(v0.9.0.9010) Support R 4.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.9.0.9009
-Date: 2020-01-08
+Version: 0.9.0.9010
+Date: 2020-01-15
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 0.9.0.9009
-## <small>Last updated: 08-Jan-2020</small>
+# AMR 0.9.0.9010
+## <small>Last updated: 15-Jan-2020</small>
 
 ### Changes
 * Speed improvement for `as.mo()` (and consequently all `mo_*` functions that use `as.mo()` internally), especially for the *G. species* format (G for genus), like *E. coli* and *K penumoniae*
@@ -13,6 +13,7 @@
 
 ### Other
 * Add a `CITATION` file
+* Full support for the upcoming R 4.0
 
 # AMR 0.9.0
 

data-raw/country_analysis.R

@@ -26,7 +26,7 @@ library(maps)
 library(httr)
 
 GET_df <- function(ip) {
-  ip <- paste0("https://ipinfo.io/", ip, "?token=089aa7765ee912")
+  ip <- paste0("https://ipinfo.io/", ip, "?token=", ipinfo_token)
   result <- ip %>% GET()
   stop_for_status(result)
   result %>%
@@ -57,6 +57,8 @@ for (i in 2:length(unique_ip)) {
     bind_rows(GET_df(unique_ip[i]))
 }
 
+ip_tbl.bak <- ip_tbl
+
 # how many?
 n_distinct(ip_tbl$country)
 
@@ -90,6 +92,9 @@ countries_geometry <- sf::st_as_sf(map('world', plot = FALSE, fill = TRUE)) %>%
          not_antarctica = as.integer(ID != "Antarctica"),
          countries_name = ifelse(included == 1, ID, NA))
 
+# how many?
+countries_geometry %>% filter(included == 1) %>% nrow()
+
 countries_plot <- ggplot(countries_geometry) +
     geom_sf(aes(fill = included, colour = not_antarctica),
             size = 0.25, 
@@ -107,7 +112,9 @@ countries_plot_mini$data <- countries_plot_mini$data %>% filter(ID != "Antarctic
 countries_plot_mini <- countries_plot_mini + scale_colour_gradient(low = "#81899B", high = "#81899B")
 countries_plot_big <- countries_plot +
   labs(title = tools::toTitleCase("Countries where the AMR package for R was downloaded from"),
-       subtitle = paste0("Between March 2018 (first release) and ", format(Sys.Date(), "%B %Y"), ". The dots denote visitors on our website https://gitlab.io/msberends/AMR.")) +
+       subtitle = paste0("Between March 2018 (first release) and ", format(Sys.Date(), "%B %Y"), "." #,
+                         #"The dots denote visitors on our website https://gitlab.io/msberends/AMR."
+                         )) +
   theme(plot.title = element_text(size = 16, hjust = 0.5),
         plot.subtitle = element_text(size = 12, hjust = 0.5)) +
   geom_text(aes(x = -170,
@@ -117,12 +124,12 @@ countries_plot_big <- countries_plot +
                                                  paste(countries_name[!is.na(countries_name)], collapse = ", ")),
                                           200)),
             hjust = 0,
-            size = 4) +
-  # points of visitors
-  geom_point(data = ip_tbl,
-             aes(x = x, y = y), 
-             size = 1,
-             colour = "#81899B")
+             size = 4) # +
+  # # points of visitors
+  # geom_point(data = ip_tbl,
+  #            aes(x = x, y = y), 
+  #            size = 1,
+  #            colour = "#81899B")
 
 # main website page
 ggsave("pkgdown/logos/countries.png",
@@ -143,6 +150,14 @@ ggsave("pkgdown/logos/countries_large.png",
 
 
 # Gibberish ---------------------------------------------------------------
+
+data %>%
+  left_join(ip_tbl, by = c("ipaddress" = "ip")) %>% 
+  group_by(country = countrycode::countrycode(country, 
+                                              origin = 'iso2c', 
+                                              destination = 'country.name')) %>%
+  summarise(first = min(timestamp_server)) %>%
+  arrange(desc(first))
 # 
 # p1 <- data %>%
 #   group_by(country) %>%

docs/404.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9010</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9010</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9010</span>
       </span>
     </div>
 

docs/authors.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9010</span>
       </span>
     </div>
 

docs/index.html

@@ -45,7 +45,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9010</span>
       </span>
     </div>
 

docs/news/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9010</span>
       </span>
     </div>
 
@@ -231,13 +231,13 @@
       
     </div>
 
-    <div id="amr-0-9-0-9009" class="section level1">
+    <div id="amr-0-9-0-9010" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-9-0-9009" class="anchor"></a>AMR 0.9.0.9009<small> Unreleased </small>
+<a href="#amr-0-9-0-9010" class="anchor"></a>AMR 0.9.0.9010<small> Unreleased </small>
 </h1>
-<div id="last-updated-08-jan-2020" class="section level2">
+<div id="last-updated-15-jan-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-08-jan-2020" class="anchor"></a><small>Last updated: 08-Jan-2020</small>
+<a href="#last-updated-15-jan-2020" class="anchor"></a><small>Last updated: 15-Jan-2020</small>
 </h2>
 <div id="changes" class="section level3">
 <h3 class="hasAnchor">
@@ -263,6 +263,7 @@
 <a href="#other" class="anchor"></a>Other</h3>
 <ul>
 <li>Add a <code>CITATION</code> file</li>
+<li>Full support for the upcoming R 4.0</li>
 </ul>
 </div>
 </div>
@@ -1426,7 +1427,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#amr-0-9-0-9009">0.9.0.9009</a></li>
+        <li><a href="#amr-0-9-0-9010">0.9.0.9010</a></li>
         <li><a href="#amr-0-9-0">0.9.0</a></li>
         <li><a href="#amr-0-8-0">0.8.0</a></li>
         <li><a href="#amr-0-7-1">0.7.1</a></li>

docs/reference/ab_property.html

@@ -85,7 +85,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9010</span>
       </span>
     </div>
 

docs/reference/as.ab.html

@@ -85,7 +85,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9010</span>
       </span>
     </div>
 

docs/reference/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9010</span>
       </span>
     </div>