Clean and fix

.Rbuildignore

@@ -7,3 +7,4 @@
 ^doc$
 ^Meta$
 ^miscellaneous_files$
+^LICENSE\.md$

DESCRIPTION

@@ -6,25 +6,27 @@ Authors@R: c(
            comment = c(ORCID = "0000-0002-5213-4364")),
     person("Christian", "Morgenstern", email = "c.morgenstern@imperial.ac.uk", role = "aut",
            comment = c(ORCID = "0000-0003-3735-1130")),
-    person("Gina", "Cuomo-Dannenburg",role = "ctb", comment = c(ORCID = "0000-0001-6821-0352")),
-    person("Ruth", "McCabe", role = "ctb", comment = c(ORCID = "0000-0002-6368-9103")),
-    person("Kelly", "McCain", role = "ctb", comment = c(ORCID = "0000-0003-2393-2217")))
+    person("Gina", "Cuomo-Dannenburg", role = "aut", comment = c(ORCID = "0000-0001-6821-0352")),
+    person("Ruth", "McCabe", role = "aut", comment = c(ORCID = "0000-0002-6368-9103")),
+    person("Kelly", "McCain", role = "aut", comment = c(ORCID = "0000-0003-2393-2217")))
 Description: Contains the latest open access pathogen data from the Pathogen Epidemiology Review Group (PERG). Tools are available to update pathogen databases with new peer-reviewed data as it becomes available, and to summarise the latest data using tables and figures.
-License: GPL (>=2)
+License: GPL (>= 3)
 Imports:
     ggplot2,
-    tidyverse,
     tibble,
     dplyr,
     tidyr,
     readr,
     patchwork,
     flextable,
     tm,
-    validate,
-    meta
+    officer,
+    stringr,
+    validate
 Suggests:
     knitr,
+    meta,
+    tidyverse,
     testthat (>= 3.0.0)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -5,47 +5,103 @@ export(create_new_article_entry)
 export(create_new_model_entry)
 export(create_new_outbreak_entry)
 export(create_new_parameter_entry)
+export(data_forest_plots)
+export(data_outbreak_table)
+export(data_param_table)
 export(date_start)
 export(delay_table)
-export(forest_plot_R)
 export(forest_plot_delay)
 export(forest_plot_mutations)
+export(forest_plot_r)
 export(forest_plot_severity)
-export(get_available_table_field_options)
-export(load_data)
+export(get_table_field_options)
+export(load_epidata)
 export(outbreak_table)
 export(quality_assessment_plots)
 export(risk_table)
 export(sero_table)
 importFrom(dplyr,"%>%")
+importFrom(dplyr,across)
+importFrom(dplyr,arrange)
 importFrom(dplyr,case_when)
 importFrom(dplyr,count)
+importFrom(dplyr,desc)
+importFrom(dplyr,distinct)
+importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,if_else)
+importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,n)
+importFrom(dplyr,row_number)
+importFrom(dplyr,rowwise)
+importFrom(dplyr,select)
 importFrom(dplyr,starts_with)
+importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
+importFrom(flextable,add_footer_lines)
+importFrom(flextable,autofit)
+importFrom(flextable,bold)
+importFrom(flextable,border_remove)
+importFrom(flextable,flextable)
+importFrom(flextable,fontsize)
+importFrom(flextable,hline)
+importFrom(flextable,set_flextable_defaults)
+importFrom(flextable,theme_booktabs)
+importFrom(flextable,vline)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,coord_flip)
+importFrom(ggplot2,element_text)
 importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,geom_errorbar)
 importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_segment)
 importFrom(ggplot2,geom_smooth)
+importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggplot_add)
+importFrom(ggplot2,guide_legend)
+importFrom(ggplot2,guides)
 importFrom(ggplot2,labs)
+importFrom(ggplot2,position_dodge)
+importFrom(ggplot2,scale_color_brewer)
+importFrom(ggplot2,scale_colour_manual)
 importFrom(ggplot2,scale_fill_manual)
+importFrom(ggplot2,scale_linetype_manual)
+importFrom(ggplot2,scale_shape_manual)
 importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_y_discrete)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,xlab)
+importFrom(ggplot2,xlim)
 importFrom(ggplot2,ylab)
+importFrom(officer,fp_border)
 importFrom(patchwork,wrap_plots)
 importFrom(readr,read_csv)
+importFrom(stats,median)
+importFrom(stats,na.omit)
+importFrom(stats,reorder)
+importFrom(stats,setNames)
+importFrom(stringr,str_replace)
+importFrom(stringr,str_replace_all)
+importFrom(stringr,str_split)
+importFrom(stringr,str_split_fixed)
+importFrom(stringr,str_starts)
+importFrom(stringr,str_to_sentence)
+importFrom(stringr,str_to_title)
+importFrom(stringr,str_wrap)
 importFrom(tibble,as_tibble)
 importFrom(tibble,as_tibble_row)
 importFrom(tidyr,pivot_longer)
+importFrom(tidyr,pivot_wider)
+importFrom(tidyr,replace_na)
+importFrom(tm,removeNumbers)
+importFrom(utils,globalVariables)
+importFrom(utils,write.csv)
+importFrom(validate,"%vin%")
 importFrom(validate,confront)
 importFrom(validate,summary)
 importFrom(validate,validator)

