From 4bf6a069352bfb4f9761c3480e53f94b5c8c0956 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Thu, 23 May 2019 18:53:18 +0200 Subject: [PATCH] website update --- docs/articles/MDR.html | 96 ++++++++++++++++++++++---------- docs/articles/freq.html | 2 +- docs/index.html | 3 +- docs/reference/antibiotics.html | 2 +- docs/reference/as.rsi.html | 2 +- docs/reference/count.html | 2 +- docs/reference/eucast_rules.html | 2 +- docs/reference/ggplot_rsi.html | 2 +- index.md | 2 +- vignettes/MDR.Rmd | 2 +- 10 files changed, 77 insertions(+), 38 deletions(-) diff --git a/docs/articles/MDR.html b/docs/articles/MDR.html index a9bbdf47..53017aa5 100644 --- a/docs/articles/MDR.html +++ b/docs/articles/MDR.html @@ -40,7 +40,7 @@ AMR (for R) - 0.6.1.9035 + 0.6.1.9037 @@ -242,19 +242,19 @@

The data set looks like this now:

head(my_TB_data)
 #   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin
-# 1          R         R            R          R            R            S
-# 2          S         R            R          S            R            S
-# 3          R         S            S          I            S            S
-# 4          R         S            S          R            S            S
-# 5          R         R            S          I            I            R
-# 6          R         S            S          S            S            S
+# 1          R         R            S          I            S            S
+# 2          S         R            I          R            S            R
+# 3          S         S            S          S            R            R
+# 4          R         S            R          S            S            S
+# 5          I         R            R          S            R            R
+# 6          S         S            S          S            S            S
 #   kanamycin
 # 1         S
 # 2         R
 # 3         S
 # 4         R
-# 5         S
-# 6         I
+# 5 R +# 6 R

We can now add the interpretation of MDR-TB to our data set:

my_TB_data$mdr <- mdr_tb(my_TB_data)
 # NOTE: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.
@@ -267,25 +267,65 @@
 # would be available too: `CAP` (capreomycin), `RIB` (rifabutin), `RFP`
 # (rifapentine)

And review the result with a frequency table:

-
freq(my_TB_data$mdr)
-# 
-# 
-# **Frequency table of `mdr` from `my_TB_data` (5,000 x 8)**   
-# 
-# Class:   `factor` > `ordered` (`numeric`)  
-# Length:  5,000 (of which NA: 0 = 0.00%)  
-# Levels:  5: `Negative` < `Mono-resistance` < `Poly-resistance` < `Multidrug res...`  
-# Unique:  5
-# 
-# 
-# |   |Item                      | Count| Percent| Cum. Count| Cum. Percent|
-# |:--|:-------------------------|-----:|-------:|----------:|------------:|
-# |1  |Mono-resistance           | 3,297|   65.9%|      3,297|        65.9%|
-# |2  |Negative                  |   627|   12.5%|      3,924|        78.5%|
-# |3  |Multidrug resistance      |   612|   12.2%|      4,536|        90.7%|
-# |4  |Poly-resistance           |   263|    5.3%|      4,799|        96.0%|
-# |5  |Extensive drug resistance |   201|    4.0%|      5,000|       100.0%|
- +
freq(my_TB_data$mdr)
+

Frequency table of mdr from my_TB_data (5,000 x 8)

+

Class: factor > ordered (numeric)
+Length: 5,000 (of which NA: 0 = 0.00%)
+Levels: 5: Negative < Mono-resistance < Poly-resistance < Multidrug res...
+Unique: 5

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ItemCountPercentCum. CountCum. Percent
1Mono-resistance3,28865.8%3,28865.8%
2Negative68613.7%3,97479.5%
3Multidrug resistance56011.2%4,53490.7%
4Poly-resistance2695.4%4,80396.1%
5Extensive drug resistance1973.9%5,000100.0%
+ diff --git a/docs/articles/freq.html b/docs/articles/freq.html index 6fc26e20..42b0863e 100644 --- a/docs/articles/freq.html +++ b/docs/articles/freq.html @@ -40,7 +40,7 @@ AMR (for R) - 0.6.1.9035 + 0.6.1.9037 diff --git a/docs/index.html b/docs/index.html index 1795c31d..01ed7319 100644 --- a/docs/index.html +++ b/docs/index.html @@ -219,8 +219,7 @@
  • Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name) (manual)
  • Plotting antimicrobial resistance (tutorial)
  • Determining first isolates to be used for AMR analysis (manual)
    • -
  • Applying EUCAST expert rules (manual -
    • +
  • Applying EUCAST expert rules (manual)
  • Descriptive statistics: frequency tables, kurtosis and skewness (tutorial)

    • This package is ready-to-use for a professional environment by specialists in the following fields:

    diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html index 124bdc1a..c1bcb191 100644 --- a/docs/reference/antibiotics.html +++ b/docs/reference/antibiotics.html @@ -80,7 +80,7 @@ AMR (for R) - 0.6.1.9035 + 0.6.1.9037 diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index c3a6641a..fb78156b 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -80,7 +80,7 @@ AMR (for R) - 0.6.1.9035 + 0.6.1.9037 diff --git a/docs/reference/count.html b/docs/reference/count.html index 37d638bc..251c2833 100644 --- a/docs/reference/count.html +++ b/docs/reference/count.html @@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_ AMR (for R) - 0.6.1.9035 + 0.6.1.9037 diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html index b516af56..f33e1baf 100644 --- a/docs/reference/eucast_rules.html +++ b/docs/reference/eucast_rules.html @@ -80,7 +80,7 @@ AMR (for R) - 0.6.1.9035 + 0.6.1.9037 diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html index e98045ed..7885783e 100644 --- a/docs/reference/ggplot_rsi.html +++ b/docs/reference/ggplot_rsi.html @@ -80,7 +80,7 @@ AMR (for R) - 0.6.1.9035 + 0.6.1.9037 diff --git a/index.md b/index.md index 8a31f550..34b027a6 100644 --- a/index.md +++ b/index.md @@ -25,7 +25,7 @@ This package can be used for: * Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name) ([manual](./reference/ab_property.html)) * Plotting antimicrobial resistance ([tutorial](./articles/AMR.html)) * Determining first isolates to be used for AMR analysis ([manual](./reference/first_isolate.html)) - * Applying EUCAST expert rules ([manual](./reference/eucast_rules.html) + * Applying EUCAST expert rules ([manual](./reference/eucast_rules.html)) * Descriptive statistics: frequency tables, kurtosis and skewness ([tutorial](./articles/freq.html)) This package is ready-to-use for a professional environment by specialists in the following fields: diff --git a/vignettes/MDR.Rmd b/vignettes/MDR.Rmd index c7d9781a..356389b6 100644 --- a/vignettes/MDR.Rmd +++ b/vignettes/MDR.Rmd @@ -74,6 +74,6 @@ my_TB_data$mdr <- mdr_tb(my_TB_data) And review the result with a frequency table: -```{r} +```{r, results = 'asis'} freq(my_TB_data$mdr) ```