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biomodhub / biomod2

BIOMOD is a computer platform for ensemble forecasting of species distributions, enabling the treatment of a range of methodological uncertainties in models and the examination of species-environment relationships.
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Maxent Species Distribution Modelling in R: Error in data.frame(..., check.names = FALSE) #539

Open Kaikash777 opened 2 weeks ago

Kaikash777 commented 2 weeks ago

Issue:

I have two dataframes with 15325 rows, and they have no NAs:

dat_Winter: contains environmental variables dolphin_coords_xy: contains longitude and latitude positions in decimal degrees

I am trying to run a Maxent model using the function maxent() from the dismo package. Whenever I run the maxent model, I keep on getting this error message (below).

Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 1, 2, 0

This message means that I'm trying to create a data.frame from vectors or columns that have a mismatched number of rows. However, both data frames have the same number of rows.

I don't understand why I'm getting this error message as I've met the requirements of 'x' and 'p', I have no NA's, I don't have any duplicates, the rows aren't mismatched in theory. Am I missing something?

I can't share the data due to ownership issues but I can provide a copy of the first 5 rows to show what my data looks like and some dummy data.

Select the presence points from the dataframe 'dolphin_coords1"

dolphin_coords_xy <- dolphin_coords1 %>% dplyr::select(1, 2) dolphin_coords_xy<-as.data.frame(dolphin_coords_xy) p=dolphin_coords_xy

make model

max1_Winter <- maxent(x = dat_Winter, p = dolphin_coords_xy)

------------Do some troubleshooting--------------------------

Check that the rows are of equal length

nrow(dat_Winter) #15325 rows nrow(dolphin_coords_xy) #15325 rows

Check for NA values in columns

sum(is.na(dolphin_coords_xy$x)) # Count NA values (NAs = 0) sum(is.na(dolphin_coords_xy$y)) # Count NA values (NAs = 0)

Check the class of the two data frames

class(dat_Winter) #data.frame class(dolphin_coords_xy) #dataframe

Check Requirements

x = Predictors can either be a Raster* object or SpatialGridDataFrame or a dataframe, in which each column should be a predictor variable and each row a presence or background record

p = If p is a data.frame or matrix it represents a set of point locations; and it must have two columns with the first being the x-coordinate (longitude) and the second the y-coordinate (latitude). Dataframe 1 dat_Winter:

     SST   Chlor.a       Slope  Distance Depth

1 26.03596 0.2764387 3.12927913 0.0000 5 2 25.84813 0.3505107 0.54305966 412.0501 9 3 25.79146 0.3326796 0.96003758 4175.7593 62 4 26.03121 0.2818667 2.14737457 412.5744 5 5 26.03596 0.2764387 3.12927913 0.0000 5

Dataframe 2 coords_dolphins_xy:

     x        y

1 33.89083 27.26778 2 33.86782 27.40854 3 33.86230 27.44623 4 33.88653 27.26957 5 33.88766 27.26848

Dummy data:

structure(list(x = c(33.7250201948918, 33.0372212855145, 33.1162582356483, 33.1780943416525, 33.325465941336, 33.1426498885266, 33.372344966745, 33.7141977476422, 33.5114065359812, 33.4723861014936), y = c(28.0621412244625, 27.6205332666635, 28.0223171819933, 27.5313555219211, 27.1894561205059, 27.5307895665988, 28.1612804006785, 27.5815055153333, 27.3029501273297, 27.3116279762238), Calf_Presence = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), SSS = c(1027.47942044867, 1026.32734772185, 1027.6889518555, 1026.61821882308, 1026.73625519967, 1026.99284255489, 1026.50956621722, 1026.42982337421, 1026.87068500051, 1026.71667900492), SST = c(25.0228688765572, 27.6068648373514, 23.5967889237256, 26.6370548686025, 26.2696984540073, 24.8069121214026, 27.1928669289746, 27.3427573793279, 26.2358166318412, 26.8545404103531), Chlor.a = c(0.234918360422555, 0.552972766326481, 0.372645556572673, 0.158839964433605, 0.155691480776937, 0.322592780862786, 0.16285265978558, 0.155731527084381, 0.207670826649629, 0.174525638280348 ), Slope = c(4.50732010781271, 0.262136190366096, 0.164475474050542, 0.725271958307515, 0.793811857372093, 0.0233933381961778, 2.86868026925737, 2.04465639865241, 1.15032474698361, 0.930412189550645), Distance = c(102293.714232872, 332276.294160756, 126047.003446403, 146918.398130579, 158796.57696904, 27015.5468157929, 190039.211871486, 265043.121310163, 105894.776220919, 98221.3073956403), Depth = c(27, 2, 52, 810, 1081, 76, 819, 879, 705, 738)), row.names = c(NA, 10L), class = "data.frame")Please make sure to close the issue once you consider it as solved

MayaGueguen commented 2 weeks ago

Hello there 👋

I'm afraid I won't be of much help : this is the biomod2 issue page here. Have you tried posting on the dismo issue page ?

Maya