Commit 47834a7b authored by GAREL Marc's avatar GAREL Marc
Browse files

Ajout des fichier RData Rapp.history et Rhistory .Rapp.history et folder rsconnect

parent 78f8e880
File added
install.packages("oce")
install.packages("Rgl")
install.packages("rgl")
install.packages("vegan")
install.packages("ade4")
install.packages("cobs")
install.packages("chron")
install.packages("quantreg")
install.packages("shiny")
shiny::runGitHub("shiny-phyloseq","joey711")
shiny::runGitHub("shiny-phyloseq","joey711")
View(install_missing_packages)
View(install_missing_packages)
View(install_missing_packages)
gas_solubility(t = 1:20,S = 35, species = "CO2")
gas_solubility(t = 0:5,S = 35,species = "O2")
Temp <- seq(from = 0, to = 30, by = 0.1)
mf <- par(mfrow = c(1, 2))
gs <- gas_solubility(t = Temp)
species <- c("CCl4", "CO2", "N2O", "Rn", "CCl2F2")
matplot(Temp, gs[, species], type = "l", lty = 1, lwd = 2,
xlab = "temperature", ylab = "mmol/m3", main = "solubility (S=35)")
legend("topright", col = 1:5, lwd = 2, legend = species)
species2 <- c("Kr", "CH4", "Ar", "O2", "N2", "Ne")
matplot(Temp, gs[, species2], type = "l", lty = 1, lwd = 2,
xlab = "temperature", ylab = "mmol/m3", main = "solubility (S=35)")
legend("topright", col = 1:6, lwd = 2, legend = species2)
plot(Temp,gas_solubility(t = Temp, species = "CCl4"), xlab = "temperature",
ylab = "mmol/m3/atm", main = "solubility (S=35)",
type = "l", lwd = 2, ylim = c(0, 100000))
lines(Temp,gas_solubility(t = Temp, species = "CO2"), col = "red", lwd = 2)
lines(Temp,gas_solubility(t = Temp, species = "N2O"), col = "blue", lwd = 2)
lines(Temp,gas_solubility(t = Temp, species = "Rn"), col = "green", lwd = 2)
lines(Temp,gas_solubility(t = Temp, species = "CCl2F2"), col = "yellow", lwd = 2)
library("marelac", lib.loc="/Library/Frameworks/R.framework/Versions/3.3/Resources/library")
gas_solubility(t = 1:20,S = 35, species = "CO2")
gas_solubility(t = 0:5,S = 35,species = "O2")
Temp <- seq(from = 0, to = 30, by = 0.1)
mf <- par(mfrow = c(1, 2))
gs <- gas_solubility(t = Temp)
species <- c("CCl4", "CO2", "N2O", "Rn", "CCl2F2")
matplot(Temp, gs[, species], type = "l", lty = 1, lwd = 2,
xlab = "temperature", ylab = "mmol/m3", main = "solubility (S=35)")
legend("topright", col = 1:5, lwd = 2, legend = species)
species2 <- c("Kr", "CH4", "Ar", "O2", "N2", "Ne")
matplot(Temp, gs[, species2], type = "l", lty = 1, lwd = 2,
xlab = "temperature", ylab = "mmol/m3", main = "solubility (S=35)")
legend("topright", col = 1:6, lwd = 2, legend = species2)
plot(Temp,gas_solubility(t = Temp, species = "CCl4"), xlab = "temperature",
ylab = "mmol/m3/atm", main = "solubility (S=35)",
type = "l", lwd = 2, ylim = c(0, 100000))
lines(Temp,gas_solubility(t = Temp, species = "CO2"), col = "red", lwd = 2)
lines(Temp,gas_solubility(t = Temp, species = "N2O"), col = "blue", lwd = 2)
lines(Temp,gas_solubility(t = Temp, species = "Rn"), col = "green", lwd = 2)
lines(Temp,gas_solubility(t = Temp, species = "CCl2F2"), col = "yellow", lwd = 2)
install.packages("OceanView")
