BiostatR Blog

When you change R version, you must reinstall manually all your installed packages. # before to update pkgins <- rownames(installed.packages()) save(pkgins, file = "pkgins.Rdata") # after updating load(file = "pkgins.Rdata") for (pkg in pkgins[is.na(match(pkgins, rownames(installed.packages())))]) {   if (pkg %in% pkgins[is.na(match(pkgins, rownames(installed.packages())))]) {     install.packages(pkg)   } } The packages shown with: pkgins[is.na(match(pkgins, rownames(installed.packages())))] Are not available in CRAN or produced an error when installed with new version.

When I update the packages, I get this error: mise à jour de la liste HTML des packages dans '.Library' Warning messages: 1: In file.create(f.tg) :   impossible de créer le fichier '/usr/share/R/doc/html/packages.html', à cause de 'Permission denied' 2: In make.packages.html(.Library) :   impossible de mettre à jour l'index HTML des packages I tried to solve the problem using  sudo chmod -R 777 /usr/share/R/

Let do a binomial glm with cbind(success, failure) First, I prepare the data: factor <- rnorm(7, 10, 2) dta <- data.frame(p=c(2, 7, 8, 9, 10, 18, 7),                   n=c(20, 20, 20, 20, 20, 20, 20)) dta cannot be used directly; it must be a matrix, not a data.frame: g <- glm(dta ~ factor,           family = binomial(link = "logit")) # Error in model.frame.default(formula = dta ~ factor, drop.unused.levels = TRUE) :  #     type (list) incorrect pour la variable 'dta' g <- glm(as.matrix(dta) ~ factor,           family = binomial(link = "logit")) coef(g)  (Intercept)       factor  -0.767901152 -0.006062598  Great, it works. But if you try to plot the effects with visreg package, it produced an error: library(visreg) visreg(g, xvar ="factor") # Error in dimnames(x) ...

In a recent blog post, a simple problem (called “FizzBuzz“) is solved. This problem is asked by some employers in data scientist job interviews. The question seeks to ascertain the applicant’s familiarity with basic programming concepts.  https://www.r-bloggers.com/fizzbuzz-in-r-and-python/ The FizzBuzz Question I came across the FizzBuzz question in this excellent blog post on conducting data scientist interviews and have seen it referenced elsewhere on the web. The intent of the question is to probe the job applicant’s knowledge of basic programming concepts. The prompt of the question is as follows: In pseudo-code or whatever language you would like: write a program that prints the numbers from 1 to 100. But for multiples of three print “Fizz” instead of the number and for the multiples of five print “Buzz”. For numbers which are multiples of both three and five print “FizzBuzz”. The Solution in R We will first solve the problem in R. We will make use of control struc...

In conclusion, if no progress bar is necessary on unix system, mclapply with  mc.preschedule =  TRUE  is very good. Don't forget to indicate mc.cores because the default is only 2 cores. If you work in windows system, you must use  parLapply . However it is more complicated as you must transfer variable and which packages must be loaded. # No parallel computing; give a reference st1 <- system.time(f <- lapply(1:10000, FUN=function(x) {Sys.sleep(0.001)})) library(parallel) # Parallel computing using 4 cores with fork and mc.preschedule being TRUE st2 <- system.time(f <- mclapply(1:10000, FUN=function(x) {Sys.sleep(0.001)}, mc.cores = 4)) # Parallel computing using 4 cores with fork and mc.preschedule being FALSE st3 <- system.time(f <- mclapply(1:10000, FUN=function(x) {Sys.sleep(0.001)}, mc.cores = 4, mc.preschedule = FALSE)) # Parallel computing using 4 cores without fork st4 <- system.time({cl <- parallel::makeCluster(4);...

To be able to build packages from source in Mojave, after the install of Xcode, run: open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

If you want unselected all checkboxes defined using  updateCheckboxGroupInput , the syntax should be: updateCheckboxGroupInput(session, inputId, selected = NULL) However, it does not work. You must indicate again the parameter choices explicitly Look at this code: rm(list = ls()) library(shiny) runApp(list(   ui = basicPage(     checkboxGroupInput('chkGrp',                         label="Choix",                         choices=list("A"="a", "B"="b", "C"="c", "D"="d", "E"="e")),     actionButton("all","All"),     actionButton("noneWithChoices","None With Choices"),     actionButton("noneWithoutChoices","None Without Choices"),     actionButton("partial","Partial"),     verbatimTextOutput("value")   ),   server = function(input, output, session) {   ...