From 9c1deab414804846d0d35743ee7bed06a1fe8293 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Tue, 6 Aug 2019 16:12:45 +0200 Subject: [PATCH] git error --- docs/reference/itis.html | 43 ++++++++++++++++++++++++++++++---------- 1 file changed, 32 insertions(+), 11 deletions(-) diff --git a/docs/reference/itis.html b/docs/reference/itis.html index abe4b60b..12a08129 100644 --- a/docs/reference/itis.html +++ b/docs/reference/itis.html @@ -6,7 +6,7 @@ -ITIS: Integrated Taxonomic Information System — itis • AMR (for R) +ITIS: Integrated Taxonomic Information System — ITIS • AMR (for R) @@ -45,7 +45,7 @@ - + @@ -80,7 +80,7 @@ AMR (for R) - 0.5.0.9009 + 0.5.0.9018 @@ -110,12 +110,26 @@
  • - + Predict antimicrobial resistance
    • +
  • + + + + Work with WHONET data + +
    • +
  • + + + + Import data from SPSS/SAS/Stata + +
  • @@ -124,14 +138,14 @@
  • - + Get properties of a microorganism
  • - + Get properties of an antibiotic @@ -151,6 +165,13 @@ Use the G-test
    • +
  • + + + + Other: benchmarks + +
  • @@ -211,7 +232,7 @@

    ITIS: Integrated Taxonomic Information System

    - +
    @@ -224,23 +245,23 @@

    ITIS

    -


    +


    This package contains the complete microbial taxonomic data (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov).

    -

    All (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.

    +

    All ~20,000 (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since ITIS honours the taxonomic branching order of bacterial phyla according to Cavalier-Smith (2002), which defines that all bacteria are classified into either subkingdom Negibacteria or subkingdom Posibacteria.

    ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].

    Read more on our website!


    -On our website https://msberends.gitlab.io/AMR you can find a omprehensive tutorial about how to conduct AMR analysis and find the complete documentation of all functions, which reads a lot easier than in R.

    +On our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

    Examples

    # NOT RUN {
 # Get a note when a species was renamed
 mo_shortname("Chlamydia psittaci")
-# Note: 'Chlamydia psittaci' (Page, 1968) was renamed 
+# Note: 'Chlamydia psittaci' (Page, 1968) was renamed
 #       'Chlamydophila psittaci' (Everett et al., 1999)
 # [1] "C. psittaci"