAMESPACE
index fb6c891..3025c5a 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/FIN_plot.R b/R/FIN_plot.R
index 1233111..508b8a6 100644
--- a/R/FIN_plot.R
+++ b/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))
diff --git a/R/original_plot_models.R b/R/original_plot_models.R
index 74a1a20..049b888 100644
--- a/R/original_plot_models.R
+++ b/R/original_plot_models.R
@@ -15,7 +15,6 @@
#'
#' @return ggplot2 object
#'
-#' @import dplyr
#' @importFrom tidyr pivot_longer
plot_models <- function(sims = baseline_sim,
diff --git a/man/add_known.Rd b/man/add_known.Rd
index 5369f4e..2f3af39 100644
--- a/man/add_known.Rd
+++ b/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
diff --git a/man/format_sims.Rd b/man/format_sims.Rd
index 7bdc033..9a3735f 100644
--- a/man/format_sims.Rd
+++ b/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}}.}
diff --git a/man/get_ci.Rd b/man/get_ci.Rd
index 005e0af..faee92f 100644
--- a/man/get_ci.Rd
+++ b/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{
diff --git a/man/plot_sirplus.Rd b/man/plot_sirplus.Rd
index 408aa3b..24e9f70 100644
--- a/man/plot_sirplus.Rd
+++ b/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,
...
)
}
--
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