create_dictionary.R

# -----------------------------------------------------------------------------#
# COMBINE THE FILES
# -----------------------------------------------------------------------------#
library(tidyverse)
library(ggplot2)
library(ggsci)
library(lubridate)

# set the path where you save the 2 large csv files (pronet_all and 
# prescient_all) including all individuals
setwd('C:/Users/Nora/Documents/Harvard/U24/Outcomes/testOutcomesNew/')
# -----------------------------------------------------------------------------#
# create a distribution plot for each variable

pronet_all <- read.csv('pronet_outcome_new.csv')
prescient_all <- read.csv('prescient_all.csv')

# divide the data based on their data-types
pronet_all_integer <- pronet_all %>%
  filter(data_type == 'Integer')%>%
  mutate(value = case_when(data_type == 'Integer' ~ as.integer(value)))

pronet_all_float <- pronet_all %>%
  filter(data_type == 'Float')%>%
  mutate(value = case_when(data_type == 'Float' ~ as.numeric(value)))

pronet_all_date <- pronet_all %>%
  filter(data_type == 'Date')%>%
  mutate(value = case_when(data_type == 'Date' ~ as.Date(ymd_hms(value))))

prescient_all_integer <- prescient_all %>%
  filter(data_type == 'Integer')%>%
  mutate(value = case_when(data_type == 'Integer' ~ as.integer(value)))

prescient_all_float <- prescient_all %>%
  filter(data_type == 'Float')%>%
  mutate(value = case_when(data_type == 'Float' ~ as.numeric(value)))

prescient_all_date <- prescient_all %>%
  filter(data_type == 'Date')%>%
  mutate(value = case_when(data_type == 'Date' ~ as.Date(ymd_hms(value))))

# combine the data from the two dataframes
outcomes_integer <- pronet_all_integer %>%
  rbind(., prescient_all_integer)%>%
  dplyr::select(-data_type)%>%
  pivot_wider(names_from = 'variable', values_from = 'value')

outcomes_date <- pronet_all_date %>%
  rbind(., prescient_all_date)%>%
  dplyr::select(-data_type)%>%
  pivot_wider(names_from = 'variable', values_from = 'value')

outcomes_float <- pronet_all_float %>%
  rbind(., prescient_all_float)%>%
  dplyr::select(-data_type)%>%
  pivot_wider(names_from = 'variable', values_from = 'value')

# -----------------------------------------------------------------------------#
# Create the dictionary of the data
# -----------------------------------------------------------------------------#

# combine the data from the two dataframes
outcomes_integer_long <- pronet_all_integer %>%
#  rbind(., prescient_all_integer)%>%
  group_by(variable) %>%
  arrange(value)%>%
  summarize(distinct_values = paste(unique(value), collapse = "; "))%>%
  mutate(n_distinct_values = str_count(distinct_values, ";\\s?") + 1)%>%
  mutate(distinct_values_list = str_extract_all(distinct_values, "-?\\d+"),
         distinct_values_list_no_missing = lapply(distinct_values_list, function(x) x[x != "-300" & x != "-900"]),
         distinct_values_list_numeric = lapply(distinct_values_list_no_missing, as.numeric),
         min_value = sapply(distinct_values_list_numeric, min),
         max_value = sapply(distinct_values_list_numeric, max))%>%
  dplyr::select(variable, distinct_values, n_distinct_values, min_value, max_value)%>%
  mutate_all(as.character)

outcomes_date_long <- pronet_all_date %>%
#  rbind(., prescient_all_date)%>%
  group_by(variable) %>%
  arrange(value)%>%
  summarize(distinct_values = paste(unique(value), collapse = "; "))%>%
  mutate(n_distinct_values = str_count(distinct_values, ";\\s?") + 1)%>%
  mutate(distinct_values_list = str_extract_all(distinct_values, "\\d{4}-\\d{2}-\\d{2}"),
         distinct_values_list_no_missing = 
           lapply(distinct_values_list, function(x) x[x != "1903-03-03" & x != "1909-09-09"]),
         distinct_values_list_numeric = lapply(distinct_values_list_no_missing, function(x) as.Date(x, format = "%Y-%m-%d")),
         min_value = sapply(distinct_values_list_numeric, min, na.rm = TRUE),
         max_value = sapply(distinct_values_list_numeric, max, na.rm = TRUE))%>%
  dplyr::select(variable, distinct_values, n_distinct_values, min_value, max_value)%>%
  mutate(min_value = as.Date(min_value, origin = "1970-01-01"),
         max_value = as.Date(max_value, origin = "1970-01-01"))%>%
  mutate_all(as.character)

