stack() in R does not include all .tiff files in my directory

Question

I am trying to perform stack() in R using enhanced vegetation index (EVI) time-series maps but it doesn't include all the .tiff files in my directory. Here's the list of files when I dir(files.evi):

[1] "MOD13Q1_EVI_2019_001.tif" "MOD13Q1_EVI_2019_017.tif"

[3] "MOD13Q1_EVI_2019_033.tif" "MOD13Q1_EVI_2019_049.tif"

[5] "MOD13Q1_EVI_2019_065.tif" "MOD13Q1_EVI_2019_081.tif"

[7] "MOD13Q1_EVI_2019_097.tif" "MOD13Q1_EVI_2019_113.tif"

[9] "MOD13Q1_EVI_2019_129.tif" "MOD13Q1_EVI_2019_145.tif"

[11] "MOD13Q1_EVI_2019_161.tif" "MYD13Q1_EVI_2019_009.tif"

[13] "MYD13Q1_EVI_2019_025.tif" "MYD13Q1_EVI_2019_041.tif"

[15] "MYD13Q1_EVI_2019_057.tif" "MYD13Q1_EVI_2019_073.tif"

[17] "MYD13Q1_EVI_2019_089.tif" "MYD13Q1_EVI_2019_105.tif"

[19] "MYD13Q1_EVI_2019_121.tif" "MYD13Q1_EVI_2019_137.tif"

[21] "MYD13Q1_EVI_2019_153.tif" "MYD13Q1_EVI_2019_169.tif"

However, when I do

evi <- list.files(files.evi, pattern = glob2rx("*MYD13Q1*.tif$"), full.names = TRUE)
all_evi_st <- stack(evi)

it only stack half of the files on my list:

class : RasterStack

dimensions : 668, 1105, 738140, 11 (nrow, ncol, ncell, nlayers)

resolution : 231.6564, 231.6564 (x, y)

extent : 11251086, 11507066, 1348703, 1503450 (xmin, xmax, ymin, ymax)

crs : +proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs

names : MYD13Q1_EVI_2019_009, MYD13Q1_EVI_2019_025, MYD13Q1_EVI_2019_041, MYD13Q1_EVI_2019_057, MYD13Q1_EVI_2019_073, MYD13Q1_EVI_2019_089, MYD13Q1_EVI_2019_105, MYD13Q1_EVI_2019_121, MYD13Q1_EVI_2019_137, MYD13Q1_EVI_2019_153, MYD13Q1_EVI_2019_169

Can anyone tell me what's happening and what's the workaround? I am new in remote sensing and still shabby with R.

Other info I can give about the time-series images is that they are from MODIS TERRA and AQUA time series derived from the 250 m 16-day composite vegetation index products (MOD13Q1/MYD13Q1).

Answer 1

In your code example

 evi <- list.files(files.evi, pattern = glob2rx("*MYD13Q1*.tif$"), full.names = TRUE)

in the part after "pattern = ..." you specifically select only the second part of your files, starting with "MYD". the not selected files start with "MOD13Q1", so they are not selected by your code :) You need to change it to:

 evi <- list.files(files.evi, pattern = glob2rx("*13Q1*.tif$"), full.names = TRUE)

then it should work as desired :)

Answer 2

It isn't clear how you generated files.evi, but in this case I feel like an easy solution to the problem is using what you know works: If dir(files.evi) returns the list of files you want to work with, then use that object to create your raster stack with:

d = dir(files.evi)
myraster = raster::stack(d)

To expand on the actual problem you have, I'm trying to replicate it on my computer, and I think it somehow relates to file structure. Here, I navigate to a working directory on my computer and then make a path to a subdirectory analagous to what returns when you print(files.evi) in the comments. I have a series of .tif files in the subdirectory, with no similarly-names files in the base directory. Trying to use stack(files.evi) may because the full names are not generated with this instance of dir(), unless you set full.names = TRUE. Both your use of list.files() and sn1ks solution work, but the "solution" that works above for you in the comments (in the absence of dir(x, full.names = TRUE) actually only works when I set the working directory to the same subdirectory that contains my images of interest.

setwd('PATH/TO/DIRECTORY/')

list.files()
files.evi = "PATH/TO/DIRECTORY/SUBDIRECTORY"
dir(files.evi)

evi <- list.files(files.evi, pattern = glob2rx("*STARTNAME*.tif$"), full.names = TRUE)
evi

evi.b <- list.files(files.evi, pattern = glob2rx("*MIDNAME*.tif$"), full.names = TRUE)
evi.b

myrastera = raster::stack(evi)
myrasterb = raster::stack(evi.b)
myrasterc = raster::stack(dir(files.evi, full.names = TRUE))
myrasterd = raster::stack(dir(files.evi)) 

If line 1 = setwd("PATH/TO/DIRECTORY"),myrasterd = ras... returns an error because files don't exist in current working directory BUT if line 1 = setwd("PATH/TO/DIRECTORY/SUBDIRECTORY"), myrasterd = ras... works fine.