From cf80ff9f6a5bb12bdf63f964ded2bcf8a7c72725 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Fri, 8 Feb 2019 10:45:55 +0100 Subject: [PATCH] Change names of the *.q functions to *_q --- NAMESPACE | 12 +++---- R/entropy.R | 16 ++++----- R/generalized_log.R | 4 +-- index.Rmd | 61 +++++++++++++++++++++++----------- index.html | 68 ++++++++++++++++++++------------------ man/{exp.q.Rd => exp_q.Rd} | 6 ++-- man/{log.q.Rd => log_q.Rd} | 6 ++-- 7 files changed, 100 insertions(+), 73 deletions(-) rename man/{exp.q.Rd => exp_q.Rd} (80%) rename man/{log.q.Rd => log_q.Rd} (84%) diff --git a/NAMESPACE b/NAMESPACE index f3e04da..835f9f3 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,11 +1,11 @@ # Generated by roxygen2: do not edit by hand -S3method(exp,q) -S3method(log,q) -export(D.q) -export(D.spectrum) -export(H.q) -export(H.spectrum) +export(D_q) +export(D_spectrum) +export(H_q) +export(H_spectrum) +export(exp_q) +export(log_q) export(mode) export(tag_bad_pcr) importFrom(Rdpack,reprompt) diff --git a/R/entropy.R b/R/entropy.R index 581a85e..d662970 100644 --- a/R/entropy.R +++ b/R/entropy.R @@ -1,23 +1,23 @@ #' @author Eric Coissac #' @export -H.q = function(x,q=1) { - sum(x * log.q(1/x,q),na.rm = TRUE) +H_q = function(x,q=1) { + sum(x * log_q(1/x,q),na.rm = TRUE) } #' @author Eric Coissac #' @export -D.q = function(x,q=1) { - exp.q(H.q(x,q),q) +D_q = function(x,q=1) { + exp_q(H_q(x,q),q) } #' @author Eric Coissac #' @export -H.spectrum = function(x,q=1) { - sapply(q,function(Q) H.q(x,Q)) +H_spectrum = function(x,q=1) { + sapply(q,function(Q) H_q(x,Q)) } #' @author Eric Coissac #' @export -D.spectrum = function(x,q=1) { - sapply(q,function(Q) D.q(x,Q)) +D_spectrum = function(x,q=1) { + sapply(q,function(Q) D_q(x,Q)) } diff --git a/R/generalized_log.R b/R/generalized_log.R index 7d5006a..982585b 100644 --- a/R/generalized_log.R +++ b/R/generalized_log.R @@ -13,7 +13,7 @@ NULL #' #' @author Eric Coissac #' @export -log.q = function(x,q=1) { +log_q = function(x,q=1) { if (q==1) log(x) else (x^(1-q)-1)/(1-q) @@ -27,7 +27,7 @@ log.q = function(x,q=1) { #' #' @author Eric Coissac #' @export -exp.q = function(x,q=1,base=exp(1)) { +exp_q = function(x,q=1,base=exp(1)) { if (q==1) exp(x) else diff --git a/index.Rmd b/index.Rmd index a37cdaf..cf2940b 100644 --- a/index.Rmd +++ b/index.Rmd @@ -18,6 +18,7 @@ library(knitr) library(tidyverse) library(kableExtra) library(latex2exp) +library(MetabarSchool) opts_chunk$set(echo = FALSE, cache = TRUE, @@ -498,7 +499,7 @@ $$ $$ ```{r echo=TRUE, eval=FALSE} -log.q = function(x,q=1) { +log_q = function(x,q=1) { if (q==1) log(x) else @@ -506,6 +507,28 @@ log.q = function(x,q=1) { } ``` +## Impact of $q$ on the `log_q` function + +```{r} +layout(matrix(c(1,1,2),nrow=1)) +qs = seq(0,5,by=1) +x = seq(0.001,1,length.out = 100) +plot(x,log_q(x,0),lty=2,lwd=3,col=0,type="l", + ylab = TeX("$^q\\log$"), + ylim=c(-10,0)) + +for (i in seq_along(qs)) { + points(x,log_q(x,qs[i]),lty=1,lwd=1,col=i,type="l") +} + +points(x,log(x),lty=2,lwd=3,col="red",type="l") + +plot(0,type='n',axes=FALSE,ann=FALSE) +legend("topleft",legend = qs,fill = seq_along(qs),cex=1.5) + + +``` + ## And its inverse function {.flexbox .vcenter} $$ @@ -517,7 +540,7 @@ $$ \right. $$ ```{r echo=TRUE, eval=FALSE} -exp.q = function(x,q=1) { +exp_q = function(x,q=1) { if (q==1) exp(x) else @@ -532,8 +555,8 @@ $$ $$ ```{r echo=TRUE, eval=FALSE} -H.q = function(x,q=1) { - sum(x * log.q(1/x,q),na.rm = TRUE) +H_q = function(x,q=1) { + sum(x * log_q(1/x,q),na.rm = TRUE) } ``` @@ -544,22 +567,22 @@ $$ ^qD=^qe^{^qH} $$ ```{r echo=TRUE, eval=FALSE} - D.q = function(x,q=1) { - exp.q(H.q(x,q),q) + D_q = function(x,q=1) { + exp_q(H_q(x,q),q) } ``` ## Biodiversity spectrum (1) {.flexbox .vcenter} ```{r echo=TRUE, eval=FALSE} -H.spectrum = function(x,q=1) { - sapply(q,function(Q) H.q(x,Q)) +H_spectrum = function(x,q=1) { + sapply(q,function(Q) H_q(x,Q)) } ``` ```{r echo=TRUE, eval=FALSE} -D.spectrum = function(x,q=1) { - sapply(q,function(Q) D.q(x,Q)) +D_spectrum = function(x,q=1) { + sapply(q,function(Q) D_q(x,Q)) } ``` @@ -568,8 +591,8 @@ D.spectrum = function(x,q=1) { ```{r echo=TRUE,warning=FALSE,error=FALSE} library(MetabarSchool) qs = seq(from=0,to=3,by=0.1) -environments.hq = apply(environments,MARGIN = 1,H.spectrum,q=qs) -environments.dq = apply(environments,MARGIN = 1,D.spectrum,q=qs) +environments.hq = apply(environments,MARGIN = 1,H_spectrum,q=qs) +environments.dq = apply(environments,MARGIN = 1,D_spectrum,q=qs) ``` ```{r} @@ -616,8 +639,8 @@ $q$ can be considered as a penality you give to rare species ## Biodiversity spectrum of the mock community ```{r echo=TRUE} -H.mock = H.spectrum(plants.16$dilution,qs) -D.mock = D.spectrum(plants.16$dilution,qs) +H.mock = H_spectrum(plants.16$dilution,qs) +D.mock = D_spectrum(plants.16$dilution,qs) ``` ```{r} @@ -640,7 +663,7 @@ abline(v=c(0,1,2),lty=2,col=4:6) ```{r echo=TRUE} positive.H = apply(positive.count.relfreq, MARGIN = 1, - FUN = H.spectrum, + FUN = H_spectrum, q=qs) ``` ```{r} @@ -672,7 +695,7 @@ positive.H.means = rowMeans(positive.H) ```{r echo=TRUE} positive.D = apply(positive.count.relfreq, MARGIN = 1, - FUN = D.spectrum, + FUN = D_spectrum, q=qs) ``` @@ -720,7 +743,7 @@ positive.clean.count.relfreq = decostand(positive.clean.count, positive.clean.H = apply(positive.clean.count.relfreq, MARGIN = 1, - FUN = H.spectrum, + FUN = H_spectrum, q=qs) ``` @@ -738,7 +761,7 @@ points(H.mock,col="red",type="l") ```{r echo=TRUE} positive.clean.D = apply(positive.clean.count.relfreq, MARGIN = 1, - FUN = D.spectrum, + FUN = D_spectrum, q=qs) ``` @@ -1144,7 +1167,7 @@ legend("topleft",legend = levels(samples.type),fill = 1:4,cex=1.2) ```{r} guiana.relfreq.final = apply(guiana.relfreq.final, MARGIN = 1, - FUN = H.spectrum, + FUN = H_spectrum, q=qs) ``` diff --git a/index.html b/index.html index 5a22cb7..eeb275f 100644 --- a/index.html +++ b/index.html @@ -1842,13 +1842,17 @@ Environment.2 \right. \]

