diff --git a/.Rbuildignore b/.Rbuildignore index ed90ba8..4c27e6e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -5,5 +5,7 @@ ^docs$ ^pkgdown$ -^logo$ -^help$ \ No newline at end of file + +^setup_help\.R$ +^logo\.R$ +^ver_upd\.R$ diff --git a/DESCRIPTION b/DESCRIPTION index 65ae5b3..dd727cd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,4 +17,6 @@ Suggests: Language: en-US Config/testthat/edition: 3 Imports: + ggplot2, + MASS, stats diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 0c97efd..0000000 --- a/LICENSE +++ /dev/null @@ -1,235 +0,0 @@ -GNU AFFERO GENERAL PUBLIC LICENSE -Version 3, 19 November 2007 - -Copyright (C) 2007 Free Software Foundation, Inc. - -Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. - - Preamble - -The GNU Affero General Public License is a free, copyleft license for software and other kinds of works, specifically designed to ensure cooperation with the community in the case of network server software. - -The licenses for most software and other practical works are designed to take away your freedom to share and change the works. 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For more information on this, and how to apply and follow the GNU AGPL, see . diff --git a/NAMESPACE b/NAMESPACE index ffb6799..baa1609 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,5 +4,8 @@ export(age_calc) export(cpr_check) export(cpr_dob) export(cpr_female) -export(plot_ord_odds) +export(plot_olr) export(quantile_cut) +import(MASS) +import(ggplot2) +import(stats) diff --git a/R/cpr_tools.R b/R/cpr_tools.R index 398dc28..d0dac79 100644 --- a/R/cpr_tools.R +++ b/R/cpr_tools.R @@ -1,7 +1,7 @@ #' CPR check #' #' Checking validity of cpr number. Vectorised. -#' @param cpr cpr-numbers as ddmmyy[-.]xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column. +#' @param cpr cpr-numbers as ddmmyy"-."xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column. #' @keywords cpr #' #' @return Logical vector of cpr validity @@ -38,7 +38,7 @@ cpr_check<-function(cpr){ #' Extracting date of birth from CPR #' #' For easy calculation. -#' @param cpr cpr-numbers as ddmmyy[-.]xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column. +#' @param cpr cpr-numbers as ddmmyy"-."xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column. #' @keywords cpr #' #' @return vector of Date elements. Format yyyy-mm-dd @@ -114,7 +114,7 @@ cpr_dob<-function(cpr){ #' Determine female sex from CPR #' #' Just checking if last number of a string is equal or not. -#' @param cpr cpr-numbers as ddmmyy[-.]xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column. +#' @param cpr cpr-numbers as ddmmyy"-."xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column. #' @keywords cpr #' #' @return Logical vector diff --git a/R/plot_olr.R b/R/plot_olr.R index d69f973..d508428 100644 --- a/R/plot_olr.R +++ b/R/plot_olr.R @@ -1,3 +1,5 @@ +utils::globalVariables(c("or","ord","lo","up")) + #' Forrest plot from ordinal logistic regression. #' #' Heavily inspired by https://www.r-bloggers.com/plotting-odds-ratios-aka-a-forrestplot-with-ggplot2/ @@ -14,29 +16,30 @@ #' @return gg object #' @keywords forest plot #' +#' @import ggplot2 stats MASS +#' #' @export #' #' @examples -#' +#' iris$ord<-factor(sample(1:3,size=nrow(iris),replace=TRUE),ordered=TRUE) +#' lm <- MASS::polr(ord~., data=iris, Hess=TRUE, method="logistic") +#' plot_olr(lm, input="model") -plot_ord_odds<-function(x, title = NULL,dec=3,lbls=NULL,hori="OR (95 % CI)",vert="Variables",short=FALSE,input=c("model","df")){ - - require(ggplot2) +plot_olr<-function(x, title = NULL, dec=3, lbls=NULL, hori="OR (95 % CI)", vert="Variables", short=FALSE, input=c("model","df")){ if (input=="model"){ - odds<-data.frame(cbind(exp(coef(x)), exp(confint(x)))) + odds <- data.frame(cbind(exp(coef(x)), exp(confint(x)))) } if (input=="df"){ - odds<-x + odds <- x } names(odds)<-c("or", "lo", "up") - rodds<-round(odds,digits = dec) + rodds<-round(odds, digits = dec) if (!is.null(lbls)){ odds$vars<-paste0(lbls," \n",paste0(rodds$or," [",rodds$lo,":",rodds$up,"]")) - } - else { + } else { odds$vars<-paste0(row.names(odds)," \n",paste0(rodds$or," [",rodds$lo,":",rodds$up,"]")) } @@ -45,16 +48,16 @@ plot_ord_odds<-function(x, title = NULL,dec=3,lbls=NULL,hori="OR (95 % CI)",vert if (short==TRUE){ ticks<-ticks[seq(1, length(ticks), 2)] } - else {ticks<-ticks} odds$ord<-c(nrow(odds):1) - ggplot(odds, aes(y= or, x = reorder(vars,ord))) + - geom_point() + - geom_errorbar(aes(ymin=lo, ymax=up), width=.2) + - scale_y_log10(breaks=ticks, labels = ticks) + - geom_hline(yintercept = 1, linetype=2) + - coord_flip() + - labs(title = title, x = vert, y = hori) + - theme_bw() + odds|> + ggplot2::ggplot(mapping = ggplot2::aes(y = or, x = reorder(vars,ord))) + + ggplot2::geom_point() + + ggplot2::geom_errorbar(mapping = ggplot2::aes(ymin=lo, ymax=up), width=.2) + + ggplot2::scale_y_log10(breaks=ticks, labels = ticks) + + ggplot2::geom_hline(yintercept = 1, linetype=2) + + ggplot2::coord_flip() + + ggplot2::labs(title = title, x = vert, y = hori) + + ggplot2::theme_bw(14) } diff --git a/R/quantile_cut.R b/R/quantile_cut.R index 0ca66d9..32b96a1 100644 --- a/R/quantile_cut.R +++ b/R/quantile_cut.R @@ -8,10 +8,10 @@ #' @param na.rm Remove NA's. Default is TRUE. #' @param group.names Names of groups to split to. Default is NULL, giving intervals as names. #' @param ordered.f Set resulting vector as ordered. Default is FALSE. -#' @param detail.list +#' @param detail.list flag to include details or not #' @param inc.outs Flag to include min(x) and max(x) as boarders in case of y!=NULL. #' -#' @return +#' @return vector or list with vector and details (length 2) #' #' @keywords quantile #' @export @@ -20,7 +20,7 @@ #' x <- 1:450 #' y <- 6:750 #' summary(quantile_cut(aa,groups=4,detail.list=FALSE)) ## Cuts quartiles -quantile_cut<-function (x, groups, y=NULL, na.rm = TRUE, group.names = NULL, ordered.f = FALSE, inc.outs=FALSE,detail.list=TRUE){ +quantile_cut<-function (x, groups, y=NULL, na.rm = TRUE, group.names = NULL, ordered.f = FALSE, inc.outs=FALSE, detail.list=FALSE){ if (!is.null(y)){ q<-quantile(y, probs = seq(0, 1, 1/groups), na.rm = na.rm, names = TRUE, type = 7) if (inc.outs){ # Setting cut boardes to include outliers in x compared to y. diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index d546fbe..fa70867 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,5 +2,5 @@ pandoc: 2.19.2 pkgdown: 2.0.6 pkgdown_sha: ~ articles: {} -last_built: 2022-09-23T09:18Z +last_built: 2022-09-23T10:04Z diff --git a/docs/reference/cpr_check.html b/docs/reference/cpr_check.html index 18c916e..d269183 100644 --- a/docs/reference/cpr_check.html +++ b/docs/reference/cpr_check.html @@ -48,7 +48,7 @@

