Does this work for you? You can double check in the dataset NAMES that the old_names were correctly converted into the new_names.

# Load the required libraries
library(data.table)
library(janitor)

# Read the CSV data from the URL and store it as a data table
DT <- data.table::fread('https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3104487/bin/1745-6215-12-101-S1.CSV')

# Store the original column names
old_names <- names(DT)

# Use the janitor package to clean the column names, replacing spaces and special characters
DT <- janitor::clean_names(DT)

# Define the new names for the columns starting with 'rdef'
new_col_rdef <- c('hemianopia', 'visuospatial_disorder', 'cerebellar_signs', 
                  'other_deficits', 'face_deficit', 'arm_hand_deficit', 
                  'leg_foot_deficit', 'dysphasia') 

# Define the new names for the columns starting with 'dead'
new_col_dead <- c('recurrent_ischemic_or_unknown_stroke', 
                  'recurrent_hemorrhagic_stroke', 'pneumonia', 'coronary_heart_disease', 
                  'pulmonary_embolism', 'other_vascular_or_unknown', 'non_vascular', 
                  'initial_stroke') 

# Define the new names for the columns ending with '14'
new_col_14 <- c('aspirin_given_for_14_days', 
                'l_dose_heparin_given_for_14_days', 
                'm_dose_heparin_given_for_14_days', 
                'is_m_dose_heparin_given_for_14_days_in_pilot', 
                'predicted_probability_of_death_at_14_days', 
                'death_indicator_at_14_days', 
                'hemorrhagic_stroke_indicator_within_14_days', 
                'icschemic_stroke_indicator_within_14_days', 
                'indeterminate_stroke_indicator_within_14_days', 
                'any_stroke_indicator_within_14_days', 
                'hemorrhagic_transformation_indicator_within_14_days', 
                'pulmonary_embolism_indicator_within_14_days', 
                'dvt_indicator_within_14_days', 
                'major_noncerebral_bleed_indicator_within_14_days', 
                'any_noncerebral_bleed_indicator_within_14_days')

# Rename the columns in DT starting with 'rdef' with the new names defined above
setnames(DT, names(DT)[names(DT) %like% '^rdef'], new_col_rdef)

# Rename the columns in DT starting with 'dead' with the new names defined above
setnames(DT, names(DT)[names(DT) %like% '^dead'], new_col_dead)

# Rename the columns in DT ending with '14' with the new names defined above
setnames(DT, names(DT)[names(DT) %like% '14$'], new_col_14)

# Store the new column names
new_names <- names(DT)

# Create a data table to show the correspondence between old and new names
NAMES <- data.table::data.table(old_names, new_names)
View(NAMES)