outcomes_float_long <- pronet_all_float %>%
#  rbind(., prescient_all_float)%>%
  group_by(variable) %>%
  arrange(value)%>%
  summarize(distinct_values = paste(unique(value), collapse = "; "))%>%
  mutate(n_distinct_values = str_count(distinct_values, ";\\s?") + 1)%>%
  mutate(distinct_values_list = str_extract_all(distinct_values, "(?<!-)[0-9]+(?:\\.[0-9]+)?"),
         distinct_values_list_no_missing = lapply(distinct_values_list, function(x) x[x != "-300" & x != "-900"]),
         distinct_values_list_numeric = lapply(distinct_values_list_no_missing, as.double),
         min_value = sapply(distinct_values_list_numeric, min),
         max_value = sapply(distinct_values_list_numeric, max))%>%
  dplyr::select(variable, distinct_values, n_distinct_values, min_value, max_value)%>%
  mutate_all(as.character)


outcomes_long_types <- outcomes_float_long %>%
  rbind(., outcomes_integer_long)%>%
  rbind(., outcomes_date_long)%>%
  dplyr::select(-n_distinct_values)

# -----------------------------------------------------------------------------#

outcome_long <- pronet_all %>%
  distinct(variable, data_type, .keep_all = FALSE)%>%
  left_join(., outcomes_long_types, by = 'variable')

# Email from Sylvain with the indications for the dictionary

# Nora, if it's not already done could you generate a data dictionary that has the following information:
#   
# Variable name (use REDCap name if it already exists) - update for the psychs variables!
# Data type (integer, date, etc.) - DONE
# Description (something readable: e.g., "Anxiety score") - UPDATE
# Value range if applicable (e.g., 1-10 or M;F or 0;1) - DONE
# Notes (the formula used to calculate the score, perhaps note your code but the information originally provided by the expert?) DONE
# Aliases:  If an expert has given you a variable name that is different than the one in REDCap, put it here.

