Persistence homogy

[lindasheila]

Dear All,

Please how do I read data from and external file to obtain the persistence homology:

The file has 4 columns: x y z. and it is in a certain directory let's say /home/linda/Destop/file.

Thank you!

[rrrlw]

I would use either read.table from the utils package or one of the read_* functions from the readr package. The exact function you use will depend on the format of your external data file. For instance, if you have a CSV, you would use one of the following blocks of code:

# code block using base R
library(TDAstats)

# read in data (change my_file.csv to your actual file name)
input_data <- read.csv("/home/linda/Desktop/file/my_file.csv")

# select the columns of interest and store in a new data frame
df_data <- input_data[, c("x", "y", "z")]

# convert that data frame to a numeric matrix
mat_data <- as.matrix(df_data)

# calculate persistent homology
homology_output <- calculate_homology(mat_data)

# code block using tidyverse
library(tidyverse)
library(TDAstats)

# read in data (change my_file.csv to your actual file name)
input_data <- read_csv("/home/linda/Desktop/file/my_file.csv")

# select the numeric columns of interest, convert to a matrix, and calculate persistent homology
homology_output <- input_data %>%
  select(x, y, z) %>%
  as.matrix() %>%
  calculate_homology()

Best of luck!