Arguments

cpr
-

cpr-numbers as ddmmyy-.xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column.

+

cpr-numbers as ddmmyy"-."xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column.

diff --git a/docs/reference/cpr_dob.html b/docs/reference/cpr_dob.html index a9fea9c..3954559 100644 --- a/docs/reference/cpr_dob.html +++ b/docs/reference/cpr_dob.html @@ -48,7 +48,7 @@

Arguments

cpr
-

cpr-numbers as ddmmyy-.xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column.

+

cpr-numbers as ddmmyy"-."xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column.

diff --git a/docs/reference/cpr_female.html b/docs/reference/cpr_female.html index 8c85fcd..f15a551 100644 --- a/docs/reference/cpr_female.html +++ b/docs/reference/cpr_female.html @@ -48,7 +48,7 @@

Arguments

cpr
-

cpr-numbers as ddmmyy-.xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column.

+

cpr-numbers as ddmmyy"-."xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column.

diff --git a/docs/reference/index.html b/docs/reference/index.html index 7f91f88..2f7fc56 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -67,7 +67,7 @@
Determine female sex from CPR
- plot_ord_odds() + plot_olr()
Forrest plot from ordinal logistic regression.
diff --git a/docs/reference/plot_olr-1.png b/docs/reference/plot_olr-1.png new file mode 100644 index 0000000..3006139 Binary files /dev/null and b/docs/reference/plot_olr-1.png differ diff --git a/docs/reference/plot_olr.html b/docs/reference/plot_olr.html new file mode 100644 index 0000000..e9dbab9 --- /dev/null +++ b/docs/reference/plot_olr.html @@ -0,0 +1,126 @@ + +Forrest plot from ordinal logistic regression. — plot_olr • stRoke + Skip to contents + + +
+
+
+

Forrest plot from ordinal logistic regression.

+ +
plot_olr.Rd
+
+ +
+

Heavily inspired by https://www.r-bloggers.com/plotting-odds-ratios-aka-a-forrestplot-with-ggplot2/

+
+ +
+

Usage

+ 
plot_olr(
+  x,
+  title = NULL,
+  dec = 3,
+  lbls = NULL,
+  hori = "OR (95 % CI)",
+  vert = "Variables",
+  short = FALSE,
+  input = c("model", "df")
+)
+
+ +
+

Arguments

+
x
+

input data.

+ + +
title
+

plot title

+ + +
dec
+

decimals for labels

+ + +
lbls
+

labels for variable names. Carefull, as the right order is not checked automatically!

+ + +
hori
+

labels the horizontal axis (this i the y axis as the plot is rotated)

+ + +
vert
+

labels the horizontal axis (this i the x axis as the plot is rotated)

+ + +
short
+

flag to half number of ticks on horizontal axis.

+ + +
input
+

can be either "model", which is a olr model (polr()), or "df", which is a dataframe whith three columns for OR, lower CI and upper CI.

+ +
+
+

Value

+ + +

gg object

+
+ +
+

Examples

+ 
iris$ord<-factor(sample(1:3,size=nrow(iris),replace=TRUE),ordered=TRUE)
+lm <- MASS::polr(ord~., data=iris, Hess=TRUE, method="logistic")
+plot_olr(lm, input="model")
+#> Waiting for profiling to be done...
+
+
+
+
+ + +
+

Developed by Andreas Gammelgaard Damsbo.

+
+ +
+

Site built with pkgdown 2.0.6.

+
+ +
+ + + + + + + diff --git a/docs/reference/quantile_cut.html b/docs/reference/quantile_cut.html index 3297e71..6ab168e 100644 --- a/docs/reference/quantile_cut.html +++ b/docs/reference/quantile_cut.html @@ -50,7 +50,7 @@ group.names = NULL, ordered.f = FALSE, inc.outs = FALSE, - detail.list = TRUE + detail.list = FALSE )
@@ -85,9 +85,15 @@
detail.list
-
+

flag to include details or not

+
+

Value

+ + +

vector or list with vector and details (length 2)