# I have added the name of the csv and the name of the expert as well.

variables_outcome <- outcome_long %>% 
  mutate(csv_names = 
           case_when(
             str_detect(variable, 'pds_total_score|chrpds_pds_f5b_p') ~ 'pubertal_developmental_scale.csv',
             str_detect(variable, 'global_role') ~ 'global_functioning_role_scale.csv',
             str_detect(variable, 'global_social') ~ 'global_functioning_social_scale.csv',
             str_detect(variable, 'bprs') ~ 'bprs.csv',
             str_detect(variable, 'perceived_stress') ~ 'perceived_stress_scale.csv',
             str_detect(variable, 'oasis') ~ 'oasis.csv',
             str_detect(variable, 'perceived_disc') ~ 'perceived_discrimination_scale.csv',
             str_detect(variable, 'cdss') ~ 'cdss.csv',
             str_detect(variable, 'chrsofas_currscore_fu|chrsofas_currscore12mo_fu') ~ 'sofas_followup.csv',
             str_detect(variable, 'chrsofas_premorbid|chrsofas_currscore12mo|chrsofas_currscore|chrsofas_lowscore') ~ 'sofas_screening.csv',
             str_detect(variable, 'psychs|sips|caarms|psychosis|dsm_schizo|first_degree_relative|drop30_sofas|premorbid_less90|conversion_date|sofas_premorbid') ~ 'psychs.csv',
             variable == 'sofas_oneyearago' | variable == 'sofas_pasyear' | variable == 'sofas_pastmonth' ~ 'psychs.csv',
             str_detect(variable, 'nsipr') ~ 'nsipr.csv',
             str_detect(variable, 'promis') ~ 'item_promis_for_sleep.csv',
             str_detect(variable, 'chrpgi_2') ~ 'pgis.csv',
             str_detect(variable, 'promis') ~ 'item_promis_for_sleep.csv',
             str_detect(variable, 'cssrs') ~ 'cssrs_baseline.csv',
             str_detect(variable, 'chrpps') ~ 'psychosis_polyrisk_score.csv',
             str_detect(variable, 'tobac|alco|cannab|cocaine|ampheta|inhalant|sedative|halluc|opiod|other') ~ 'assist.csv',
             str_detect(variable, 'chrpred') ~ 'ra_prediction.csv',
             str_detect(variable, 'childhood_subtotal|adolescence_sub|adulthood_sub|only_childhood|upto_') ~ 'premorbid_adjustment_scale.csv'))%>%
  mutate(description = 
           case_when(variable == "psychs_pos_tot"                            ~ 'PSYCHS Total Score',
                     variable == "psychs_sips_p1"                            ~ 'SIPS P1 Severity Score: Unusual Thought Content/Delusional Ideas',
                     variable == "psychs_sips_p2"                            ~ 'SIPS P2 Severity Score: Suspiciousness/Persecutory Ideas',
                     variable == "psychs_sips_p3"                            ~ 'SIPS P3 Severity Score: Grandiose Ideas',
                     variable == "psychs_sips_p4"                            ~ 'SIPS P4 Severity Score: Perceptual Abnormalities/Hallucinations',
                     variable == "psychs_sips_p5"                            ~ 'SIPS P5 Severity Score: Disorganized Communication',
                     variable == "sips_pos_tot"                              ~ 'SIPS Positive Severity Score',
                     variable == "psychs_caarms_p1"                          ~ 'product of frequency by intensity of positive scale P1',
                     variable == "psychs_caarms_p2"                          ~ 'product of frequency by intensity of positive scale P2',
                     variable == "psychs_caarms_p3"                          ~ 'product of frequency by intensity of positive scale P3',
                     variable == "psychs_caarms_p4"                          ~ 'product of frequency by intensity of positive scale P4',
                     variable == "caarms_pos_tot"                            ~ 'sum of Caarms P1-4',
                     variable == "psychosis_onset_date"                      ~ 'earliest date (minimum) of all psychosis onset dates measured',
                     variable == "sips_"                      ~ 'earliest date (minimum) of all psychosis onset dates measured',
                     variable == "chrpsychs_scr_ac1"                         ~ 'Psychosis',
                     variable == "chrpsychs_scr_ac2"                         ~ 'CAARMS BLIPS',
                     variable == "chrpsychs_scr_ac3"                         ~ 'CAARMS APS subthreshold frequency',
                     variable == "chrpsychs_scr_ac4"                         ~ 'CAARMS APS subthreshold intensity',
                     variable == "chrpsychs_scr_ac5"                         ~ 'CAARMS APS',
                     variable == "chrpsychs_scr_ac6"                         ~ 'CAARMS Vulnerability',
                     variable == "chrpsychs_scr_ac7"                         ~ 'CAARMS ultra high risk group',
