#2: Decreasing calculation time

Nadege Belouard¹

2024-08-22

Aim and setup

In case of extremely large species occurrence datasets, it may take a long time to run the analyses. Any number of sectors will provide the accurate results. However, computational time may be decreased by increasing the number of sectors considered. The higher the number of sectors, the larger the invasion radius at which points are compared by pairs in find_thresholds, so the fewer distances need to be calculated. However, the lower the number of sectors, the better pre-identification of spatial discontinuities and the more pruned the list of potential jumps, so the faster find_jumps. The lowest computational time is therefore obtained by a trade-off between dataset size, invasion radius, and number of sectors.

We demonstrate the effect of the number of sectors on computational time on the SLF dataset.

Load the grid data created in the first vignette

grid_data <- read.csv(file.path(here::here(), "exported-data", "grid_data.csv"))  

Compare calculation times

Run the jumpID functions successively for 16, 40, and 80 sectors and compare computation times.

## [1] "Sectors: 16"
## 2024-08-22 14:53:41.64369 Start sector attribution... Sector attribution completed. 
## 2024-08-22 14:53:41.686407 Start finding thresholds... Sector 1/16...  2/16...  3/16...  4/16...  5/16...  6/16...  7/16...  8/16...  9/16...  10/16...  11/16...  12/16...  13/16...  14/16...  15/16...  16/16
## Threshold analysis done. 4243 potential jumps were found. 
## 2024-08-22 14:59:53.712392 Start finding jumps... Year 2014 ... Year 2015 ... Year 2016 ... Year 2017 ... Year 2018 ... Year 2019 ... Year 2020 ... Year 2021 ... Year 2022 ... Jump analysis done. 387 jumps were identified.
## 2024-08-22 15:00:15.857648 Start finding secondary diffusion... Year 2017 ...Year 2018 ...Year 2019 ...Year 2020 ...Year 2021 ...Year 2022 ...Analysis of secondary diffusion done. 
## [1] "Sectors: 40"
## 2024-08-22 15:01:23.338102 Start sector attribution... Sector attribution completed. 
## 2024-08-22 15:01:23.357757 Start finding thresholds... Sector 1/40...  2/40...  3/40...  4/40...  5/40...  6/40...  7/40...  8/40...  9/40...  10/40...  11/40...  12/40...  13/40...  14/40...  15/40...  16/40...  17/40...  18/40...  19/40...  20/40...  21/40...  22/40...  23/40...  24/40...  25/40...  26/40...  27/40...  28/40...  29/40...  30/40...  31/40...  32/40...  33/40...  34/40...  35/40...  36/40...  37/40...  38/40...  39/40...  40/40
## Threshold analysis done. 3747 potential jumps were found. 
## 2024-08-22 15:03:14.950368 Start finding jumps... Year 2014 ... Year 2015 ... Year 2016 ... Year 2017 ... Year 2018 ... Year 2019 ... Year 2020 ... Year 2021 ... Year 2022 ... Jump analysis done. 387 jumps were identified.
## 2024-08-22 15:03:36.875957 Start finding secondary diffusion... Year 2016 ...Year 2017 ...Year 2018 ...Year 2019 ...Year 2020 ...Year 2021 ...Year 2022 ...Analysis of secondary diffusion done. 
## [1] "Sectors: 80"
## 2024-08-22 15:04:21.741394 Start sector attribution... Sector attribution completed. 
## 2024-08-22 15:04:21.760537 Start finding thresholds... Sector 1/80...  2/80...  3/80...  4/80...  5/80...  6/80...  7/80...  8/80...  9/80...  10/80...  11/80...  12/80...  13/80...  14/80...  15/80...  16/80...  17/80...  18/80...  19/80...  20/80...  21/80...  22/80...  23/80... Warning: no negative survey in the gap identified in sector 23 and year 2021 after 106 km. The spatial discontinuity that is identified may be due to few surveys done in this area, or space divided into too many sectors. Consider decreasing the number of sectors 
## Warning: no negative survey in the gap identified in sector 23 and year 2022 after 106 km. The spatial discontinuity that is identified may be due to few surveys done in this area, or space divided into too many sectors. Consider decreasing the number of sectors 
##  24/80...  25/80...  26/80...  27/80...  28/80...  29/80...  30/80...  31/80...  32/80...  33/80... Warning: no negative survey in the gap identified in sector 33 and year 2019 after 113 km. The spatial discontinuity that is identified may be due to few surveys done in this area, or space divided into too many sectors. Consider decreasing the number of sectors 
## Warning: no negative survey in the gap identified in sector 33 and year 2020 after 113 km. The spatial discontinuity that is identified may be due to few surveys done in this area, or space divided into too many sectors. Consider decreasing the number of sectors 
##  34/80...  35/80...  36/80...  37/80...  38/80...  39/80...  40/80...  41/80...  42/80...  43/80...  44/80...  45/80...  46/80...  47/80...  48/80...  49/80...  50/80...  51/80...  52/80...  53/80...  54/80...  55/80...  56/80...  57/80...  58/80...  59/80...  60/80...  61/80...  62/80...  63/80...  64/80...  65/80...  66/80...  67/80...  68/80...  69/80...  70/80...  71/80...  72/80...  73/80...  74/80...  75/80...  76/80...  77/80...  78/80...  79/80...  80/80
## Threshold analysis done. 5034 potential jumps were found. 
## 2024-08-22 15:04:40.929554 Start finding jumps... Year 2014 ... Year 2015 ... Year 2016 ... Year 2017 ... Year 2018 ... Year 2019 ... Year 2020 ... Year 2021 ... Year 2022 ... Jump analysis done. 387 jumps were identified.
## 2024-08-22 15:05:14.605223 Start finding secondary diffusion... Year 2016 ...Year 2017 ...Year 2018 ...Year 2019 ...Year 2020 ...Year 2021 ...Year 2022 ...Analysis of secondary diffusion done.

##    s potJumps Jumps    Total_time
## 1 16     4243   387 7.694898 mins
## 2 40     3747   387 2.973373 mins
## 3 80     5034   387 2.109599 mins

For this dataset, all computational times are decreased by dividing space into 40 sectors instead of 16. Data is not dense enough for dividing space into 80 sectors, as indicated by multiple warning messages from find_threshold.

– end of vignette –