From 95f7c78fd6c64ffee850c6a3a3e5c17bcec03b61 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Mon, 14 May 2018 11:54:08 +0200 Subject: [PATCH] edit vignette title --- NEWS.md | 2 +- vignettes/.gitignore | 4 + vignettes/freq.Rmd | 2 +- vignettes/freq.html | 344 ------------------------------------------- 4 files changed, 6 insertions(+), 346 deletions(-) create mode 100644 vignettes/.gitignore delete mode 100644 vignettes/freq.html diff --git a/NEWS.md b/NEWS.md index cffdf5e7..afacac0b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ # 0.2.9000 (development version) #### New -* Vignettes about frequency tables: [vignettes/freq.html](vignettes/freq.html) +* 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)` #### Changed diff --git a/vignettes/.gitignore b/vignettes/.gitignore new file mode 100644 index 00000000..5a5283f9 --- /dev/null +++ b/vignettes/.gitignore @@ -0,0 +1,4 @@ +figure +*.html +*.md +rsconnect diff --git a/vignettes/freq.Rmd b/vignettes/freq.Rmd index 7eb895e7..04702aac 100644 --- a/vignettes/freq.Rmd +++ b/vignettes/freq.Rmd @@ -5,7 +5,7 @@ output: rmarkdown::html_vignette: toc: true vignette: > - %\VignetteIndexEntry{Vignette Title} + %\VignetteIndexEntry{Creating Frequency Tables} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- diff --git a/vignettes/freq.html b/vignettes/freq.html deleted file mode 100644 index f956a698..00000000 --- a/vignettes/freq.html +++ /dev/null @@ -1,344 +0,0 @@ - - - - - - - - - - - - - - - -Creating Frequency Tables - - - - - - - - - - - - - - - - - -

Creating Frequency Tables

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Matthijs S. Berends

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Introduction

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Frequency tables (or frequency distributions) are summaries of the distribution of values in a sample. With the freq function, you can create univariate frequency tables. Multiple variables will be pasted into one variable, so it forces a univariate distribution. We take the septic_patients dataset (included in this AMR package) as example.

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Frequencies of one variable

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To only show and quickly review the content of one variable, you can just select this variable in various ways. Let’s say we want to get the frequencies of the sex variable of the septic_patients dataset:

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# # just using base R
-freq(septic_patients$sex)
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-# # using base R to select the variable and pass it on with a pipe
-septic_patients$sex %>% freq()
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-# # do it all with pipes, using the `select` function of the dplyr package
-septic_patients %>%
-  select(sex) %>%
-  freq()
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This will all lead to the following table:

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freq(septic_patients$sex)
-# Class:     character
-# Length:    2000 (of which NA: 0 = 0.0%)
-# Unique:    2
-# 
-# Item    Count   Percent   Cum. Count   Cum. Percent
-# -----  ------  --------  -----------  -------------
-# M        1112     55.6%         1112          55.6%
-# F         888     44.4%         2000         100.0%
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This immediately shows the class of the variable, its length and availability (i.e. the amount of NA), the amount of unique values and (most importantly) that among septic patients men are more prevalent than women.

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Frequencies of more than one variable

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Multiple variables will be pasted into one variable to review individual cases, keeping a univariate frequency table.

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For illustration, we could add some more variables to the septic_patients dataset to learn about bacterial properties:

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my_patients <- septic_patients %>% 
-  left_join_microorganisms()
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Now all variables of the microorganisms dataset have been joined to the septic_patients dataset. The microorganisms dataset consists of the following variables:

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colnames(microorganisms)
-#  [1] "bactid"       "bactsys"      "family"       "genus"       
-#  [5] "species"      "subspecies"   "fullname"     "type"        
-#  [9] "gramstain"    "aerobic"      "type_nl"      "gramstain_nl"
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If we compare the dimensions between the old and new dataset, we can see that these 11 variables were added:

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dim(septic_patients)
-# [1] 2000   47
-dim(my_patients)
-# [1] 2000   58
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So now the genus and species variables are available. A frequency table of these combined variables can be created like this:

