prevent dplyr:row_number warning

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.2.0.9001
-Date: 2018-05-30
+Version: 0.2.0.9002
+Date: 2018-05-31
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(

NEWS.md

@@ -1,4 +1,4 @@
-# 0.2.0.9000 (development version)
+# 0.2.0.90xx (development version)
 #### New
 * Vignettes about frequency tables
 * Possibility to globally set the default for the amount of items to print in frequency tables (`freq` function), with `options(max.print.freq = n)`
@@ -6,6 +6,8 @@
 #### Changed
 * Renamed `toConsole` parameter of `freq` to `as.data.frame`
 * Small translational improvements to the `septic_patients` dataset
+* Coerce RSI values from combined MIC/RSI values: `as.rsi("<=0.002; S")` will now return `"S"`
+* Fix for warning `hybrid evaluation forced for row_number` from the `dplyr` package v0.7.5 and above.
 
 # 0.2.0 (latest stable version)
 #### New

R/classes.R

@@ -44,7 +44,7 @@ as.rsi <- function(x) {
     # remove all spaces
     x <- gsub(' +', '', x)
     # remove all MIC-like values: numbers, operators and periods
-    x <- gsub('[0-9.,<=>]+', '', x)
+    x <- gsub('[0-9.,;:<=>]+', '', x)
     # disallow more than 3 characters
     x[nchar(x) > 3] <- NA
     # set to capitals

R/first_isolates.R

@@ -292,12 +292,15 @@ first_isolate <- function(tbl,
   }
 
   scope.size <- tbl %>%
-    filter(row_number() %>%
-             between(row.start,
-                     row.end),
+    filter(
+      suppressWarnings(
+        row_number() %>% between(row.start,
+                                 row.end)
+      ),
       genus != '') %>%
     nrow()
 
+
   # Analysis of first isolate ----
   all_first <- tbl %>%
     mutate(other_pat_or_mo = if_else(patient_id == lag(patient_id)
@@ -336,13 +339,14 @@ first_isolate <- function(tbl,
       mutate(
         real_first_isolate =
           if_else(
-            between(row_number(), row.start, row.end)
+            suppressWarnings(between(row_number(), row.start, row.end))
             & genus != ''
             & (other_pat_or_mo
                | days_diff >= episode_days
                | key_ab_other),
             TRUE,
             FALSE))
+
     if (info == TRUE) {
       cat('\n')
     }
@@ -351,7 +355,7 @@ first_isolate <- function(tbl,
       mutate(
         real_first_isolate =
           if_else(
-            between(row_number(), row.start, row.end)
+            suppressWarnings(between(row_number(), row.start, row.end))
             & genus != ''
             & (other_pat_or_mo
                | days_diff >= episode_days),

R/freq.R

@@ -349,7 +349,6 @@ freq <- function(x,
         ' (',
         (Count.rest / length(x)) %>% percent(force_zero = TRUE),
         ') ]\n', sep = '')
-    cat('\n')
 
   } else {
     print(

R/print.R

@@ -204,7 +204,12 @@ prettyprint_df <- function(x,
     # class will be marked up per column
     if (NROW(x.bak) > 0) {
       rownames.x <- rownames(x)
-      x <- x %>% filter(row_number() == 1) %>% rbind(x, stringsAsFactors = FALSE)
+      x <- x %>%
+        filter(
+          suppressWarnings(
+            row_number() == 1)
+        ) %>%
+        rbind(x, stringsAsFactors = FALSE)
       rownames(x) <- c('*', rownames.x)
     }