-
log.q = function(x,q=1) {
+
log_q = function(x,q=1) {
   if (q==1)
     log(x)
   else 
     (x^(1-q)-1)/(1-q)
 }

 
+
Impact of \(q\) on the log_q function

+
+

+
 
And its inverse function

 
 
\[
@@ -1860,7 +1864,7 @@ Environment.2
            \right.
 \]

 
-
exp.q = function(x,q=1) {
+
exp_q = function(x,q=1) {
   if (q==1)
     exp(x)
   else
@@ -1873,8 +1877,8 @@ Environment.2
 ^qH = - \sum_{i=1}^S pi \times ^q\log pi
 \]

 
-
H.q = function(x,q=1) {
-  sum(x * log.q(1/x,q),na.rm = TRUE)
+
H_q = function(x,q=1) {
+  sum(x * log_q(1/x,q),na.rm = TRUE)
 }

 
 
and generalized the previously presented Hill's number

@@ -1883,28 +1887,28 @@ Environment.2
 ^qD=^qe^{^qH}
 \]

 
-
 D.q = function(x,q=1) {
-  exp.q(H.q(x,q),q)
+
 D_q = function(x,q=1) {
+  exp_q(H_q(x,q),q)
 }

 
 
Biodiversity spectrum (1)

 
-
H.spectrum = function(x,q=1) {
-  sapply(q,function(Q) H.q(x,Q))
+
H_spectrum = function(x,q=1) {
+  sapply(q,function(Q) H_q(x,Q))
 }

