[Seqinr-commits] r2114 - in pkg: . R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue May 18 14:53:14 CEST 2021
Author: simonpenel
Date: 2021-05-18 14:53:14 +0200 (Tue, 18 May 2021)
New Revision: 2114
Modified:
pkg/DESCRIPTION
pkg/R/dia.bactgensize.R
Log:
replace ftp by https in dia.bactgensize.R
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2021-05-18 12:29:27 UTC (rev 2113)
+++ pkg/DESCRIPTION 2021-05-18 12:53:14 UTC (rev 2114)
@@ -1,7 +1,7 @@
Encoding: UTF-8
Package: seqinr
Version: 4.2-8
-Date: 2021-03-17
+Date: 2021-05-18
Title: Biological Sequences Retrieval and Analysis
Authors at R: c(person("Delphine", "Charif", role = "aut"),
person("Olivier", "Clerc", role = "ctb"),
Modified: pkg/R/dia.bactgensize.R
===================================================================
--- pkg/R/dia.bactgensize.R 2021-05-18 12:29:27 UTC (rev 2113)
+++ pkg/R/dia.bactgensize.R 2021-05-18 12:53:14 UTC (rev 2114)
@@ -1,7 +1,7 @@
dia.bactgensize <- function(
fit = 2, p = 0.5, m1 = 2000, sd1 = 600, m2 = 4500, sd2 = 1000, p3 = 0.05,
m3 = 9000, sd3 = 1000, maxgensize = 20000,
- source = c("ftp://pbil.univ-lyon1.fr/pub/seqinr/data/goldtable15Dec07.txt",
+ source = c("https://pbil.univ-lyon1.fr/datasets/seqinr/data/goldtable15Dec07.txt",
"http://www.genomesonline.org/DBs/goldtable.txt"))
{
#
@@ -11,7 +11,7 @@
#
# Build source of data string:
#
- if(source == "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/goldtable15Dec07.txt"){
+ if(source == "https://pbil.univ-lyon1.fr/datasets/seqinr/data/goldtable15Dec07.txt"){
sodtxt <- "Source of data: GOLD (Genomes OnLine Database) 15 Dec 2007"
} else {
sodtxt <- paste("Source of data: GOLD (Genomes OnLine Database)",date())
@@ -45,7 +45,7 @@
if(fit == 0)
{
- hst <- hist(sizeKb, freq = TRUE,
+ hst <- hist(sizeKb, freq = TRUE,
breaks = mybreaks,
main=paste("Genome size distribution for", n, "bacterial genomes"),
xlab="Genome size [Kb]",
@@ -56,7 +56,7 @@
lines(x=dst$x, y=vscale*dst$y)
legend(x = max(sizeKb)/2, y = 0.75*max(hst$counts), lty=1,
"Gaussian kernel density estimation")
-
+
mtext(sodtxt)
}
##########################################
@@ -66,7 +66,7 @@
###########################################
if(fit == 2)
{
- logvraineg <- function(param, obs)
+ logvraineg <- function(param, obs)
{
p <- param[1]
m1 <- param[2]
@@ -84,10 +84,10 @@
y2 <- vscale*(1-estimate[1])*dnorm(x, estimate[4], estimate[5])
dst <- density(sizeKb)
- hst <- hist(sizeKb, plot = FALSE, breaks = mybreaks)
+ hst <- hist(sizeKb, plot = FALSE, breaks = mybreaks)
ymax <- max(y1, y2, hst$counts, vscale*dst$y)
-
-
+
+
hist(sizeKb, freq = TRUE, ylim=c(0,ymax),
breaks = mybreaks,
main=paste("Genome size distribution for", n, "bacterial genomes"),
@@ -94,7 +94,7 @@
xlab="Genome size [Kb]",
ylab="Genome count",
col="lightgrey")
-
+
lines(x, y1, col="red", lwd=2)
lines(x, y2, col="blue", lwd=2)
@@ -101,21 +101,21 @@
text(x = max(sizeKb)/2, y = ymax, pos=4, "Maximum likelihood estimates:")