+

Examples

@@ -95,7 +101,7 @@ x <- 1:450 y <- 6:750 summary(quantile_cut(aa,groups=4,detail.list=FALSE)) ## Cuts quartiles -#> [1,250] (250,500] (500,752] (752,1e+03] +#> [1,238] (238,496] (496,745] (745,1e+03] #> 500 500 501 499
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Vector data frame column.","code":""},{"path":"/reference/cpr_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"CPR check — cpr_check","text":"Logical vector cpr validity","code":""},{"path":"/reference/cpr_check.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"CPR check — cpr_check","text":"","code":"fsd<-c(\"2310450637\", \"010115-4000\", \"0101896000\",\"010189-3000\",\"300450-1030\",\"010150-4021\") cpr_check(fsd) #> OBS: according to new description, not all valid CPR numbers apply to this modulus 11 rule. #> Please refer to: https://cpr.dk/media/12066/personnummeret-i-cpr.pdf #> [1] TRUE FALSE FALSE FALSE FALSE FALSE all(cpr_check(fsd)) #> OBS: according to new description, not all valid CPR numbers apply to this modulus 11 rule. #> Please refer to: https://cpr.dk/media/12066/personnummeret-i-cpr.pdf #> [1] FALSE"},{"path":"/reference/cpr_dob.html","id":null,"dir":"Reference","previous_headings":"","what":"Extracting date of birth from CPR — cpr_dob","title":"Extracting date of birth from CPR — cpr_dob","text":"easy calculation.","code":""},{"path":"/reference/cpr_dob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extracting date of birth from CPR — cpr_dob","text":"","code":"cpr_dob(cpr)"},{"path":"/reference/cpr_dob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extracting date of birth from CPR — cpr_dob","text":"cpr cpr-numbers ddmmyy\"-.\"xxxx ddmmyyxxxx. Also mixed formatting. Vector data frame column.","code":""},{"path":"/reference/cpr_dob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extracting date of birth from CPR — cpr_dob","text":"vector Date elements. Format yyyy-mm-dd","code":""},{"path":"/reference/cpr_dob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extracting date of birth from CPR — cpr_dob","text":"","code":"cpr_dob(\"231045-0637\") #> [1] \"1945-10-23\" fsd<-c(\"010190-2000\", \"010115-4000\", \"0101896000\",\"010189-3000\",\"300450-1030\",\"010150-4021\") cpr_dob(fsd) #> [1] \"1990-01-01\" \"2015-01-01\" \"1889-01-01\" \"1989-01-01\" \"1950-04-30\" #> [6] \"1950-01-01\""},{"path":"/reference/cpr_female.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine female sex from CPR — cpr_female","title":"Determine female sex from CPR — cpr_female","text":"Just checking last number string equal .","code":""},{"path":"/reference/cpr_female.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine female sex from CPR — cpr_female","text":"","code":"cpr_female(cpr)"},{"path":"/reference/cpr_female.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine female sex from CPR — cpr_female","text":"cpr cpr-numbers ddmmyy\"-.\"xxxx ddmmyyxxxx. Also mixed formatting. Vector data frame column.","code":""},{"path":"/reference/cpr_female.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine female sex from CPR — cpr_female","text":"Logical vector","code":""},{"path":"/reference/cpr_female.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine female sex from CPR — cpr_female","text":"","code":"cpr_female(\"231045-0637\") #> [1] TRUE"},{"path":"/reference/plot_olr.html","id":null,"dir":"Reference","previous_headings":"","what":"Forrest plot from ordinal logistic regression. — plot_olr","title":"Forrest plot from ordinal logistic regression. — plot_olr","text":"Heavily inspired https://www.r-bloggers.com/plotting-odds-ratios-aka--forrestplot--ggplot2/","code":""},{"path":"/reference/plot_olr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Forrest plot from ordinal logistic regression. — plot_olr","text":"","code":"plot_olr( x, title = NULL, dec = 3, lbls = NULL, hori = \"OR (95 % CI)\", vert = \"Variables\", short = FALSE, input = c(\"model\", \"df\") )"},{"path":"/reference/plot_olr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Forrest plot from ordinal logistic regression. — plot_olr","text":"x input data. title plot title dec decimals labels lbls labels variable names. Carefull, right order checked automatically! hori labels horizontal axis (y axis plot rotated) vert labels horizontal axis (x axis plot rotated) short flag half number ticks horizontal axis. input can either \"model\", olr model (polr()), \"df\", dataframe whith three columns , lower CI upper CI.","code":""},{"path":"/reference/plot_olr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Forrest plot from ordinal logistic regression. — plot_olr","text":"gg object","code":""},{"path":"/reference/plot_olr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Forrest plot from ordinal logistic regression. — plot_olr","text":"","code":"iris$ord<-factor(sample(1:3,size=nrow(iris),replace=TRUE),ordered=TRUE) lm <- MASS::polr(ord~., data=iris, Hess=TRUE, method=\"logistic\") plot_olr(lm, input=\"model\") #> Waiting for profiling to be done..."},{"path":"/reference/plot_ord_odds.html","id":null,"dir":"Reference","previous_headings":"","what":"Forrest plot from ordinal logistic regression. — plot_ord_odds","title":"Forrest plot from ordinal logistic regression. — plot_ord_odds","text":"Heavily inspired https://www.r-bloggers.com/plotting-odds-ratios-aka--forrestplot--ggplot2/","code":""},{"path":"/reference/plot_ord_odds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Forrest plot from ordinal logistic regression. — plot_ord_odds","text":"","code":"plot_ord_odds( x, title = NULL, dec = 3, lbls = NULL, hori = \"OR (95 % CI)\", vert = \"Variables\", short = FALSE, input = c(\"model\", \"df\") )"},{"path":"/reference/plot_ord_odds.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Forrest plot from ordinal logistic regression. — plot_ord_odds","text":"x input data. title plot title dec decimals labels lbls labels variable names. Carefull, right order checked automatically! hori labels horizontal axis (y axis plot rotated) vert labels horizontal axis (x axis plot rotated) short flag half number ticks horizontal axis. input can either \"model\", olr model (polr()), \"df\", dataframe whith three columns , lower CI upper CI.","code":""},{"path":"/reference/plot_ord_odds.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Forrest plot from ordinal logistic regression. — plot_ord_odds","text":"gg object","code":""},{"path":"/reference/quantile_cut.html","id":null,"dir":"Reference","previous_headings":"","what":"Easy function for splitting numeric variable in quantiles — quantile_cut","title":"Easy function for splitting numeric variable in quantiles — quantile_cut","text":"Using base/stats functions cut() quantile().","code":""},{"path":"/reference/quantile_cut.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Easy function for splitting numeric variable in quantiles — quantile_cut","text":"","code":"quantile_cut( x, groups, y = NULL, na.rm = TRUE, group.names = NULL, ordered.f = FALSE, inc.outs = FALSE, detail.list = FALSE )"},{"path":"/reference/quantile_cut.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Easy function for splitting numeric variable in quantiles — quantile_cut","text":"x Variable cut. groups Number groups. y alternative vector draw quantile cuts . Limits within x. Default NULL. na.rm Remove NA's. Default TRUE. group.names Names groups split . Default NULL, giving intervals names. ordered.f Set resulting vector ordered. Default FALSE. inc.outs Flag include min(x) max(x) boarders case y!=NULL. detail.list flag include details ","code":""},{"path":"/reference/quantile_cut.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Easy function for splitting numeric variable in quantiles — quantile_cut","text":"vector list vector details (length 2)","code":""},{"path":"/reference/quantile_cut.