romunov - Developer IT

improve my code for collapsing a list of data.frames

- by romunov

Dear StackOverFlowers (flowers in short), I have a list of data.frames (walk.sample) that I would like to collapse into a single (giant) data.frame. While collapsing, I would like to mark (adding another column) which rows have came from which element of the list. This is what I've got so far. This is the data.frame that needs to be collapsed/stacked. > walk.sample [[1]] walker x y 1073 3 228.8756 -726.9198 1086 3 226.7393 -722.5561 1081 3 219.8005 -728.3990 1089 3 225.2239 -727.7422 1032 3 233.1753 -731.5526 [[2]] walker x y 1008 3 205.9104 -775.7488 1022 3 208.3638 -723.8616 1072 3 233.8807 -718.0974 1064 3 217.0028 -689.7917 1026 3 234.1824 -723.7423 [[3]] [1] 3 [[4]] walker x y 546 2 629.9041 831.0852 524 2 627.8698 873.3774 578 2 572.3312 838.7587 513 2 633.0598 871.7559 538 2 636.3088 836.6325 1079 3 206.3683 -729.6257 1095 3 239.9884 -748.2637 1005 3 197.2960 -780.4704 1045 3 245.1900 -694.3566 1026 3 234.1824 -723.7423 I have written a function to add a column that denote from which element the rows came followed by appending it to an existing data.frame. collapseToDataFrame <- function(x) { # collapse list to a dataframe with a twist walk.df <- data.frame() for (i in 1:length(x)) { n.rows <- nrow(x[[i]]) if (length(x[[i]])>1) { temp.df <- cbind(x[[i]], rep(i, n.rows)) names(temp.df) <- c("walker", "x", "y", "session") walk.df <- rbind(walk.df, temp.df) } else { cat("Empty list", "\n") } } return(walk.df) } > collapseToDataFrame(walk.sample) Empty list Empty list walker x y session 3 1 -604.5055 -123.18759 1 60 1 -562.0078 -61.24912 1 84 1 -594.4661 -57.20730 1 9 1 -604.2893 -110.09168 1 43 1 -632.2491 -54.52548 1 1028 3 240.3905 -724.67284 1 1040 3 232.5545 -681.61225 1 1073 3 228.8756 -726.91980 1 1091 3 209.0373 -740.96173 1 1036 3 248.7123 -694.47380 1 I'm curious whether this can be done more elegantly, with perhaps do.call() or some other more generic function?

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tidy/efficient function writing in R

- by romunov

Excuse my ignorance, as I'm not a computer engineer but with roots in biology. I have become a great fan of pre-allocating objects (kudos to SO and R inferno by Patrick Burns) and would like to improve my coding habits. In lieu of this fact, I've been thinking about writing more efficient functions and have the following question. Is there any benefits in removing variables that will be overwritten at the start of the next loop, or is this just a waste of time? For the sake of argument, let's assume that the size of old and new variables is very similar or identical.

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using OOoWrite, i would like to add custom html elements

- by romunov

I have 35 pages list of scientific references. In order to upload them to a webpage, I would like to add custom fields before and after each reference. I would also like to find italicized text and add around it. For instance, I would like this paragraph Alouf N., 1973. Biotope et description de Niphargus altagahizi n. sp., Amphipode Gammaridé souterrain du Liban, International Journal of Speleology 5: 49-61. to look like: <p class="cite">Alouf N., 1973. Biotope et description de <em>Niphargus altagahizi</em> n. sp., Amphipode Gammaridé souterrain du Liban, International Journal of Speleology 5: 49-61.</p> Any suggestions how to do this in OOoWriter macros perhaps, or any other application?

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how to substract numbers from levels

- by romunov

Dear SOFers, I would like to cut a vector of values ranging 0-70 to x number of categories, and would like the upper limit of each category. So far, I have tried this using cut() and am trying to extract the limits from levels. I have a list of levels, from which I would like to extract the second number from each level. How can I extract the values between space and ] (which is the number I'm interested in)? I have: > levels(bins) [1] "(-0.07,6.94]" "(6.94,14]" "(14,21]" "(21,28]" "(28,35]" [6] "(35,42]" "(42,49]" "(49,56]" "(56,63.1]" "(63.1,70.1]" and would like to get: [1] 6.94 14 21 28 35 42 49 56 63.1 70.1 Or is there a better way of calculating the upper bounds of categories?