require(OceanView)
require(shape)
cols <- ramp.col(c( "lightblue1", "grey10"), n = 100)
par(mar = c(0, 0, 0, 1))
image2D(Hypsometry, col = cols, shade = 0.1, rasterImage = TRUE,
contour = list(levels = 0, draw = F), axes = FALSE, xlab = "", ylab = "",
colkey = list(width = 0.5, length = 0.5, cex.axis = 0.7))
require(OceanView)
require(shape)
cols <- ramp.col(c( "lightblue1", "grey10"), n = 100)
par(mar = c(0, 0, 0, 1))
image2D(Hypsometry, col = cols, shade = 0.1, rasterImage = TRUE,
contour = list(levels = 0, draw = F), axes = FALSE, xlab = "", ylab = "",
colkey = list(width = 0.5, length = 0.5, cex.axis = 0.7))
install.packages("ode")
install.packages("deSolve")
co2=o2_unit_conv(x[,8], from = "percent_a.s.", to = "umol_per_l", S, x[,7],p)
shiny::runApp('OSU/Growth_APP')
runApp('OSU/Growth_APP')
runApp('OSU/Growth_APP')
runApp('OSU/Growth_APP')
source("https://bioconductor.org/biocLite.R")
biocLite("cytofkit")
library("cytofkit")
cytofkit()
cytofkit_GUI()
cytofkit_GUI()
library("cytofkit")
## simple contour plot
contour(GvHD[[1]])
## overlay with existing plot
plot(GvHD[[1]], c("FSC-H", "SSC-H"))
contour(GvHD[[1]], add=TRUE, col="lightgray", lty=3)
## colored contours
contour(GvHD[[1]], fill="red")
cols <- rainbow(3, alpha=0.1)
contour(GvHD[[1]], fill=cols, col=cols)
## overlay of multiple flowFrames in a flowSet
contour(GvHD[1:3], col=cols, fill=cols)
library("flowViz", lib.loc="/Library/Frameworks/R.framework/Versions/3.3/Resources/library")
## simple contour plot
contour(GvHD[[1]])
## overlay with existing plot
plot(GvHD[[1]], c("FSC-H", "SSC-H"))
contour(GvHD[[1]], add=TRUE, col="lightgray", lty=3)
## colored contours
contour(GvHD[[1]], fill="red")
cols <- rainbow(3, alpha=0.1)
contour(GvHD[[1]], fill=cols, col=cols)
## overlay of multiple flowFrames in a flowSet
contour(GvHD[1:3], col=cols, fill=cols)
data(GvHD)
GvHD <- GvHD[pData(GvHD)$Patient %in% 6:7]
densityplot(~ `FSC-H`, GvHD)
densityplot(~ `FSC-H` + `SSC-H`, GvHD)
densityplot(~ ., GvHD[1:3])
library("lattice")
library("lattice")
library("lattice", lib.loc="/Library/Frameworks/R.framework/Versions/3.3/Resources/library")
## Tonga Trench Earthquakes
Depth <- equal.count(quakes$depth, number=8, overlap=.1)
xyplot(lat ~ long | Depth, data = quakes)
update(trellis.last.object(),
strip = strip.custom(strip.names = TRUE, strip.levels = TRUE),
par.strip.text = list(cex = 0.75),
aspect = "iso")
R
version(à)
version()
runApp('OSU/Growth_APP')
shiny::runApp('OSU/Growth_APP')
b1 = installed.packages()[, 1]
write.talbe(b1, "all_my_packages.txt")
getwd()
write.table(b1, "all_my_packages.txt")
shiny::runApp('GitHub/logistic_microbio')
runApp('GitHub/logistic_microbio')
runApp('OSU/Growth_APP')
runApp('GitHub/logistic_microbio')
runApp('GitHub/logistic_microbio')
runApp('OSU/Growth_APP')
runApp('GitHub/logistic_microbio')
runApp('GitHub/logistic_microbio')
runApp('GitHub/logistic_microbio')
ll
library("cytofkit", lib.loc="/Library/Frameworks/R.framework/Versions/3.3/Resources/library")
install.packages("XQuartz")