                     variable == "chrpsychs_scr_ac9"                         ~ 'SIPS - BIPS Progression',
                     variable == "chrpsychs_scr_ac10"                        ~ 'SIPS - BIPS Persistence',
                     variable == "chrpsychs_scr_ac11"                        ~ 'SIPS - BIPS Partial Remission',
                     variable == "chrpsychs_scr_ac12"                        ~ 'SIPS - BIPS Full Remission',
                     variable == "chrpsychs_scr_ac15"                        ~ 'SIPS - APSS Progression',
                     variable == "chrpsychs_scr_ac16"                        ~ 'SIPS - APSS Persistence',
                     variable == "chrpsychs_scr_ac17"                        ~ 'SIPS - APSS Partial Remission',
                     variable == "chrpsychs_scr_ac18"                        ~ 'SIPS - APSS Full Remission',
                     variable == "chrpsychs_scr_ac21"                        ~ 'SIPS - GRD Progression',
                     variable == "chrpsychs_scr_ac22"                        ~ 'SIPS - GRD Persistence',
                     variable == "chrpsychs_scr_ac23"                        ~ 'SIPS - GRD Partial Remission',
                     variable == "chrpsychs_scr_ac24"                        ~ 'SIPS - GRD Full Remission',
                     variable == "chrpsychs_scr_ac27"                        ~ 'SIPS - CHR Progression',
                     variable == "chrpsychs_scr_ac28"                        ~ 'SIPS - CHR Persistence',
                     variable == "chrpsychs_scr_ac29"                        ~ 'SIPS - CHR Partial Remission',
                     variable == "chrpsychs_scr_ac30"                        ~ 'SIPS - CHR Full Remission',
                     variable == "chrpsychs_scr_ac31"                        ~ 'SIPS - Current Status',
                     variable == "chrpsychs_scr_ac32"                        ~ 'DSM5 - Attenuated Psychosis',
                     variable == "conversion_date"                           ~ 'Date of Conversion',
                     variable == "hcpsychs_fu_ac1"              ~ 'Psychosis',
                     variable == "hcpsychs_fu_ac1_curr"         ~ 'Psychosis at any time since the previous visit',
                     variable == "hcpsychs_fu_ac1_prev"         ~ 'Psychosis at previous visit',
                     variable == "hcpsychs_fu_ac1_first"        ~ 'Psychosis for the first time at the current visit',
                     variable == "hcpsychs_fu_ac1_conv"         ~ 'Psychosis for the first time at the current visit and no psychosis before',
                     variable == "hcpsychs_fu_ac9"              ~ 'SIPS BIPS Progression',
                     variable == "hcpsychs_fu_ac10"             ~ 'SIPS BIPS Persistence',
                     variable == "hcpsychs_fu_ac11"             ~ 'SIPS BIPS Partial Remission',
                     variable == "hcpsychs_fu_ac12"             ~ 'SIPS BIPS Full Remission',
                     variable == "hcpsychs_fu_ac15"             ~ 'SIPS APSS Progression',
                     variable == "hcpsychs_fu_ac16"             ~ 'SIPS APSS Persistence',
                     variable == "hcpsychs_fu_ac17"             ~ 'SIPS APSS Partial Remission',
                     variable == "hcpsychs_fu_ac18"             ~ 'SIPS APSS Full Remission',
                     variable == "hcpsychs_fu_ac21"             ~ 'SIPS GRD Progression',
                     variable == "hcpsychs_fu_ac22"             ~ 'SIPS GRD Persistence',
                     variable == "hcpsychs_fu_ac23"             ~ 'SIPS GRD Partial Remission',
                     variable == "hcpsychs_fu_ac24"             ~ 'SIPS GRD Full Remission',
                     variable == "hcpsychs_fu_ac27"             ~ 'SIPS CHR Progression',
                     variable == "hcpsychs_fu_ac28"             ~ 'SIPS CHR Persistence',
                     variable == "hcpsychs_fu_ac29"             ~ 'SIPS CHR Partial Remission',
                     variable == "hcpsychs_fu_ac30"             ~ 'SIPS CHR Full Remission',
                     variable == "hcpsychs_fu_ac31"             ~ 'SIPS Current Status',
                     variable == "hcpsychs_fu_ac32"             ~ 'DSM-5 Attenuated Psychosis Syndrome',
                     variable == "chrpsychs_fu_ac1"              ~ 'Psychosis',
                     variable == "chrpsychs_fu_ac1_curr"         ~ 'Psychosis at any time since the previous visit',
                     variable == "chrpsychs_fu_ac1_prev"         ~ 'Psychosis at previous visit',
                     variable == "chrpsychs_fu_ac1_first"        ~ 'Psychosis for the first time at the current visit',