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my_patients %>%
-  select(genus, species) %>%
-  freq()
-# Columns:   2
-# Length:    2000 (of which NA: 0 = 0.0%)
-# Unique:    137
-# 
-# Item                                 Count   Percent   Cum. Count   Cum. Percent
-# ----------------------------------  ------  --------  -----------  -------------
-# Escherichia coli                       485     24.2%          485          24.2%
-# Staphylococcus coagulase negatief      297     14.8%          782          39.1%
-# Staphylococcus aureus                  200     10.0%          982          49.1%
-# Staphylococcus epidermidis             150      7.5%         1132          56.6%
-# Streptococcus pneumoniae                97      4.9%         1229          61.5%
-# Staphylococcus hominis                  67      3.4%         1296          64.8%
-# Klebsiella pneumoniae                   65      3.2%         1361          68.0%
-# Enterococcus faecalis                   44      2.2%         1405          70.2%
-# Proteus mirabilis                       33      1.7%         1438          71.9%
-# Pseudomonas aeruginosa                  31      1.6%         1469          73.5%
-# Streptococcus pyogenes                  30      1.5%         1499          75.0%
-# Enterococcus faecium                    27      1.4%         1526          76.3%
-# Bacteroides fragilis                    26      1.3%         1552          77.6%
-# Enterobacter cloacae                    25      1.2%         1577          78.8%
-# Klebsiella oxytoca                      23      1.1%         1600          80.0%
-# ... and 122 more (n = 400; 20.0%). Use `nmax` to show more or less rows.
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Frequencies of numeric values

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Frequency tables can be created of any input.

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In case of numeric values (like integers, doubles, etc.) additional descriptive statistics will be calculated and shown into the header:

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# # get age distribution of unique patients
-septic_patients %>% 
-  distinct(patient_id, .keep_all = TRUE) %>% 
-  select(age) %>% 
-  freq(nmax = 5)
-# Class:     integer
-# Length:    1920 (of which NA: 0 = 0.0%)
-# Unique:    94
-#   
-# Mean:      68
-# Std. dev.: 18 (CV: 0.27)
-# Five-Num:  0  |  61  |  72  |  80  |  101 (CQV: 0.13)
-# Outliers:  94 (unique: 26)
-# 
-#  Item   Count   Percent   Cum. Count   Cum. Percent
-# -----  ------  --------  -----------  -------------
-#     0      34      1.8%           34           1.8%
-#     1       5      0.3%           39           2.0%
-#     2       5      0.3%           44           2.3%
-#     3       2      0.1%           46           2.4%
-#     4       1      0.1%           47           2.4%
-# ... and 89 more (n = 1873; 97.6%).
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So the following properties are determined, where NA values are always ignored:

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So for example, the above frequency table quickly shows the median age of patients being 72.

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Frequencies of factors

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Frequencies of factors will be sorted on factor level instead of item count by default. This can be changed with the sort.count parameter. Frequency tables of factors always show the factor level as an additional last column.

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sort.count is TRUE by default, except for factors. Compare this default behaviour:

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septic_patients %>%
-  select(hospital_id) %>% 
-  freq()
-# Class:     factor
-# Length:    2000 (of which NA: 0 = 0.0%)
-# Unique:    5
-# 
-# Item    Count   Percent   Cum. Count   Cum. Percent   (Factor Level)
-# -----  ------  --------  -----------  -------------  ---------------
-# A         233     11.7%          233          11.7%                1
-# B         583     29.1%          816          40.8%                2
-# C         221     11.1%         1037          51.8%                3
-# D         650     32.5%         1687          84.4%                4
-# E         313     15.7%         2000         100.0%                5
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To this, where items are now sorted on item count:

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septic_patients %>%
-  select(hospital_id) %>% 
-  freq(sort.count = TRUE)
-# Class:     factor
-# Length:    2000 (of which NA: 0 = 0.0%)
-# Unique:    5
-# 
-# Item    Count   Percent   Cum. Count   Cum. Percent   (Factor Level)
-# -----  ------  --------  -----------  -------------  ---------------
-# D         650     32.5%          650          32.5%                4
-# B         583     29.1%         1233          61.7%                2
-# E         313     15.7%         1546          77.3%                5
-# A         233     11.7%         1779          88.9%                1
-# C         221     11.1%         2000         100.0%                3
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All classes will be printed into the header. Variables with the new rsi class of this AMR package are actually ordered factors and have three classes (look at Class in the header):