library("cytofkit", lib.loc="/Library/Frameworks/R.framework/Versions/3.3/Resources/library")
install.packages("VGAM", dependencies = FALSE)
library("cytofkit", lib.loc="/Library/Frameworks/R.framework/Versions/3.3/Resources/library")
install.packages("~/Downloads/VGAM_1.0-3.tar.gz", repos = NULL, type = "source")
library("vegan", lib.loc="/Library/Frameworks/R.framework/Versions/3.4/Resources/library")
S <- specnumber(BCI) # observed number of species
(raremax <- min(rowSums(BCI)))
Srare <- rarefy(BCI, raremax)
plot(S, Srare, xlab = "Observed No. of Species", ylab = "Rarefied No. of Species")
abline(0, 1)
rarecurve(BCI, step = 20, sample = raremax, col = "blue", cex = 0.6)
data(BCI)
S <- specnumber(BCI) # observed number of species
(raremax <- min(rowSums(BCI)))
Srare <- rarefy(BCI, raremax)
plot(S, Srare, xlab = "Observed No. of Species", ylab = "Rarefied No. of Species")
abline(0, 1)
rarecurve(BCI, step = 20, sample = raremax, col = "blue", cex = 0.6)
View(BCI)
data(BCI)
S <- specnumber(BCI) # observed number of species
(raremax <- min(rowSums(BCI)))
Srare <- rarefy(BCI, raremax)
plot(S, Srare, xlab = "Observed No. of Species", ylab = "Rarefied No. of Species")
abline(0, 1)
rarecurve(BCI, step = 20, sample = raremax, col = "blue", cex = 0.6)
data(BCI)
S <- specnumber(BCI) # observed number of species
(raremax <- min(rowSums(BCI)))
Srare <- rarefy(BCI, raremax)
plot(S, Srare, xlab = "Observed No. of Species", ylab = "Rarefied No. of Species")
abline(0, 1)
rarecurve(BCI, step = 20, sample = raremax, col = "blue", cex = 0.6)
library("knitr", lib.loc="/Library/Frameworks/R.framework/Versions/3.4/Resources/library")
knitr::opts_chunk$set(echo = TRUE)
summary(cars)
plot(pressure)
knitr::opts_chunk$set(echo = TRUE)
summary(cars)
plot(pressure)
data(BCI)
S <- specnumber(BCI) # observed number of species
(raremax <- min(rowSums(BCI)))
Srare <- rarefy(BCI, raremax)
plot(S, Srare, xlab = "Observed No. of Species", ylab = "Rarefied No. of Species")
abline(0, 1)
rarecurve(BCI, step = 20, sample = raremax, col = "blue", cex = 0.6)
data(BCI)
S <- specnumber(BCI) # observed number of species
(raremax <- min(rowSums(BCI)))
Srare <- rarefy(BCI, raremax)
plot(S, Srare, xlab = "Observed No. of Species", ylab = "Rarefied No. of Species")
abline(0, 1)
rarecurve(BCI, step = 20, sample = raremax, col = "blue", cex = 0.6)
help("plot")
?? plot
library("phyloseq", lib.loc="/Library/Frameworks/R.framework/Versions/3.4/Resources/library")
data("GlobalPatterns")
gp.ch = subset_taxa(GlobalPatterns, Phylum == "Chlamydiae")
plot_bar(gp.ch)
shiny::runApp('CNRS/BD_test/bd_test')
shiny::runApp('CNRS/BD_test/bd_test')
setwd("~/GitHub/logistic_microbio")
shiny::runApp()
name: logistic_microbio
title: logistic_microbio
username:
account: hpteam
server: shinyapps.io
hostUrl: https://api.shinyapps.io/v1
appId: 325933
bundleId: 1327097
url: https://hpteam.shinyapps.io/logistic_microbio/
when: 1524126472.021
asMultiple: FALSE
asStatic: FALSE
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment