diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 33835b4..f5557e6 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -47,7 +47,7 @@ jobs: -m '📄 Render README.Rmd' || echo "No changes to commit" - name: Docs run: | - Rscript -e "devtools::build_site()" + Rscript -e "pkgdown::build_reference; devtools::build_site()" git add docs git commit \ --author="github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>" \ diff --git a/NAMESPACE b/NAMESPACE index be0b72b..588b83d 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -2,9 +2,11 @@ export("%>%") export(.data) +export(close_enough) export(format_number) export(inline_hook) export(is_nearly_whole) +export(is_nondesc) export(load_deps) export(paste_oxford_list) export(read_dist) diff --git a/NEWS.md b/NEWS.md index 5f807c2..a46fc74 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,10 +2,14 @@ - Added a `NEWS.md` file to track changes to the package. - Major new functions: - - `read_dist()` - - `read_tax()` - - `inline_hook()` - - `paste_oxford_list()` - - `format_number()` + - `read_dist()` (#10, @NLesniak) + - `read_tax()` (#22, @NLesniak) + - `set_knitr_opts()` (#21, @pschloss, @kelly-sovacool) + - `inline_hook()` (#21, @pschloss, @kelly-sovacool) + - `paste_oxford_list()` (#21, @pschloss, @kelly-sovacool) + - `format_number()` (#24, @pschloss, @kelly-sovacool) + - `is_nearly_whole()` (#24, @pschloss, @kelly-sovacool) + - `close_enough()` (#26, @kelly-sovacool) + - `is_nondesc()` (#28, @kelly-sovacool) - New vignettes: - `introduction` diff --git a/R/utils.R b/R/utils.R index eae7e3a..7c2cff0 100644 --- a/R/utils.R +++ b/R/utils.R @@ -35,6 +35,31 @@ close_enough <- function(x, y, tol = 10^-3) { all(dplyr::near(x, y, tol = tol)) } +#' Check whether all elements given are sorted in non-descending order +#' +#' @param ... anything! +#' +#' @return `TRUE` if the elements are sorted in non-descending order, otherwise `FALSE` +#' @export +#' @author Kelly Sovacool \email{sovacool@@umich.edu} +#' +#' @examples +#' +#' is_nondesc(1, 2, 3) +#' is_nondesc(c(1, 2), 3) +#' is_nondesc(6, 4, 1) +#' is_nondesc("a", "b", "c") +#' is_nondesc(c("z", "y")) +is_nondesc <- function(...) { + things <- c(...) + if (length(things) < 1) { + warning("Zero elements were given to `is_nondesc()`") + } + first <- things[1] + last <- things[length(things)] + !is.unsorted(things) & first <= last +} + #' Install & load packages #' @param ... package names to install & load #' @export diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index ef934f9..df8d83a 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -136,9 +136,9 @@

Pull request process

diff --git a/docs/articles/introduction_files/header-attrs-2.7/header-attrs.js b/docs/articles/introduction_files/header-attrs-2.10/header-attrs.js similarity index 100% rename from docs/articles/introduction_files/header-attrs-2.7/header-attrs.js rename to docs/articles/introduction_files/header-attrs-2.10/header-attrs.js diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 23817c1..31f52e9 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 1.6.1 pkgdown_sha: ~ articles: introduction: introduction.html -last_built: 2021-10-25T18:09Z +last_built: 2021-11-08T17:31Z diff --git a/docs/reference/DistCalc-package.html b/docs/reference/DistCalc-package.html deleted file mode 100644 index d607044..0000000 --- a/docs/reference/DistCalc-package.html +++ /dev/null @@ -1,170 +0,0 @@ - - - - - - - - -What the package does (short line) -~~ package title ~~ — DistCalc-package • mothuR - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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What the package does (short line) -~~ package title ~~

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More about what it does (maybe more than one line) -~~ A concise (1-5 lines) description of the package ~~

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Package:DistCalc
Type:Package
Version:1.0
Date:2012-12-14
License:What license is it under?
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~~ An overview of how to use the package, including the most important functions ~~

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References

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~~ Literature or other references for background information ~~

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~~ Optional links to other man pages, e.g. ~~ -~~ <pkg> ~~

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Examples

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Plot the pcoa.axes output from mothur. Can accept a design file for groups.

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-Axis=TRUE, Tick.marks=TRUE, Label.tick.marks=TRUE, X.ticklabs=NULL,
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Arguments

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The .pcoa.axes file from mothur's pcoa function.

design

The .design file for the groups you which to color the points by. defaults to no design file.

ax1, ax2, ax3

The axes you wish to plot. Defaults to the 3 most relevant according to mothur.

Lab1, Lab2, Lab3

titles for the 1st/x, 2nd/y and 3rd/z axis.

Pch

plotting "character", i.e. symbol to use. Defaults to 19 (solid circles)

Main

an overall title for the plot.

Sub

sub-title.

Scale.y

scale of y axis related to x- and z axis.

Angle

angle between x and y axis (Attention: result depends on scaling).

Axis

a logical value indicating whether axes should be drawn on the plot.

Tick.marks

a logical value indicating whether tick marks should be drawn on the plot (only if axis = TRUE).

Label.tick.marks

a logical value indicating whether tick marks should be labeled on the plot (only if axis = TRUE and tick.marks = TRUE).

X.ticklabs, Y.ticklabs, Z.ticklabs

vector of tick mark labels.

Y.margin.add

add additional space between tick mark labels and axis label of the y axis.

Grid

a logical value indicating whether a grid should be drawn on the plot.

Box

a logical value indicating whether a box should be drawn around the plot.

Lab

a numerical vector of the form c(x, y, len). The values of x and y give the (approximate) number of tickmarks on the x and y axes.

Lab.z

the same as lab, but for z axis.

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character indicating the type of plot: "p" for points, "l" for lines, "h" for vertical lines to x-y-plane, etc.

LX, LY

the x and y co-ordinates to be used to position the legend. They can be specified by keyword or in any way which is accepted by xy.coords.

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diff --git a/docs/reference/RarePlot.html b/docs/reference/RarePlot.html
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The .group.rarefaction file which you wish to plot. Only works for the output of rarefaction.single from mothur.
groups
The specific groups within x which you wish to plot, in list form c("Examplegroup1", "Examplegroup2'). either the names ie c("m24626d36", "Day3") or the number the group falls in the list of all groups. ie c(1,4,7) (the 1st 4th and 7th group).
ylab
Title for y axis. Defaults to "Number of Different OTUs"
xlab
Title for x axis. Defaults to "Number of Tags Sampled"
pch
Character string or vector of 1-characters or integers for plotting characters, see points. The first character is the plotting-character for the first plot, the second for the second, etc. The default is nothing. Change to NULL if you want the digits 1:9 then the lowercase and uppercase letters
xlim
Range of x axis
ylim
Range of y axis
error
If error = TRUE then plot the Lower and Upperbounds for each group.
delNum
The number of excess characters before each name generally X0.03. or something similiar. Set delNum to the number you which to delete.

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RarePlot("example.groups.shared",c("Examplegroup1","Examplegroup2","ExampleGroup3"))
#> Error in RarePlot("example.groups.shared", c("Examplegroup1", "Examplegroup2",     "ExampleGroup3")): could not find function "RarePlot"
RarePlot("example2.groups.shared",c(14,11,30,"ExampleGroup4"),error=TRUE,pch=NULL)
#> Error in RarePlot("example2.groups.shared", c(14, 11, 30, "ExampleGroup4"),     error = TRUE, pch = NULL): could not find function "RarePlot"

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diff --git a/docs/reference/between.dist.html b/docs/reference/between.dist.html
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between.dist(dist, design, groups, subgroups=FALSE)

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Either a file containing a phylip formatted distance matrix with ThetaYC, UniFrac, or some other distance metric between samples or a variable representing the distance matrix that was imported using the read.dist function.
design
a '.design' file, i.e. a file containing two columns separated by a tab, with the sample names in the left column and the name of their group in the right column.
groups
a vector of strings containing the names of the groups to be analyzed.  There is no limit to the number of groups that can be analyzed.  The parameter 'all' can be used to analyze the relationships between all groups.
subgroups
a logical value determing whether to use the group column or the subgroup column in the analysis (FALSE is groups TRUE is subgroups). (which subgroups to use are determined by the groups vector.)

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If the dist paramater is a phylip file, then the function will start by using the read.dist function to import the distance matrix.  The function will then parse distance matrix into smaller matrices each containing the columns from one group of interest and the rows of another.  The distances in each of the smaller matrices are then used to calculated the minimum, maximum, median, mean, and standard deviation of the distances between each group.  The statistics are printed to the screen.
	