 
-
D.spectrum = function(x,q=1) {
-  sapply(q,function(Q) D.q(x,Q))
+
D_spectrum = function(x,q=1) {
+  sapply(q,function(Q) D_q(x,Q))
 }

 
 
Biodiversity spectrum (2)

 
 
library(MetabarSchool)
 qs = seq(from=0,to=3,by=0.1)
-environments.hq = apply(environments,MARGIN = 1,H.spectrum,q=qs)
-environments.dq = apply(environments,MARGIN = 1,D.spectrum,q=qs)

+environments.hq = apply(environments,MARGIN = 1,H_spectrum,q=qs)
+environments.dq = apply(environments,MARGIN = 1,D_spectrum,q=qs)
-

+

Generalized entropy \(vs\) \(\alpha\)-diversity indices

@@ -1934,32 +1938,32 @@ environments.dq = apply(environments,MARGIN = 1,D.spectrum,q=qs)

Biodiversity spectrum of the mock community

-
H.mock = H.spectrum(plants.16$dilution,qs)
-D.mock = D.spectrum(plants.16$dilution,qs)
+
H.mock = H_spectrum(plants.16$dilution,qs)
+D.mock = D_spectrum(plants.16$dilution,qs)
-

+

Biodiversity spectrum and metabarcoding (1)

positive.H = apply(positive.count.relfreq,
                    MARGIN = 1,
-                   FUN = H.spectrum,
+                   FUN = H_spectrum,
                    q=qs)
-

+

Biodiversity spectrum and metabarcoding (2)

-

+

Biodiversity spectrum and metabarcoding (3)

positive.D = apply(positive.count.relfreq,
                    MARGIN = 1,
-                   FUN = D.spectrum,
+                   FUN = D_spectrum,
                    q=qs)
-

+

Impact of data cleaning on \(\alpha\)-diversity (1)

@@ -1992,19 +1996,19 @@ positive.clean.count.relfreq = decostand(positive.clean.count, positive.clean.H = apply(positive.clean.count.relfreq, MARGIN = 1, - FUN = H.spectrum, + FUN = H_spectrum, q=qs) -

+

Impact of data cleaning on \(\alpha\)-diversity (3)

positive.clean.D = apply(positive.clean.count.relfreq,
                          MARGIN = 1,
-                         FUN = D.spectrum,
+                         FUN = D_spectrum,
                          q=qs)
-

+

\(\beta\)-diversity

@@ -2163,7 +2167,7 @@ data("guiana.samples") 
s = tag_bad_pcr(guiana.samples$sample,guiana.count)
-

+

guiana.count.clean = guiana.count[s$keep,]
 guiana.samples.clean = guiana.samples[s$keep,]
@@ -2178,7 +2182,7 @@ guiana.samples.clean = guiana.samples[s$keep,] 
s = tag_bad_pcr(guiana.samples.clean$sample,guiana.count.clean)
-

+

guiana.count.clean = guiana.count.clean[s$keep,]
 guiana.samples.clean = guiana.samples.clean[s$keep,]
@@ -2193,7 +2197,7 @@ guiana.samples.clean = guiana.samples.clean[s$keep,] 
s = tag_bad_pcr(guiana.samples.clean$sample,guiana.count.clean)
-

+

guiana.count.clean = guiana.count.clean[s$keep,]
 guiana.samples.clean = guiana.samples.clean[s$keep,]
@@ -2260,7 +2264,7 @@ xy = xy[,1:2] xy.hellinger = decostand(xy,method = "hellinger")
-

+

@@ -2301,17 +2305,17 @@ guiana.jac.50.pcoa = cmdscale(guiana.jac.50.dist,k=3,eig = TRUE)

Principale coordinate analysis (2)

-

+

Principale composante analysis

guiana.hellinger.pca = prcomp(guiana.hellinger.final,center = TRUE, scale. = FALSE)
-

+

Comparing diversity of the environments

-

+

Bibliography

diff --git a/man/exp.q.Rd b/man/exp_q.Rd similarity index 80% rename from man/exp.q.Rd rename to man/exp_q.Rd index 21590c8..b2f7575 100644 --- a/man/exp.q.Rd +++ b/man/exp_q.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/generalized_log.R -\name{exp.q} -\alias{exp.q} +\name{exp_q} +\alias{exp_q} \title{Generalized exponential function.} \usage{ -\method{exp}{q}(x, q = 1, base = exp(1)) +exp_q(x, q = 1, base = exp(1)) } \description{ Generalized exponential function. diff --git a/man/log.q.Rd b/man/log_q.Rd similarity index 84% rename from man/log.q.Rd rename to man/log_q.Rd index d1fb77e..8fc1667 100644 --- a/man/log.q.Rd +++ b/man/log_q.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/generalized_log.R -\name{log.q} -\alias{log.q} +\name{log_q} +\alias{log_q} \title{Generalized logaritmic function.} \usage{ -\method{log}{q}(x, q = 1) +log_q(x, q = 1) } \description{ \deqn{x \longmapsto 1 : \log(x) \approx x-1}