                     variable == "chrpsychs_fu_ac1_conv"         ~ 'Psychosis for the first time at the current visit and no psychosis before',
                     variable == "chrpsychs_fu_ac9"              ~ 'SIPS BIPS Progression',
                     variable == "chrpsychs_fu_ac10"             ~ 'SIPS BIPS Persistence',
                     variable == "chrpsychs_fu_ac11"             ~ 'SIPS BIPS Partial Remission',
                     variable == "chrpsychs_fu_ac12"             ~ 'SIPS BIPS Full Remission',
                     variable == "chrpsychs_fu_ac15"             ~ 'SIPS APSS Progression',
                     variable == "chrpsychs_fu_ac16"             ~ 'SIPS APSS Persistence',
                     variable == "chrpsychs_fu_ac17"             ~ 'SIPS APSS Partial Remission',
                     variable == "chrpsychs_fu_ac18"             ~ 'SIPS APSS Full Remission',
                     variable == "chrpsychs_fu_ac21"             ~ 'SIPS GRD Progression',
                     variable == "chrpsychs_fu_ac22"             ~ 'SIPS GRD Persistence',
                     variable == "chrpsychs_fu_ac23"             ~ 'SIPS GRD Partial Remission',
                     variable == "chrpsychs_fu_ac24"             ~ 'SIPS GRD Full Remission',
                     variable == "chrpsychs_fu_ac27"             ~ 'SIPS CHR Progression',
                     variable == "chrpsychs_fu_ac28"             ~ 'SIPS CHR Persistence',
                     variable == "chrpsychs_fu_ac29"             ~ 'SIPS CHR Partial Remission',
                     variable == "chrpsychs_fu_ac30"             ~ 'SIPS CHR Full Remission',
                     variable == "chrpsychs_fu_ac31"             ~ 'SIPS Current Status',
                     variable == "chrpsychs_fu_ac32"             ~ 'DSM-5 Attenuated Psychosis Syndrome',
                     variable == "psychosis_current"           ~ 'Psychosis Current',
                     variable == "psychosis_previous"          ~ 'Psychosis Previous',
                     variable == "psychosis_first"             ~ 'Psychosis First',
                     variable == "psychosis_conversion"        ~ 'Psychosis Conversion',
                     variable == "chrpps_sum1" ~ 'Risk 1 based on Sex/Age',
                     variable == "chrpps_sum2" ~ 'Risk 2 based on handedness',                             
                     variable == "chrpps_sum7" ~ 'Risk 7 based on paternal age',
                     variable == "chrpps_sum8" ~ 'Risk 8 based on social economic status',                             
                     variable == "chrpps_sum9" ~ 'Risk 9 based on parental severe mental illness',
                     variable == "chrpps_sum10" ~ 'Risk 10 based on adult life events',                            
                     variable == "chrpps_sum11" ~ 'Risk 11 based on daily smoking',
                     variable == "chrpps_sum12" ~ 'Risk 12 based on heavy cannabis use',                            
                     variable == "chrpps_sum13" ~ 'Risk 13 based on childhood trauma',
                     variable == "chrpps_sum14" ~ 'Risk 14 based on Trait anhedonia',                            
                     variable == "chrassist_tobacco"       ~ 'Severity of use: tobacco',
                     variable == "chrassist_alcohol"       ~ 'Severity of use: alcohol',                                 
                     variable == "chrassist_cannabis"      ~ 'Severity of use: cannabis',
                     variable == "chrassist_cocaine"       ~ 'Severity of use: cocaine',                                 
                     variable == "chrassist_amphetamines"  ~ 'Severity of use: amphetamines',
                     variable == "chrassist_inhalants"     ~ 'Severity of use: inhalants',                               
                     variable == "chrassist_sedatives"     ~ 'Severity of use: sedatives',
                     variable == "chrassist_hallucinogens" ~ 'Severity of use: hallucinogens',
                     variable == "chrassist_opiods"        ~ 'Severity of use: opiods',
                     variable == "chrassist_other"         ~ 'Severity of use: other',                                   
                     variable == "chrpas_childhood_subtotal"                 ~ 'PAS: Childhood',
                     variable == "chrpas_early_adolescence_subtotal"         ~ 'PAS: Early Adolescence',              
                     variable == "chrpas_late_adolescence_subtotal"          ~ 'PAS: Late Adolescence',
                     variable == "chrpas_adulthood_subtotal"                 ~ 'PAS: Adulthood',                      