R/append_new_entry_to_table.R

@@ -1,41 +1,67 @@
-#' append_new_entry_to_table
+#' Append new entry to article, outbreak, model, or parameter table
+#'
+#' NOTE: This can only be run in a locally cloned repository
 #'
 #' @param pathogen name of pathogen
-#' @param table_type
-#' @param new_row all the required details for the new row
+#' @param table_type table to be updated, either "article", "outbreak", "model"
+#' or "parameter"
+#' @param new_row the new row of data to be added to the table, this can be
+#' generated using either create_new_article_entry(), create_new_model_entry(),
+#' create_new_outbreak_entry(), or create_new_parameter_entry() (must contain
+#' the same number of variables as the table to be updated)
 #' @param validate check if the new row to be added passes minimum criteria
-#' @param write_table  write appended table
-#' @return Null (updates table)
-#' @examples
+#' (either TRUE or FALSE)
+#' @param write_table write appended table (either TRUE or FALSE). If TRUE the
+#' new table will be written as a csv file in the data folder of a locally
+#' cloned repository.
+#' @param vignette_prepend string to allow loading data in vignettes
+#' @return table with new entry (if write_table = TRUE the relevant table in a
+#' locally cloned repository is updated)
+#' @importFrom utils write.csv
 #'
 #' @export
-append_new_entry_to_table <- function(pathogen=NA, table_type=NA, new_row=NA, validate = TRUE, write_table = FALSE, vignette_prepend = "")
-{
-  old_table <- load_data(table_type =table_type,pathogen = pathogen, vignette_prepend = vignette_prepend)
+append_new_entry_to_table <- function(pathogen = NA,
+                                      table_type = NA,
+                                      new_row = NA,
+                                      validate = TRUE,
+                                      write_table = FALSE,
+                                      vignette_prepend = "") {
+
+  old_table <- load_epidata(table_type = table_type,
+                            pathogen = pathogen,
+                            vignette_prepend = vignette_prepend)
 
-  # check that schemas match
-  if(!((sum( colnames(new_row) == colnames(old_table) ) / length( colnames(new_row )) ) == 1))
-    stop('Schemas of new row and data sets do not match')
+  if (!((sum(colnames(new_row) == colnames(old_table)) /
+        length(colnames(new_row))) == 1))
+    stop("Schemas of new row and data sets do not match")
 
-  # check that the entry doesn't exist already -- create same for other table types as well
-  if( table_type=='article' & new_row$article_id %in% old_table$article_id)
-    stop('article_id already exists in the data set')
+  if (table_type == "article" && new_row$article_id %in% old_table$article_id)
+    stop("article_id already exists in the data set")
 
-  new_table <- rbind(old_table,new_row)
+  new_table <- rbind(old_table, new_row)
 
-  if(validate)
-  {
-    if(table_type=='article')     # if not valid it will fail here.
-      create_new_article_entry(pathogen = pathogen, new_article = new_row %>% as.vector(), vignette_prepend =  vignette_prepend)
-    if(table_type=='outbreak')     # if not valid it will fail here.
-      create_new_outbreak_entry(pathogen = pathogen, new_outbreak = new_row %>% as.vector(), vignette_prepend =  vignette_prepend)
-    if(table_type=='model')     # if not valid it will fail here.
-      create_new_model_entry(pathogen = pathogen, new_model = new_row %>% as.vector(), vignette_prepend =  vignette_prepend)
-    if(table_type=='parameter')     # if not valid it will fail here.
-      create_new_parameter_entry(pathogen = pathogen, new_param = new_row %>% as.vector(), vignette_prepend =  vignette_prepend)
+  if (validate) {
+    if (table_type == "article")
+      create_new_article_entry(pathogen = pathogen,
+                               new_article = new_row %>% as.vector(),
+                               vignette_prepend = vignette_prepend)
+    if (table_type == "outbreak")
+      create_new_outbreak_entry(pathogen = pathogen,
+                                new_outbreak = new_row %>% as.vector(),
+                                vignette_prepend = vignette_prepend)
+    if (table_type == "model")
+      create_new_model_entry(pathogen = pathogen,
+                             new_model = new_row %>% as.vector(),
+                             vignette_prepend = vignette_prepend)
+    if (table_type == "parameter")
+      create_new_parameter_entry(pathogen = pathogen,
+                                 new_param = new_row %>% as.vector(),
+                                 vignette_prepend = vignette_prepend)
   }
 
-  if(write_table) write.csv(new_table,paste0(vignette_prepend, 'data/', pathogen, '_', table_type, '.csv'))
+  if (write_table)
+    write.csv(new_table, paste0(vignette_prepend, "extdata/", pathogen, "_",
+                                table_type, ".csv"))
 
   return(new_table)
 }