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Easy function for splitting numeric variable in quantiles — quantile_cut","text":"","code":"aa <- as.numeric(sample(1:1000,2000,replace = TRUE)) x <- 1:450 y <- 6:750 summary(quantile_cut(aa,groups=4,detail.list=FALSE)) ## Cuts quartiles #> [1,238] (238,496] (496,745] (745,1e+03] #> 500 500 501 499"},{"path":"/reference/stRoke-package.html","id":null,"dir":"Reference","previous_headings":"","what":"stRoke: Tools for work in clinical stroke research — stRoke-package","title":"stRoke: Tools for work in clinical stroke research — stRoke-package","text":"R functions convenient data management danalysis health research. package mainly collected personal use. start package migrates functions agdamsbo/daDoctoR-package.","code":""},{"path":"/reference/stRoke-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"stRoke: Tools for work in clinical stroke research — stRoke-package","text":"Maintainer: Andreas Gammelgaard Damsbo agdamsbo@clin.au.dk (ORCID)","code":""}] diff --git a/docs/sitemap.xml b/docs/sitemap.xml index c8bc185..a11e470 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -27,6 +27,9 @@ /reference/index.html + + /reference/plot_olr.html + /reference/plot_ord_odds.html diff --git a/man/cpr_check.Rd b/man/cpr_check.Rd index 6f06109..47095c5 100644 --- a/man/cpr_check.Rd +++ b/man/cpr_check.Rd @@ -7,7 +7,7 @@ cpr_check(cpr) } \arguments{ -\item{cpr}{cpr-numbers as ddmmyy\link{-.}xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column.} +\item{cpr}{cpr-numbers as ddmmyy"-."xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column.} } \value{ Logical vector of cpr validity diff --git a/man/cpr_dob.Rd b/man/cpr_dob.Rd index 55dad78..bb83c45 100644 --- a/man/cpr_dob.Rd +++ b/man/cpr_dob.Rd @@ -7,7 +7,7 @@ cpr_dob(cpr) } \arguments{ -\item{cpr}{cpr-numbers as ddmmyy\link{-.}xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column.} +\item{cpr}{cpr-numbers as ddmmyy"-."xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column.} } \value{ vector of Date elements. Format yyyy-mm-dd diff --git a/man/cpr_female.Rd b/man/cpr_female.Rd index 38d52ad..7cbf64f 100644 --- a/man/cpr_female.Rd +++ b/man/cpr_female.Rd @@ -7,7 +7,7 @@ cpr_female(cpr) } \arguments{ -\item{cpr}{cpr-numbers as ddmmyy\link{-.}xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column.} +\item{cpr}{cpr-numbers as ddmmyy"-."xxxx or ddmmyyxxxx. Also mixed formatting. Vector or data frame column.} } \value{ Logical vector diff --git a/man/plot_ord_odds.Rd b/man/plot_olr.Rd similarity index 82% rename from man/plot_ord_odds.Rd rename to man/plot_olr.Rd index 9d86c08..b87aec5 100644 --- a/man/plot_ord_odds.Rd +++ b/man/plot_olr.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/plot_olr.R -\name{plot_ord_odds} -\alias{plot_ord_odds} +\name{plot_olr} +\alias{plot_olr} \title{Forrest plot from ordinal logistic regression.} \usage{ -plot_ord_odds( +plot_olr( x, title = NULL, dec = 3, @@ -38,5 +38,10 @@ gg object \description{ Heavily inspired by https://www.r-bloggers.com/plotting-odds-ratios-aka-a-forrestplot-with-ggplot2/ } +\examples{ +iris$ord<-factor(sample(1:3,size=nrow(iris),replace=TRUE),ordered=TRUE) +lm <- MASS::polr(ord~., data=iris, Hess=TRUE, method="logistic") +plot_olr(lm, input="model") +} \keyword{forest} \keyword{plot} diff --git a/man/quantile_cut.Rd b/man/quantile_cut.Rd index 54431f0..dd3e2ca 100644 --- a/man/quantile_cut.Rd +++ b/man/quantile_cut.Rd @@ -12,7 +12,7 @@ quantile_cut( group.names = NULL, ordered.f = FALSE, inc.outs = FALSE, - detail.list = TRUE + detail.list = FALSE ) } \arguments{ @@ -30,7 +30,10 @@ quantile_cut( \item{inc.outs}{Flag to include min(x) and max(x) as boarders in case of y!=NULL.} -\item{detail.list}{} +\item{detail.list}{flag to include details or not} +} +\value{ +vector or list with vector and details (length 2) } \description{ Using base/stats functions cut() and quantile().