                     variable == "chrpas_total_score_only_childhood"         ~ 'PAS: Only Childhood',
                     variable == "chrpas_total_score_upto_early_adolescence" ~ 'PAS: Up to early adolescence',      
                     variable == "chrpas_total_score_upto_late_adolescence"  ~ 'PAS: Up to late adolescence',
                     variable == "chrpas_total_score_upto_adulthood"         ~ 'PAS: Up to Adulthood',              
                     variable == "chrcssrs_intensity_lifetime"           ~ 'CSSRS (Suicide intensity): Lifetime',
                     variable == "chrcssrs_intensity_pastmonth"          ~ 'CSSRS (Suicide intensity): Past Month',               
                     variable == "chrpred_transition"                 ~ 'Rater prediction Transition: Yes/No',
                     variable == "chrpred_experience"                 ~ 'Month of experience of the raters',                      
                     variable == "chrpgi_2"                              ~ 'Overall health symptoms of the last 7 days (PGI-S)',
                     variable == "chrpromis_total"                       ~ 'Sleep quality (PROMIS)',                            
                     variable == "chrgfrs_decline_in_global_role_functioning" ~ 'Decline in role functioning (highest score in lifetime - current score)',
                     variable == "chrgfss_decline_in_global_social_functioning" ~ 'Decline in social functioning (highest score in lifetime - current score)',    
                     variable == "chrnsipr_motivation_and_pleasure_dimension" ~ 'Motivation and Pleasure (NSIPR)',
                     variable == "chrnsipr_diminished_expression_dimension" ~ 'Diminished Expression Dimension (NSIPR)',  
                     variable == "chrnsipr_avolition_domain" ~ 'Avolition (NSIPR)',
                     variable == "chrnsipr_asociality_domain" ~ 'Asociality (NSIPR)',                 
                     variable == "chrnsipr_anhedonia_domain" ~ 'Anhedonia (NSIPR)',
                     variable == "chrnsipr_blunted_affect_domain" ~ 'Blunted Affect (NSIPR)',             
                     variable == "chrnsipr_item11_rating" ~ 'Alogia (NSIPR)',
                     variable == "chrsofas_premorbid" ~ 'SOFAS: Premorbid',                      
                     variable == "chrsofas_currscore12mo" ~ 'SOFAS: 12 months ago',
                     variable == "chrsofas_currscore" ~ 'SOFAS: Current score at screening',        
                     variable == "chrsofas_lowscore" ~ 'SOFAS: Lowest score in the last year',
                     variable == "chrsofas_currscore_fu" ~ 'SOFAS: current score at follow-up',        
                     variable == "chrsofas_currscore12mo_fu" ~ 'SOFAS: Score 12 months ago at follow up',
                     variable == "chrpds_total_score_female_sex" ~ 'Pubertal developmental scale: total score',                     
                     variable == "chrpds_total_score_male_sex" ~ 'Pubertal developmental scale: total score',                     
                     variable == "chrpds_pds_f5b_p" ~ 'Menarche: Yes/No',
                     variable == "chrbprs_bprs_total" ~ 'BRPS: Total score',                              
                     variable == "chrbprs_affect_subscale" ~ 'BRPS: Affect subscale',
                     variable == "chrbprs_positive_symptom_subscale" ~ 'BRPS: Positive symptoms subscale',          
                     variable == "chrbprs_negative_symptom_subscale" ~ 'BRPS: Negative symptoms subscale',
                     variable == "chrbprs_activation_subscale" ~ 'BRPS: Activation subscale',
                     variable == "chrbprs_disorganization_subscale" ~ 'BRPS: Disorganization',
                     variable == "chroasis_total" ~ 'OASIS total (Anxiety)',                             
                     variable == "chrpds_perceived_discrimination_total" ~ 'Total score of Perceived discrimination',
                     variable == "chrcdss_total" ~ 'Total of depressive symptoms (CDSS)',                              
                     variable == "chrpss_perceived_stress_scale_total" ~ 'Total of perceived stress'))%>%
  mutate(diverging_expert_variable_name = 
           case_when(variable == "psychs_pos_tot"        ~ 'PSYCHS Total Score',
                     variable == "psychs_sips_p1"        ~ 'SIPS P1 Severity Score: Unusual Thought Content/Delusional Ideas',
                     variable == "psychs_sips_p2"        ~ 'SIPS P2 Severity Score: Suspiciousness/Persecutory Ideas',
                     variable == "psychs_sips_p3"        ~ 'SIPS P3 Severity Score: Grandiose Ideas',
