rescience-archives / petchey-plebani-pennekamp-2016 Goto Github PK

Here are some other changes needed to run the code:

1. Lines 412 and 837
   The detrended <- rbind(ww1, ww2) command produced a matrix, which can't be used by the group_by command in line 423. Instead of rbind, I suggest to use dplyr::bind_rows.
2. Line 951
   The fit_GAMs function called line 948 creates an object named X, not X1. Therefore, on line 951 we have to reflect this by changing Get_LE_from_fit2(gams, X1, epsval=0.01) to Get_LE_from_fit2(gams, X, epsval=0.01)
3. Line 992
   The command cors.long <- gather(cors, key=dist, convert=F) doesn't give the expected result, as the dist column is considered as one of the variables to be "gathered". As a result, the data frame we obtain has 2 columns, the first one labeled "dist" but containing the variables, and the second one containing the "values" but with the first 12 corresponding to the distance. The correct command should be gather(cors, 2:13, key=Variable, value=Correlation, convert=F)

Trying to run the code from report.Rmd, I ran into an issue at line 193, rbind fails merging the two datasets because they don't have the same number of columns:

Error in rbind(deparse.level, ...) : numbers of columns of arguments do not match

I tried to run your code following the instructions, without much success so far. Warning: I have next to no R experience, so I am really just stupidly following your instructions.

The first time I tried to run report.Rmd in RStudio, I got an error message telling me that package devtools is not installed. I installed it as I had installed the listed dependencies before. Could it be that this package is missing from your dependency list?

On the next run, I got an error reported in line 147: Error: sum(spp.abund$Day.number == 1 + as.numeric((spp.abund$Date - .... is not TRUE Execution halted. I have no idea what to do about that.