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stored values within a custom function

- by romunov

My program takes a data.frame and crunches the numbers. At one point, values from j-th column are multiplied by a predefined values that depends on the column name (species name, actually - it's en ecological index). So far, I've been providing these values via a second data.frame by matching column names. What would be an efficient way of integrating fixed variable values within a function? I would like my program to be as portable as possible, without the need for a second data.frame file.

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trying to append a list, but something breaks

- by romunov

I'm trying to create an empty list which will have as many elements as there are num.of.walkers. I then try to append, to each created element, a new sub-list (length of new sub-list corresponds to a value in a. When I fiddle around in R everything goes smooth: list.of.dist[[1]] <- vector("list", a[1]) list.of.dist[[2]] <- vector("list", a[2]) list.of.dist[[3]] <- vector("list", a[3]) list.of.dist[[4]] <- vector("list", a[4]) I then try to write a function. Here is my feeble attempt that results in an error. Can someone chip in what am I doing wrong? countNumberOfWalks <- function(walk.df) { list.of.walkers <- sort(unique(walk.df$label)) num.of.walkers <- length(unique(walk.df$label)) #Pre-allocate objects for further manipulation list.of.dist <- vector("list", num.of.walkers) a <- c() # Count the number of walks per walker. for (i in list.of.walkers) { a[i] <- nrow(walk.df[walk.df$label == i,]) } a <- as.vector(a) # Add a sublist (length = number of walks) for each walker. for (i in i:num.of.walkers) { list.of.dist[[i]] <- vector("list", a[i]) } return(list.of.dist) } > num.of.walks.per.walker <- countNumberOfWalks(walk.df) Error in vector("list", a[i]) : vector size cannot be NA

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applying apply() to deeply embeded list elements only

- by romunov

I would like to apply my function to only elements that are deeper in the list structure. For example, I would like to apply a certain function to list elements of second order only. Is this feasible with apply()? > str(l) List of 3 $ :List of 2 ..$ : num 5 ..$ : num 10 $ :List of 2 ..$ : num 15 ..$ : num 20 $ :List of 2 ..$ : num 25 ..$ : num 30

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trying to prune down a list of files

- by romunov

I have a list of files and I'm trying to extract all layer1_*.grd files. Is there a way of doing this in one grep expression? lof <- c("layer1_1.grd", "layer1_1.gri", "layer1_2.grd", "layer1_2.gri", "layer1_3.grd", "layer1_3.gri", "layer1_4.grd", "layer1_4.gri", "layer1_5.grd", "layer1_5.gri", "layer2_1.grd", "layer2_1.gri", "layer2_2.grd", "layer2_2.gri", "layer2_3.grd", "layer2_3.gri", "layer2_4.grd", "layer2_4.gri", "layer2_5.grd", "layer2_5.gri", "layer3_1.grd", "layer3_1.gri", "layer3_2.grd", "layer3_2.gri", "layer3_3.grd", "layer3_3.gri", "layer3_4.grd", "layer3_4.gri", "layer3_5.grd", "layer3_5.gri", "layer4_1.grd", "layer4_1.gri", "layer4_2.grd", "layer4_2.gri", "layer4_3.grd", "layer4_3.gri", "layer4_4.grd", "layer4_4.gri", "layer4_5.grd", "layer4_5.gri" I tried doing this in two steps: list.of.files <- list.files(pattern = c("1_")) list.of.files <- list.of.files[grep(".grd", list.of.files)] Can someone enlighten me how to do this with grep in one step? I naively tried passing list() and c() to the grep but, as you can imagine, it doesn't work. list.of.files <- list.files() list.of.files <- list.of.files[grep(list("1_", ".grd"), list.of.files)]

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taking care of dependencies in your functions

- by romunov

How do you solve the dependencies of packages within your functions? I add require(package) into the function, but I wonder if there's a preferred way of accomplishing this task.

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StatET debugging tool

- by romunov

I think I'm just being dense, but I can't seem to figure out how to use the debugging tool while working in R in Eclipse (StatET plugin). Has anyone got any tips or tutorials on the subject?

Developer IT