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within.dist for calculating distances within groups
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Examples

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#Using a phylip file as input
-#between.dist('~/Desktop/germfree.sq.dist','~/Desktop/germfree.design', c('early','late'))
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-#Using a distance matrix that has already been read in using read.dist
-#between.dist(gf.sq.dist,'~/Desktop/germfree.design', c('early','late'))
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-#between.dist('~/Desktop/germfree.sq.dist','~/Desktop/germfree.design', 'all')
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-#btwn.list<-between.dist('~/Desktop/germfree.sq.dist','~/Desktop/germfree.design', c('early','late'))
-#plot.dists(btwn.list)
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-## The function is currently defined as
-function (dist, design, groups)
-{
-    if (length(groups) == 1) {
-        options(warn = (-1))
-        if (groups == "all") {
-            if (length(design) == 1) {
-                dsn <- read.table(design)
-            }
-            if (length(design) > 1) {
-                dsn <- design
-            }
-            groups <- as.vector(unique(dsn[, 2]))
-            options(warn = (0))
-        }
-    }
-    one.between <- function(dist, design, group1, group2) {
-        if (typeof(dist) == "character") {
-            dist <- read.dist(dist)
-        }
-        if (length(design) == 1) {
-            design <- read.design(design)
-        }
-        get.dists <- function(dist, Detailsdesign, group1, group2) {
-            group1 <<- group1
-            group2 <<- group2
-            get.grp1 <- function(d, g) {
-                c1 <- 1
-                grp1 <- c()
-                for (i in 1:nrow(d)) {
-                  if (d[i, 2] == g) {
-                    grp1[c1] <- d[i, 1]
-                    c1 <- c1 + 1
-                  }
-                }
-                invisible(grp1)
-            }
-            get.grp2 <- function(d, g) {
-                c2 <- 1
-                grp2 <- c()
-                for (i in 1:nrow(d)) {
-                  if (d[i, 2] == g) {
-                    grp2[c2] <- d[i, 1]
-                    c2 <- c2 + 1
-                  }
-                }
-                invisible(grp2)
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-            grp1 <- get.grp1(design, group1)
-            grp2 <- get.grp2(design, group2)
-            get.rows <- function(dist, grp) {
-                rows <- dist[grp[1], ]
-                for (i in 2:length(grp)) {
-                  rows <- rbind(rows, dist[grp[i], ])
-                }
-                invisible(rows)
-            }
-            rows <- get.rows(dist, grp1)
-            get.rows <- function(dist, grp) {
-                matrix <- dist[, grp[1]]
-                for (i in 2:length(grp)) {
-                  matrix <- cbind(matrix, dist[, grp[i]])
-                }
-                invisible(matrix)
-            }
-            matrix <- get.rows(rows, grp2)
-            vect <- as.vector(matrix)
-            invisible(vect)
-        }
-        dists <- get.dists(dist, design, group1, group2)
-        cat(sprintf("Stats for distances between %s and %s",
-            group1, group2), "\n", sprintf("Minimum: %f", min(dists)),
-            "\n", sprintf("Maximum: %f", max(dists)), "\n", sprintf("Median: %f",
-                median(dists)), "\n", sprintf("Mean: %f", mean(dists)),
-            "\n", sprintf("Std. Dev.: %f", sd(dists)), "\n",
-            "\n", sep = "")
-        return(dists)
-    }
-    dist.vect <- c()
-    c <- 1
-    dist.list <- vector(mode = "list", length = ((length(groups)^2 -
-        length(groups))/2))
-    list.names <- c()
-    for (i in 1:(length(groups) - 1)) {
-        for (j in (i + 1):length(groups)) {
-            list.names[c] <- paste(groups[i], "vs", groups[j])
-            dist.list[[c]] <- one.between(dist, design, groups[i],
-                groups[j])
-            c <- c + 1
-        }
-    }
-    names(dist.list) <- list.names
-    invisible(dist.list)
-  }
#> function (dist, design, groups) 
-#> {
-#>     if (length(groups) == 1) {
-#>         options(warn = (-1))
-#>         if (groups == "all") {
-#>             if (length(design) == 1) {
-#>                 dsn <- read.table(design)
-#>             }
-#>             if (length(design) > 1) {
-#>                 dsn <- design
-#>             }
-#>             groups <- as.vector(unique(dsn[, 2]))
-#>             options(warn = (0))
-#>         }
-#>     }
-#>     one.between <- function(dist, design, group1, group2) {
-#>         if (typeof(dist) == "character") {
-#>             dist <- read.dist(dist)
-#>         }
-#>         if (length(design) == 1) {
-#>             design <- read.design(design)
-#>         }
-#>         get.dists <- function(dist, Detailsdesign, group1, group2) {
-#>             group1 <<- group1
-#>             group2 <<- group2
-#>             get.grp1 <- function(d, g) {
-#>                 c1 <- 1
-#>                 grp1 <- c()
-#>                 for (i in 1:nrow(d)) {
-#>                   if (d[i, 2] == g) {
-#>                     grp1[c1] <- d[i, 1]
-#>                     c1 <- c1 + 1
-#>                   }
-#>                 }
-#>                 invisible(grp1)
-#>             }
-#>             get.grp2 <- function(d, g) {
-#>                 c2 <- 1
-#>                 grp2 <- c()
-#>                 for (i in 1:nrow(d)) {
-#>                   if (d[i, 2] == g) {
-#>                     grp2[c2] <- d[i, 1]
-#>                     c2 <- c2 + 1
-#>                   }
-#>                 }
-#>                 invisible(grp2)
-#>             }
-#>             grp1 <- get.grp1(design, group1)
-#>             grp2 <- get.grp2(design, group2)
-#>             get.rows <- function(dist, grp) {
-#>                 rows <- dist[grp[1], ]
-#>                 for (i in 2:length(grp)) {
-#>                   rows <- rbind(rows, dist[grp[i], ])
-#>                 }
-#>                 invisible(rows)
-#>             }
-#>             rows <- get.rows(dist, grp1)
-#>             get.rows <- function(dist, grp) {
-#>                 matrix <- dist[, grp[1]]
-#>                 for (i in 2:length(grp)) {
-#>                   matrix <- cbind(matrix, dist[, grp[i]])
-#>                 }
-#>                 invisible(matrix)
-#>             }
-#>             matrix <- get.rows(rows, grp2)
-#>             vect <- as.vector(matrix)
-#>             invisible(vect)
-#>         }
-#>         dists <- get.dists(dist, design, group1, group2)
-#>         cat(sprintf("Stats for distances between %s and %s", 
-#>             group1, group2), "\n", sprintf("Minimum: %f", min(dists)), 
-#>             "\n", sprintf("Maximum: %f", max(dists)), "\n", sprintf("Median: %f", 
-#>                 median(dists)), "\n", sprintf("Mean: %f", mean(dists)), 
-#>             "\n", sprintf("Std. Dev.: %f", sd(dists)), "\n", 
-#>             "\n", sep = "")
-#>         return(dists)
-#>     }
-#>     dist.vect <- c()
-#>     c <- 1
-#>     dist.list <- vector(mode = "list", length = ((length(groups)^2 - 
-#>         length(groups))/2))
-#>     list.names <- c()
-#>     for (i in 1:(length(groups) - 1)) {
-#>         for (j in (i + 1):length(groups)) {
-#>             list.names[c] <- paste(groups[i], "vs", groups[j])
-#>             dist.list[[c]] <- one.between(dist, design, groups[i], 
-#>                 groups[j])
-#>             c <- c + 1
-#>         }
-#>     }
-#>     names(dist.list) <- list.names
-#>     invisible(dist.list)
-#>   }
-#> <environment: 0x7fad4cf69e48>

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diff --git a/docs/reference/mothuR.html b/docs/reference/close_enough.html
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-mothuR: one-line description goes here — mothuR • mothuR
+Check whether two numeric vectors are close enough for gov't work. — close_enough • schtools
 
 
 
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         0.0.1.9000
       
     
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@@ -118,21 +118,51 @@
 

   

     

-    
mothuR: one-line description goes here

+    
Check whether two numeric vectors are close enough for gov't work.

     
-    
+    
     

 
     

-    
longer description (paragraph) goes here

+    
This is like dplyr::near() except with much less precision.

     

 
-
-
-    
brief overview of functions

-
-    
NA

-
+    
close_enough(x, y, tol = 10^-3)

+
+    
Arguments

+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
x
a numeric vector
y
another numeric vector
tol
tolerance (default: 10^-3.)

+
+    
Value

+
+    
TRUE if all numbers are near enough within the tolerance, otherwise FALSE

+    
Author

+
+    
Kelly Sovacool sovacool@umich.edu

+
+    
Examples

+    

+close_enough(0.0004, 0)
+#> [1] TRUE
+close_enough(0.8887, 0.8884)
+#> [1] TRUE
+close_enough(1, 2)
+#> [1] FALSE
+
+