text(x = max(sizeKb)/2, y = 0.95*ymax, col="red", pos = 4, cex=1.2,
- substitute(hat(p)[1] == e1~~hat(mu)[1] == e2~~hat(sigma)[1] == e3,
- list(e1 = round(estimate[1],3),
+ substitute(hat(p)[1] == e1~~hat(mu)[1] == e2~~hat(sigma)[1] == e3,
+ list(e1 = round(estimate[1],3),
e2 = round(estimate[2],1),
e3 = round(estimate[3],1))))
text(x = max(sizeKb)/2, y = 0.90*ymax, col="blue", pos = 4, cex=1.2,
- substitute(hat(p)[2] == q~~hat(mu)[2] == e4~~hat(sigma)[2] == e5,
- list(q = round(1 - estimate[1],3),
+ substitute(hat(p)[2] == q~~hat(mu)[2] == e4~~hat(sigma)[2] == e5,
+ list(q = round(1 - estimate[1],3),
e4 = round(estimate[4],1),
e5 = round(estimate[5],1))))
-
+
lines(x=dst$x, y=vscale*dst$y)
legend(x = max(sizeKb)/2, y = 0.75*ymax, lty=1,
"Gaussian kernel density estimation")
-
+
mtext(sodtxt)
}
##########################################
@@ -125,7 +125,7 @@
###########################################
if(fit == 3)
{
- logvraineg <- function(param, obs)
+ logvraineg <- function(param, obs)
{
p <- param[1]
m1 <- param[2]
@@ -148,7 +148,7 @@
y2 <- vscale*(1-estimate[1]-estimate[6])*dnorm(x, estimate[4], estimate[5])
y3 <- vscale*estimate[6]*dnorm(x, estimate[7], estimate[8])
- hst <- hist(sizeKb, plot = FALSE, breaks = mybreaks)
+ hst <- hist(sizeKb, plot = FALSE, breaks = mybreaks)
ymax <- max(y1, y2, y3, hst$counts)
hist(sizeKb, freq = TRUE, ylim=c(0,ymax),
@@ -157,36 +157,36 @@
xlab="Genome size [Kb]",
ylab="Genome count",
col="lightgrey")
-
+
lines(x, y1, col="red", lwd=2)
lines(x, y2, col="blue", lwd=2)
lines(x, y3, col="green3", lwd=2)
-
+
text(x = max(sizeKb)/2, y = ymax, pos=4, "Maximum likelihood estimates:")
text(x = max(sizeKb)/2, y = 0.95*ymax, col="red", pos = 4, cex=1.2,
- substitute(hat(p)[1] == e1~~hat(mu)[1] == e2~~hat(sigma)[1] == e3,
- list(e1 = round(estimate[1],3),
+ substitute(hat(p)[1] == e1~~hat(mu)[1] == e2~~hat(sigma)[1] == e3,
+ list(e1 = round(estimate[1],3),
e2 = round(estimate[2],1),
e3 = round(estimate[3],1))))
text(x = max(sizeKb)/2, y = 0.90*ymax, col="blue", pos = 4, cex=1.2,
- substitute(hat(p)[2] == q~~hat(mu)[2] == e4~~hat(sigma)[2] == e5,
- list(q = round(1 - estimate[1]-estimate[6],3),
+ substitute(hat(p)[2] == q~~hat(mu)[2] == e4~~hat(sigma)[2] == e5,
+ list(q = round(1 - estimate[1]-estimate[6],3),
e4 = round(estimate[4],1),
e5 = round(estimate[5],1))))
-
+
text(x = max(sizeKb)/2, y = 0.85*ymax, col="green3", pos = 4, cex=1.2,
- substitute(hat(p)[3] == p3~~hat(mu)[3] == e7~~hat(sigma)[3] == e8,
- list(p3 = round(estimate[6],3),
+ substitute(hat(p)[3] == p3~~hat(mu)[3] == e7~~hat(sigma)[3] == e8,
+ list(p3 = round(estimate[6],3),
e7 = round(estimate[7],1),
- e8 = round(estimate[8],1))))
-
+ e8 = round(estimate[8],1))))
+
dst <- density(sizeKb)
lines(x=dst$x, y=vscale*dst$y)
legend(x = max(sizeKb)/2, y = 0.75*ymax, lty=1,
"Gaussian kernel density estimation")
-
+
mtext(sodtxt)
}
#
@@ -194,15 +194,3 @@
#
invisible(data)
}
-
-
-
-
-
-
-
-
-
-
-
-
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