                     variable == "psychs_sips_p4"        ~ 'SIPS P4 Severity Score: Perceptual Abnormalities/Hallucinations',
                     variable == "psychs_sips_p5"        ~ 'SIPS P5 Severity Score: Disorganized Communication',
                     variable == "sips_pos_tot"          ~ 'SIPS Positive Severity Score',
                     variable == "psychs_caarms_p1"      ~ 'product of frequency by intensity of positive scale P1',
                     variable == "psychs_caarms_p2"      ~ 'product of frequency by intensity of positive scale P2',
                     variable == "psychs_caarms_p3"      ~ 'product of frequency by intensity of positive scale P3',
                     variable == "psychs_caarms_p4"      ~ 'product of frequency by intensity of positive scale P4',
                     variable == "caarms_pos_tot"        ~ 'sum of Caarms P1-4',
                     variable == "psychosis_onset_date"  ~ 'earliest date (minimum) of all psychosis onset dates measured',
                     variable == "chrpsychs_scr_ac1"   ~ 'Psychosis - yes/no',
                     variable == "chrpsychs_scr_ac2"   ~ 'CAARMS BLIPS',
                     variable == "chrpsychs_scr_ac3"   ~ 'CAARMS APS subthreshold frequency',
                     variable == "chrpsychs_scr_ac4"   ~ 'CAARMS APS subthreshold intensity',
                     variable == "chrpsychs_scr_ac5"   ~ 'CAARMS APS',
                     variable == "chrpsychs_scr_ac6"   ~ 'CAARMS Vulnerability',
                     variable == "chrpsychs_scr_ac7"   ~ 'CAARMS ultra high risk group',
                     variable == "chrpsychs_scr_ac9"   ~ 'SIPS - BIPS Progression',
                     variable == "chrpsychs_scr_ac10"  ~ 'SIPS - BIPS Persistence',
                     variable == "chrpsychs_scr_ac11"  ~ 'SIPS - BIPS Partial Remission',
                     variable == "chrpsychs_scr_ac12"  ~ 'SIPS - BIPS Full Remission',
                     variable == "chrpsychs_scr_ac15"  ~ 'SIPS - APSS Progression',
                     variable == "chrpsychs_scr_ac16"  ~ 'SIPS - APSS Persistence',
                     variable == "chrpsychs_scr_ac17"  ~ 'SIPS - APSS Partial Remission',
                     variable == "chrpsychs_scr_ac18"  ~ 'SIPS - APSS Full Remission',
                     variable == "chrpsychs_scr_ac21"  ~ 'SIPS - GRD Progression',
                     variable == "chrpsychs_scr_ac22"  ~ 'SIPS - GRD Persistence',
                     variable == "chrpsychs_scr_ac23"  ~ 'SIPS - GRD Partial Remission',
                     variable == "chrpsychs_scr_ac24"  ~ 'SIPS - GRD Full Remission',
                     variable == "chrpsychs_scr_ac27"  ~ 'SIPS - CHR Progression',
                     variable == "chrpsychs_scr_ac28"  ~ 'SIPS - CHR Persistence',
                     variable == "chrpsychs_scr_ac29"  ~ 'SIPS - CHR Partial Remission',
                     variable == "chrpsychs_scr_ac30"  ~ 'SIPS - CHR Full Remission',
                     variable == "chrpsychs_scr_ac31"  ~ 'SIPS - Current Status',
                     variable == "chrpsychs_scr_ac32"  ~ 'DSM5 - Attenuated Psychosis',
                     variable == "conversion_date"             ~ 'Date of Conversion',
                     variable == "psychosis_current"           ~ 'Psychosis Current',
                     variable == "psychosis_previous"          ~ 'Psychosis Previous',
                     variable == "psychosis_first"             ~ 'Psychosis First',
                     variable == "psychosis_conversion"        ~ 'Psychosis Conversion',
                     variable == "chrpps_sum1" ~ '',
                     variable == "chrpps_sum2" ~ '',                             
                     variable == "chrpps_sum7" ~ '',
                     variable == "chrpps_sum8" ~ '',                             
                     variable == "chrpps_sum9" ~ '',
                     variable == "chrpps_sum10" ~ '',                            
                     variable == "chrpps_sum11" ~ '',
                     variable == "chrpps_sum12" ~ '',                            
                     variable == "chrpps_sum13" ~ 'chrpps_sum14',
                     variable == "chrpps_sum14" ~ 'chrpps_sum15',                            
                     variable == "chrassist_tobacco"       ~ '',
                     variable == "chrassist_alcohol"       ~ '',                                 
                     variable == "chrassist_cannabis"      ~ '',
                     variable == "chrassist_cocaine"       ~ '',                                 
                     variable == "chrassist_amphetamines"  ~ '',
                     variable == "chrassist_inhalants"     ~ '',                               