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septic_patients %>%
-  select(amox) %>% 
-  freq()
-# Class:     factor > ordered > rsi
-# Length:    2000 (of which NA: 678 = 33.9%)
-# Unique:    3
-# 
-# Item    Count   Percent   Cum. Count   Cum. Percent   (Factor Level)
-# -----  ------  --------  -----------  -------------  ---------------
-# S         561     42.4%          561          42.4%                1
-# I          49      3.7%          610          46.1%                2
-# R         712     53.9%         1322         100.0%                3
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Frequencies of dates

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Frequencies of dates will show the oldest and newest date in the data, and the amount of days between them:

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septic_patients %>%
-  select(date) %>% 
-  freq(nmax = 5)
-# Class:     Date
-# Length:    2000 (of which NA: 0 = 0.0%)
-# Unique:    1662
-# 
-# Oldest:    2 januari 2001
-# Newest:    18 oktober 2017 (+6133)
-# 
-# Item          Count   Percent   Cum. Count   Cum. Percent
-# -----------  ------  --------  -----------  -------------
-# 2008-12-24        5      0.2%            5           0.2%
-# 2010-12-10        4      0.2%            9           0.4%
-# 2011-03-03        4      0.2%           13           0.6%
-# 2013-06-24        4      0.2%           17           0.8%
-# 2017-09-01        4      0.2%           21           1.1%
-# ... and 1657 more (n = 1979; 99.0%).
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Additional parameters

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Parameter na.rm

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With the na.rm parameter (defaults to TRUE, but they will always be shown into the header), you can include NA values in the frequency table:

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septic_patients %>%
-  select(amox) %>% 
-  freq(na.rm = FALSE)
-# Class:     factor > ordered > rsi
-# Length:    2678 (of which NA: 678 = 25.3%)
-# Unique:    4
-# 
-# Item    Count   Percent   Cum. Count   Cum. Percent   (Factor Level)
-# -----  ------  --------  -----------  -------------  ---------------
-# S         561     28.1%          561          28.1%                1
-# I          49      2.5%          610          30.5%                2
-# R         712     35.6%         1322          66.1%                3
-# <NA>      678     33.9%         2000         100.0%             <NA>
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Parameter markdown

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The markdown parameter can be used in reports created with R Markdown. This will always print all rows:

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septic_patients %>%
-  select(hospital_id) %>% 
-  freq(markdown = TRUE)
-# 
-# Class:     factor
-# 
-# Length:    2000 (of which NA: 0 = 0.0%)
-# 
-# Unique:    5
-# 
-# |Item | Count| Percent| Cum. Count| Cum. Percent| (Factor Level)|
-# |:----|-----:|-------:|----------:|------------:|--------------:|
-# |A    |   233|   11.7%|        233|        11.7%|              1|
-# |B    |   583|   29.1%|        816|        40.8%|              2|
-# |C    |   221|   11.1%|       1037|        51.8%|              3|
-# |D    |   650|   32.5%|       1687|        84.4%|              4|
-# |E    |   313|   15.7%|       2000|       100.0%|              5|
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Parameter as.data.frame

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With the as.data.frame parameter you can assign the frequency table to an object, or just print it as a data.frame to the console:

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my_df <- septic_patients %>%
-  select(hospital_id) %>% 
-  freq(as.data.frame = TRUE)
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-my_df
-#   item count percent cum_count cum_percent factor_level
-# 1    A   233  0.1165       233      0.1165            1
-# 2    B   583  0.2915       816      0.4080            2
-# 3    C   221  0.1105      1037      0.5185            3
-# 4    D   650  0.3250      1687      0.8435            4
-# 5    E   313  0.1565      2000      1.0000            5
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-class(my_df)
-# [1] "data.frame"
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AMR, (c) 2018, https://github.com/msberends/AMR

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Licensed under the GNU General Public License v2.0.

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