---
title: "Searching help pages of R packages"
author: "Spencer Graves, Sundar Dorai-Raj, and Romain François"
date: "2024-06-28"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Searching help pages of R packages}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup}
library(sos)
```


This vignette was originally published in *The R Journal*, vol. 1(2) in 2009. The package and this vignette have been changed since then to make the package easier to use and to adjust to changes in the R ecosystem. 

## Abstract

The `sos` package provides a means to quickly and flexibly search the help pages of contributed packages, finding functions and datasets in seconds or minutes that could not be found in hours or days by any other means we know.  Its `findFn` function searches [the search site `https://search.r-project.org`](https://search.r-project.org) used by the [`RSiteSearch`](https://stat.ethz.ch/R-manual/R-devel/library/utils/html/RSiteSearch.html) function but returns the matches in a [`data.frame`](https://www.stat.ethz.ch/R-manual/R-devel/library/base/html/data.frame.html) of class `findFn`, which can be further manipulated by other `sos` functions to produce, for example, an Excel file that starts with a summary sheet that makes it relatively easy to prioritize alternative packages for further study. As such, it provides a very powerful way to do a literature search for functions and packages relevant to a particular topic of interest and could become virtually mandatory for authors of new packages or papers in publications such as *The R Journal* and the *Journal of Statistical Software*.

## Introduction

The `sos` package provides a means to quickly and flexibly search the help pages of contributed packages, finding functions and datasets in seconds or minutes that could not be found in hours or days by any other means we know.

The main capability of this package is the `findFn` function, which scans the *function* entries in the `RSiteSearch` database, created originally by Jonathan Baron,^[@JB09URL]. It returns the matches in a `data.frame` of class `findFn`. This database includes options to search the help pages of R packages contributed to CRAN (the [Comprehensive R Archive Network](https://cran.r-project.org)) plus a few other publicly available packages, as well as selected mailing list archives---primarily R-help.  The `findFn` function focuses only on the *help pages* in this database, ignoring the R-help archives. (CRAN grew from 1700 contributed packages and bundles on 2009-03-11 to 1954 on 2009-09-18, adding over 40 packages per day, an annual growth rate of 31 percent.)

The [`print`](https://stat.ethz.ch/R-manual/R-devel/library/base/html/print.html) method for objects of class `findFn` displays the results as two tables in the default web browser. 

* The first is the table of individual help pages with links to those help pages, sorted by package. The key benefit of this is that they results are sorted by package, displaying first the results from the package with the most matches. This behavior differs from that of the `RSiteSearch` function in the [`utils`](https://stat.ethz.ch/R-manual/R-devel/library/utils/html/00Index.html) package in more ways than the sort order.  First, `findFn` returns the results in R as a `data.frame`, which can be further manipulated.  Second, the ultimate display in a web browser is a table, unlike the list produced by `RSiteSearch`.
* The second table is a package summary. 

Other `sos` functions provide summaries with one line for each package, support the union and intersection of `findFn` objects, and translate a `findFn` object into an Excel file with three sheets: 

# **PackageSum2**, which provides an enhanced summary of the packages with matches, 
# the **findFn** table itself, and 
# (the **call** used to produce it.

Three examples are considered below:  
* First we find a data set containing a variable `Petal.Length`}`. 
* Second, we study R capabilities for splines, including looking for a function named `spline`.  
* Third, we search for contributed R packages with capabilities for solving differential equations.

## Finding a variable in a data set

Chambers (2009)^[@JC09] uses a variable `Petal.Length` from a famous Fisher data set but without naming the data set nor indicating where it can be found nor even if it exists in any contributed R package. The sample code he provides does not work by itself.  To get his code to  work to produce his Figure 7.2, we must first obtain a copy of this famous data set in a format compatible with his code.

To look for this data set, one might first try the [`help.search`](https://stat.ethz.ch/R-manual/R-patched/library/utils/html/help.search.html) function.  Unfortunately, this function returns nothing in this case:

```{r Petal.Len}
(Petal.Length <- help.search('Petal.Length'))
```

When this failed, many users might then try 

```{r PL.RSiteSearch}
library(sos)
if(!CRAN()){
  RSiteSearch('Petal.Length')
}
```

This produced 80 matches when it was tried one day (and 62 matches a few months later).

`RSiteSearch('Petal.Length', 'function')` will identify only the help pages.  We can get something similar and for many purposes more useful, as follows:

```{r PetalLen_sos} 
library(sos)
PL <- findFn('Petal.Length')
class(PL)
dim(PL)
```

`PL` is a data frame of class `findFn` identifying all the help pages in the `RSiteSearch` database matching the search term (unless the number of matches exceeds the `20*maxPages` argument of `findFn`, assuming 20 links per page).  An alias for `findFn` is `???`. Thus, this same search can be performed as follows:

```{r PL_sos}
PL. <- ???Petal.Length
class(PL.)
dim(PL.)
```

(The `???` alias only works in an assignment, so to print immediately, you need something like `(PL <- ???Petal.Length)`.)

The `data.frame`s `PL` and `PL.` should be identical unless the search site `https://search.r-project.org` changes in the time between these two searches. 

Both `data.frame`s have columns `Count`, `MaxScore`, `TotalScore`, `Package`, `Function`, `Date`, `Score`, `Description`, and `Link`. `Function` is the name of the *help page, not* the name of the function for two reasons: 

# Multiple functions may be documented on a single
help page. 
# Some help pages document other things such as data sets.  

`Score` is the index of the strength of the match.  It is used by the `RSiteSearch` database to decide which items to display first. `Package` is the name of the package containing `Function`. `Count` gives the total number of matches in `Package` found in this `findFn` call.  By default, the `findFn` object is sorted by `Count`, `MaxScore`, `TotalScore`, and `Package` (to place the most important `Package` first), then by `Score`}` and `Function`.

The `summary` method for an object of class `FindFn` prints a table giving for each `Package` the `Count` (number of matches), `MaxScore` (max of `Score`), `TotalScore` (sum of `Score`), and `Date`, sorted like a Pareto chart to place the `Package` with the most help pages first:

```{r summary.PL,results='hide'} 
# the following table has been
# manually edited for clarity
summary(PL)
```
```{r summary.PL-print, echo=FALSE}
s <- summary(PL)
blank <- data.frame(Package = "<...>",
      Count = "", MaxScore = "", TotalScore = "",
      Date = "", pkgLink='')
s$PackageSummary[] <- lapply(s$PackageSummary[], as.character)
row.names(s$PackageSummary) <-
  as.character(s$PackageSummary$Package)
s$PackageSummary <- rbind(s$PackageSummary['yaImpute', ],
                          blank,
                          s$PackageSummary['datasets', ],
                          blank)
print(s, row.names = FALSE)
```

(The `Date` here is the date that this package was added to the `RSiteSearch` database.)

One of the listed packages is `datasets`.  Since it is part of the default R distribution, we decide to look there first.  We can select that row of `PL` just like we would select a row from any other data frame:

```{r Petal.Length.sos.3,results='hide'}
PL[PL$Package == 'datasets', 'Function']
```
```{r Petal.Length.sos.3-print,echo=FALSE}
print(PL[PL$Package == 'datasets', 'Function'], max.levels = 0)
```

Problem solved in less than a minute!  Any other method known
to the present authors would have taken substantially more time.

## Finding packages with spline capabilities

In 2005, the lead author of this article decided he needed to learn more about splines.  A literature search
began as follows:

```{r RSiteSearch-spline,results='hide'}
if(!CRAN()){
  RSiteSearch('spline')
}
```
```{r RSiteSearch-spline-numpages,results='hide',echo=FALSE}
getRSiteSearchHits <- function(description) {
  today <- format(Sys.time(), "%Y-%m-%d")
  con <- url(description)
  on.exit(close(con))
  lines <- try(readLines(con))
  if(class(lines) == 'try-error'){
    return(list(hits=0, date=today))
  }
  pattern <- "^.*<!-- HIT -->([0-9]+)<!-- HIT -->.*$"
  hits <- sub(pattern, "\\1", lines[grep(pattern, lines)])
  list(hits = hits, date = today)
}
splineHits <- getRSiteSearchHits("http://search.r-project.org/cgi-bin/namazu.cgi?query=spline&max=20&result=normal&sort=score&idxname=Rhelp08&idxname=functions&idxname=views")
```

(using the `RSiteSearch` function in the `utils` package). While preparing this manuscript, this command identified 1526 documents one day.  That is too many.  It can be restricted to functions as follows:

```{r RSiteSearch-spline-fun, results='hide'}
if(!CRAN()){
  RSiteSearch('spline', 'fun')
}
```
```{r RSiteSearch-spline-fun-numpages,results='hide',echo=FALSE} 
splineFunHits <- getRSiteSearchHits("http://search.r-project.org/cgi-bin/namazu.cgi?query=spline&max=20&result=normal&sort=score&idxname=functions")
```

This identified only 739 one day (631 earlier). That's an improvement over 739 but is still too many for convenient analysis. To get a quick overview of these matches,  can proceed as follows:

```{r RSiteSearch-spline-fun2,results='hide'}
if(!CRAN()){
  RSiteSearch('spline', 'fun')
}
```
```{r RSiteSearch-spline-fun2-numpages,results='hide',echo=FALSE}
splineFunHits <- getRSiteSearchHits("http://search.r-project.org/cgi-bin/namazu.cgi?query=spline&max=20&result=normal&sort=score&idxname=functions")
```

This downloaded a summary of the highest-scoring help pages in the `RSiteSearch` data base in roughly 5-15 seconds, depending on the speeds of the database and Internet connection.  

If the search results exceeds the `maxPages` argument, increase that argument from its default 100: 

```{r sos-spline-maxPages-999,results='hide'}
splineAll <- findFn('spline', maxPages = 999)
```

If we want to find a function named `spline`, we can proceed as follows:

```{r sos-spline-subset,results='hide'}
selSpl <- splineAll[, 'Function'] == 'spline'
splineAll[selSpl, ]
```

This has 0 rows, because there is no help page named
`spline`.  This does *not* mean that no function
with that exact name exists, only that no *help page*
has that name.

To look for help pages whose name *includes* the characters `spline`, we can use `grepFn`:

```{r sos-spline-grep,results='hide'} 
if(!CRAN()){
  grepFn('spline', splineAll, ignore.case = TRUE)
}
```
```{r sos-spline-grep2,results='hide',echo=FALSE}
g <- grepFn('spline', splineAll, ignore.case = TRUE)
gFunc6 <- as.character(g[6, "Function"])
gPac6 <- as.character(g[6, "Package"])
gScore6 <- g[6, "Score"]
gCount6 <- g[6, "Count"]
# Apparently, nlevels(splineAll$Package)
# splineAll$Package used to be a factor; not it's not
nPacSplineAll <- length(table(splineAll$Package))
```

This returned a `findFn` object identifying `r nrow(g)` help pages. When this was run while preparing this manuscript, the sixth row was `lspline` in the `assist` package, which has a Score of 1. (On another day, the results could be different, because the `RSiteSearch` database changes over time.) This was the sixth row in this table, because it is in the `assist` package, which had a total of 34 help pages matching the search term, but this was the only one whose name matched the `pattern` passed to `grepFn`.

We could next `print` the `splineAll` `findFn` object.  However, it may not be easy to digest a table with 739 rows (or however many rows it produces when you run it). 

`summary(splineAll)` would tell us that the `r nrow(splineAll)` help pages came from `r nPacSplineAll` different packages and display the first `minPackages = 12` such packages. (If other packages had the same number of matches as the twelfth package, they would also appear in this summary. `minPackages is an argument of the `summary.findFn` function and can be changed if the user wishes.) 

A more complete view can be obtained in MS Excel format using the `writeFindFn2xls` function:

```{r writeFindFn2xls-options,echo=FALSE}
op <- options(width = 80)
```
```{r writeFindFn2xls,results='hide'}
writeFindFn2xls(splineAll)
```
```{r writeFindFn2xls-options2,echo=FALSE}
options(op)
```

(`findFn2xls` is an alias for `writeFindFn2xls`.
We use the longer version here, as it may be
easier to remember.)

If either the `WriteXLS` package and compatible Perl code
are properly installed or if you are running Windows with
the `RODBC` package, this produces an Excel file in the
working directory named `splineAll.xls`, containing the
following three worksheets:

* The **PackageSum2** sheet includes one line for each
package with a matching help page, enhanced by providing
information for locally installed packages
not available in the `findFn` object.
* The **findFn** sheet contains the search results.
* The **call** sheet gives the call to `findFn` that generated these search results.

If `writeFindFn2xls` cannot produce an Excel file with
your installation, it will write three `csv`}` files with
names `splineAll-sum.csv`}`, `splineAll.csv`, and
`splineAll-call.csv`, corresponding to the three
worksheets described above. (Users who do not have MS Excel
may like to know that Open Office Calc can open a standard
`xls`}` file and can similarly create such files.)^[@CALC09MAN]

The **PackageSum2** sheet is created by the **PackageSum2** function, which adds information from installed packages not obtained by `findFn`.  The extended summary includes the package title and date, plus the names of the author and the maintainer, the number of help pages in the package, and the name(s) of any vignettes.  This can be quite valuable in prioritizing packages for further study. Other things being equal, we think most people would rather learn how to use a package being actively maintained than one that has not changed in five years.  Similarly, we might prefer to study a capability in a larger package than a smaller one, because the rest of the package might provide other useful tools or a broader context for understanding the capability of interest.

These extra fields, package title, etc., are blank for packages in the `findFn` object not installed locally. For installed packages, the `Date` refers to the *packaged* date rather than the date the package was added to the `RSiteSearch` database.

Therefore, the value of `PackageSum2` can be increased by running [`install.packages`](https://stat.ethz.ch/R-manual/R-devel/library/utils/html/install.packages.html) (from the [`utils`](https://stat.ethz.ch/R-manual/R-devel/library/utils/html/00Index.html) package) to install packages not currently available locally and `update.packages` to ensure the local availability of the latest versions for all installed packages.

To make it easier to add desired packages, the `sos` package includes an `installPackages` function, which checks all the packages in a `findFn` object for which the number of matches exceeds a second argument `minCount` and installs any of those not already available locally;  the default `minCount` is the square root of the largest `Count`.  Therefore, the results from `PackageSum2` and the `PackageSum2` sheet created by `writeFindFn2xls` will typically contain more information after running `installPackages` than before.

To summarize, three lines of code gave us a very powerful
summary of spline capabilities in contributed R
packages:

```{r install-and-write-options,echo=FALSE}
op <- options(width=80)
```
```{r install-and-write,results='hide'}
splineAll <- findFn('spline', maxPages = 999)
# Do not include in auto test
#installPackages(splineAll)
writeFindFn2xls(splineAll)
```
```{r install-and-write-options-undo,echo=FALSE}
options(op)
```

The resulting `splineAll.xls` file can help establish priorities for further study of the different packages and functions.  An analysis of this nature almost four years ago led the lead author to the `fda` package and its companion books, which further led to a collaboration that has produced joint presentations at three different conferences and a joint book.^[@RHG09]

## Combining search results 

The lead author of this article recently gave an invited presentation on "Fitting Nonlinear Differential Equations to Data in R"^[[Workshop on Statistical Methods for Dynamic System Models, Vancouver, 2009: `http://stat.sfu.ca/~dac5/workshop09/Spencer_Graves.html`](http://people.stat.sfu.ca/~dac5/workshop09/Spencer_Graves.html). A key part of preparing for that presentation was a search of
contributed R code, which proceeded roughly as follows:

```{R differntial-equations,results='hide'}
de <- findFn('differential equation')
des <- findFn('differential equations')
de. <- de | des
```

When this was run in 2009, the object `de` had 53 rows, while `des` had 105. If this search engine were simply searching for character strings, `de` would be *larger* than `des`; in this case, it was smaller. The last object `de.` is the union
of `de` and `des`;  **|** is an alias for `unionFindFn`.
In 2009 the `de.` object had 124 rows. That suggests that
the corresponding intersection must have had (53+105-124) = 34 rows. This can be confirmed via `nrow(de \& des)`. (**&** is an alias for `intersectFindFn`.)

To make everything in `de.` locally available, we can use `installPackages(de., minCount = 1)`.  This installed all referenced packages except `rmutil` and a dependency `Biobase`, which were not available on CRAN but are included in the `RSiteSearch` database.

Next, `writeFindFn2xls(de.)` produced a file `de..xls` in the working directory.  [(]The working directory can be identified via `getwd()`.]

The `PackageSum2` sheet of that Excel file provided a quick summary of packages with matches, sorted to put the package with the most matches first.  In this case, this first package was `deSolve`, which provides, "General solvers for initial value problems of ordinary differential equations (ODE), partial differential equations (PDE) and differential algebraic equations (DAE)".  This is clearly quite relevant to the subject.  The second package was `PKfit`, which is "A Data Analysis Tool for Pharmacokinetics".  This may be too specialized for general use.  I therefore would not want to study this first unless my primary interest here was in pharmacokinetic models.

By studying the summary page in this way, I was able to decide relatively quickly which packages I should consider first.  In making this decision, I gave more weight to packages with one or more vignettes and less weight to those where the `Date` was old, indicating that the code was not being actively maintained and updated.  I also checked the conference information to make sure I did not embarrass myself by overlooking a package authored or maintained by another invited speaker.

## Discussion 

We have found `findFn` in the `sos` package to be very quick, efficient and effective for finding things in contributed packages.  The `grepFn` function helps quickly look for functions (or help pages) with particular names. The capabilities in `unionFindFn` and `intersectFindFn` (especially via their **|*}** and **&** aliases) can be quite useful where a single search term seems inadequate;  they make it easy to combine multiple searches to produce something closer to what is desired.  An example of this was provided with searching for both ``differential equation'' and ``differential equations''.

The **PackageSum2** sheet of an Excel file produced by `writeFindFn2xls` (after also running the `installPackages` function) is quite valuable for understanding the general capabilities available for a particular topic. This could be of great value for authors to find what is already available so they don't duplicate something that already exists and so their new contributions appropriately consider the contents of other packages.

The `findFn` capability can also reduce the risk of "the researcher's nightmare" of being told after substantial work that someone else has already done it.

## Acknowledgments

The capabilities described here extend the power of the
R Site Search search engine originally maintained by Jonathan Baron. Without Prof. Baron's support, it would not have been feasible to develop the features described here. Duncan Murdoch, Marc Schwarz, Dirk Eddelbuettel, Gabor Grothendiek and anonymous referees contributed suggestions for improvement, but of course can not be blamed for any deficiencies.  The collaboration required to produce the current `sos` package was greatly facilitated by R-Forge^[@RFORGE09URL]. The `sos` package is part of the R Site Search project hosted there.  This project also includes code for a Firefox extension to simplify the process of finding information about R from within Firefox.  This Firefox extension is still being developed with the current version downloadable from [`http://addictedtor.free.fr/rsitesearch`](http://addictedtor.free.fr/rsitesearch/).

Spencer Graves 
EffectiveDefense.org 
Kansas City, Missouri
email spencer.graves@effectivedefense.org

Sundar Dorai-Raj 
Google 
Mountain View, CA
email sdorairaj@google.com

Romain François 
Independent R Consultant 
Montpellier, France
email francoisromain@free.fr
