[R] Calling R (GAMM) from Fortran
Hello, I am currently working on a modeling project using Fortran to run large repetitive loops (many DO loops). As part of this process I would like to use a model fit in R and currently stored as an R object. This is a rather complex model, a GAMM, and I am curious whether there is a way to call this model from Fortran. I am not sure call is correct terminology, but I would basically like to use this GAMM to make a prediction as part of each DO loop. Is this possible? I have found instructions, etc. for calling Fortran from R but not vice versa. Thank you for any information or advice. General advice to address this situation is also welcome. Thanks again! -Paul Simonin [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Create histogram from data matrix
Hello! Thanks for reading this request for assistance. I have a question regarding creating a histogram-like figure from data that are not currently in the correct format for the hist command. Specifically, my data have been processed and are in a matrix with columns containing the variables of interest and separate columns containing the number of times this variable was observed (counts). This data frame/matrix is rather large (1600 rows), and there are multiple rows corresponding to the same variable level (e.g., temperature=8, 5 observations in one row, then the next: temperature=8, 9 observations, and so on). In other words, the data are not one long vector R can read and plot as a histogram, nor are they condensed. My goal is to create a figure in which one axis is bins (e.g., temperature values) and the other is number of observations in this bin (e.g., number of organisms seen). My question is: Is there a way R can be told to read my data to create a plot like that I desire? So far I have tried several options, including bar plots with no success. If there is no way to do this with my data as the are currently arrange, is there an efficient way to re-arrange them? Thanks a lot for any assistance or advice! Sincerely, Paul Simonin -- Paul W. Simonin Graduate Research Assistant, MS Program Vermont Cooperative Fish and Wildlife Research Unit The Rubenstein School of Environment and Natural Resources University of Vermont 81 Carrigan Dr. Burlington, VT 05405 Ph:802-656-3153 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Create histogram from data matrix
Thank you all for your advice. I have received some good tips, but it was suggested I write back with a small simulated data set to better illustrate my needs. So, currently my data frame looks something like: ID (date) Temperature Number of fish 200706183 5 456 200706183 5 765 200706183 4 567 200706183 3 876 200706183 3 888 200706183 2 111 200706184 8 2345 200706184 8 654 200706184 8 7786 200706184 7 345 200706184 6 234 200706184 6 123 I need to create a plots for each ID (date) of the number of fish observed at each temperature. Obviously my data frame is much larger. These plots do not have to be in a specific histogram format, but it seems this may be appropriate. Thanks for any additional advice as to how this may be done, either using plot commands or reformatting my data. It seemed the ggplot2 options may be good but so far I have tried qplot with no success: my most recent code looks like: qplot(temp,number of fish, geom=histogram,binwidth=1) I have tried various tweaks of this, but no success. Thanks for any advice! -Paul Simonin Quoting stephen sefick ssef...@gmail.com: It would be easier if you were to make a data frame of fake values to illustrate your point, so that we could just copy it into an R session and see if we can't get it to work. So, a stab in the dark would to look at ggplot2 specifically the hist argument in qplot and the facets, the lattice package, or reshape to change the format of your data. If you want me to fool around with it use dput and take a small subset of your data or make up data to be able to be copied into an R session. hope that helps, Stephen On Fri, Apr 17, 2009 at 10:59 AM, Paul Warren Simonin paul.simo...@uvm.edu wrote: Hello! Thanks for reading this request for assistance. I have a question regarding creating a histogram-like figure from data that are not currently in the correct format for the hist command. Specifically, my data have been processed and are in a matrix with columns containing the variables of interest and separate columns containing the number of times this variable was observed (counts). This data frame/matrix is rather large (1600 rows), and there are multiple rows corresponding to the same variable level (e.g., temperature=8, 5 observations in one row, then the next: temperature=8, 9 observations, and so on). In other words, the data are not one long vector R can read and plot as a histogram, nor are they condensed. My goal is to create a figure in which one axis is bins (e.g., temperature values) and the other is number of observations in this bin (e.g., number of organisms seen). My question is: Is there a way R can be told to read my data to create a plot like that I desire? So far I have tried several options, including bar plots with no success. If there is no way to do this with my data as the are currently arrange, is there an efficient way to re-arrange them? Thanks a lot for any assistance or advice! Sincerely, Paul Simonin -- Paul W. Simonin Graduate Research Assistant, MS Program Vermont Cooperative Fish and Wildlife Research Unit The Rubenstein School of Environment and Natural Resources University of Vermont 81 Carrigan Dr. Burlington, VT 05405 Ph:802-656-3153 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis -- Paul W. Simonin Graduate Research Assistant, MS Program Vermont Cooperative Fish and Wildlife Research Unit The Rubenstein School of Environment and Natural Resources University of Vermont 81 Carrigan Dr. Burlington, VT 05405 Ph:802-656-3153 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Subset a data frame for plotting
Hello, I have a question regarding how to subset/select parts of a data frame (matrix) in order to plot data associated only with this subset. Specifically I have a large data frame in which one column contains ID values (dates), and other columns contain data I would like to plot (temperature, light, etc.). I would like to break up this large matrix so as to plot data associated with specific ID values (dates) separately. I have learned of several commands that supposedly subset matrices in this manner and have tried the following code with no success: 200706183-subset(AllData, ID = 200706183) 200706183-gx.subset(AllData, ID == 200706183) 200706183-subset(x=AllData, AllData$ID = 200706183) 200706183-gx.subset(x=AllData, AllData$ID == 200706183) In using this code my plan was to create smaller data frame objects which I could then plot. My first question, though, is whether this is the correct approach. Is there a more efficient way I can create plots conditional on certain criteria such as code = 200706183 ? If I do need to first create separate smaller data frames, how do I go about doing this? Am I missing something in the above commands? Any other advice is certainly welcome too, as I admit to being a bit new to R. Thank you very much for any answers, tips, suggestions, etc.! Best wishes, Paul Simonin -- Paul W. Simonin Graduate Research Assistant, MS Program Vermont Cooperative Fish and Wildlife Research Unit The Rubenstein School of Environment and Natural Resources University of Vermont 81 Carrigan Dr. Burlington, VT 05405 Ph:802-656-3153 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Log transformation and -Inf values for use in glm()
Hello, I am writing regarding log transformation of data in a single matrix column, and subsequent use of these data in a glm model fit. I have a data matrix in which I am using the log function to transform the values. This transformation results in -Inf values in some places, though. I then receive an error when this matrix is used in the glm function, and would like to know this can be avoided. I have attempted several methods already including the use of na.exclue commands in the glm statement: DistributionT-glm(EarlyLn$yoyras~EarlyLn$temp,family=gaussian(link = identity),na.exclude) I have also attempted to use the is.finite command: EarlyLn$yoyras-EarlyLn[is.finite(EarlyLn$yoyras)==T,] I know another option would be to use a type of find and replace command to remove entire rows of the matrix that contain 0's (before log transformation) or -Inf (after transformation), but I do not know how this is done. Thank you for any advice or tips regarding conducting this transformation and feeding the data matrix into glm. Sincerely, Paul S. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Plot with x-axis dates
Hello, I am attempting to create plots using two continuous variables and it seems I should be able to use the simple plot command. However, my x-axis values are dates, and I believe this could be the reason I am receiving error messages reading: Error in Summary.factor(c(2L, 4L, 3L, 5L, 6L, 7L, 1L), na.rm = FALSE) : range not meaningful for factors I have attempted to convert the date values to official dates within R and have done that successfully using the as.date function, but this did not help in the plots. So, how can one create plots in which the x-axis is date values? I know it would be possible to convert all my dates into a different linear scale (e.g., julian dates). However, I would like to complete this process as simply as possible. Thank you for any advice or information. Sincerely, Paul S. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
