Move vignette and data processing dependencies to suggests

DESCRIPTION

@@ -10,7 +10,12 @@ Authors@R: c(
 Description: Estimate temperature dependent R0 for a given pathogen and vector from temperature data using experimentally derived constant temperature-R0 curves.
 License: MIT + file LICENSE
 Suggests: 
+    bookdown,
+    cowplot,
+    ggplot2,
+    here,
     knitr,
+    lubridate,
     rmarkdown,
     spelling,
     testthat (>= 3.0.0)
@@ -24,13 +29,8 @@ Language: en-GB
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Imports: 
-    bookdown,
     cinterpolate,
-    cowplot,
     dplyr,
-    ggplot2,
-    here,
-    lubridate,
     rlang,
     stats,
     tibble,

data-raw/R0.R

@@ -1,6 +1,9 @@
 # Constant temperature - R0 data 
 # From Mordecai et al 2019
 
+if (!require("here")) install.packages("here")
+library(here)
+
 AeaeDENV_R0 <- read.csv(here("data-raw", "Thermal-Eco-MBD-main", "AeaeDENV.R0.csv"))
 AeaeZIKV_R0 <- read.csv(here("data-raw", "Thermal-Eco-MBD-main", "AeaeZIKV.R0.csv"))
 AealDENV_R0 <- read.csv(here("data-raw", "Thermal-Eco-MBD-main", "AealDENV.R0.csv"))

data-raw/fiji-example.R

@@ -1,6 +1,13 @@
 # Fiji dengue case study data
 # From Kucharski et al 2018, https://github.com/adamkucharski/fiji-denv3-2014
 
+if (!require("here")) install.packages("here")
+library(here)
+if (!require("lubridate")) install.packages("lubridate")
+library(lubridate)
+library(dplyr)
+library(tidyr)
+
 fiji_denv3_2014 <- read.csv(here("data-raw", "fiji-central_lab-tested_denv3-2014.csv")) |> 
   dplyr::mutate(month_date = lubridate::floor_date(as.Date(date, format = "%d/%m/%Y"), unit = "month")) |> 
   tidyr::pivot_longer(c("central", "western", "north", "east"), names_to = "geography", values_to = "cases")

vignettes/temperature_R0.Rmd

@@ -22,8 +22,10 @@ Temperature is an important driver of vector-borne disease transmission, affecti
 
 The {climateR0} package extracts temperature-dependent R0 for an input time series of mean temperature for 14 vector-pathogen combinations, focusing on mosquito-borne diseases that pose a major public health threat. Temperature dependent R~0~ is a relative measure bounded between 0 and 1, where 1 indicates maximum temperature suitability for transmission. This is a useful indicator for the epidemic potential of a vector-borne disease which can be used for situational awareness or be incorporated into forecasting models to predict future cases. Note that we use a relative measure of R~0~ as other factors affect the absolute magnitude of R~0~ such as immunity, control measures and population behaviour, which are not considered here. 
 
-```{r setup}
+```{r setup, include = FALSE}
 library(climateR0)
+library(ggplot2)
+library(cowplot)
 ```
 
 ### Case study - 2013/14 DENV3 outbreak in Fiji