                     variable == "chrassist_sedatives"     ~ '',
                     variable == "chrassist_hallucinogens" ~ '',
                     variable == "chrassist_opiods"        ~ '',
                     variable == "chrassist_other"         ~ '',                                   
                     variable == "chrpas_childhood_subtotal"                 ~ '',
                     variable == "chrpas_early_adolescence_subtotal"         ~ '',              
                     variable == "chrpas_late_adolescence_subtotal"          ~ '',
                     variable == "chrpas_adulthood_subtotal"                 ~ '',                      
                     variable == "chrpas_total_score_only_childhood"         ~ '',
                     variable == "chrpas_total_score_upto_early_adolescence" ~ '',      
                     variable == "chrpas_total_score_upto_late_adolescence"  ~ '',
                     variable == "chrpas_total_score_upto_adulthood"         ~ '',              
                     variable == "chrcssrs_intensity_lifetime"           ~ '',
                     variable == "chrcssrs_intensity_pastmonth"          ~ '',               
                     variable == "chrpred_transition"                 ~ '',
                     variable == "chrpred_experience"                 ~ '',                      
                     variable == "chrpgi_2"                           ~ '',
                     variable == "chrpromis_total"                       ~ 'A total of the 8 items with very poor being 1 and up to very good being 5',                            
                     variable == "chrgfrs_decline_in_global_role_functioning" ~ '',
                     variable == "chrgfss_decline_in_global_social_functioning" ~ '',    
                     variable == "chrnsipr_motivation_and_pleasure_dimension" ~ '',
                     variable == "chrnsipr_diminished_expression_dimension" ~ '',  
                     variable == "chrnsipr_avolition_domain" ~ '',
                     variable == "chrnsipr_asociality_domain" ~ '',                 
                     variable == "chrnsipr_anhedonia_domain" ~ '',
                     variable == "chrnsipr_blunted_affect_domain" ~ '',             
                     variable == "chrnsipr_item11_rating" ~ 'nsipr_alogia_domain',
                     variable == "chrsofas_premorbid" ~ 'SOFAS Premorbid',                      
                     variable == "chrsofas_currscore12mo" ~ 'SOFAS score 12 months ago',
                     variable == "chrsofas_currscore" ~ 'SOFAS current score at screening',        
                     variable == "chrsofas_lowscore" ~ 'SOFAS lowest score in the last year',
                     variable == "chrsofas_currscore_fu" ~ 'SOFAS current score at follow-up',        
                     variable == "chrsofas_currscore12mo_fu" ~ 'SOFAS score 12 months ago from follow up',
                     variable == "chrpds_total_score_sex" ~ 'PDS total score female sex/PDS total score male sex',                     
                     variable == "chrpds_pds_f5b_p" ~ 'pds_menarche',
                     variable == "chrbprs_bprs_total" ~ 'bprs_total',                              
                     variable == "chrbprs_affect_subscale" ~ '',
                     variable == "chrbprs_positive_symptom_subscale" ~ '',          
                     variable == "chrbprs_negative_symptom_subscale" ~ '',
                     variable == "chrbprs_activation_subscale" ~ '',
                     variable == "chrbprs_disorganization_subscale" ~ '',
                     variable == "chroasis_total" ~ '',                             
                     variable == "chrpds_perceived_discrimination_total" ~ '',
                     variable == "chrcdss_total" ~ '',                              
                     variable == "chrpss_perceived_stress_scale_total" ~ ''))%>%
  mutate(Experts = 
           case_when(
             str_detect(variable, 'pds') ~ 'Melissa Kerr',
             str_detect(variable, 'global_role') ~ 'Jean Addington',
             str_detect(variable, 'global_social') ~ 'Jean Addington',
             str_detect(variable, 'bprs') ~ 'Melissa Kerr',
             str_detect(variable, 'perceived_stress') ~ 'Jean Addington',
             str_detect(variable, 'oasis') ~ 'Jean Addington',
             str_detect(variable, 'perceived_disc') ~ 'Jean Addington',
             str_detect(variable, 'cdss') ~ 'Jean Addington',
             str_detect(variable, 'chrsofas_premorbid|chrsofas_currscore12mo|chrsofas_currscore|chrsofas_lowscore') ~ 'Melissa Kerr',
             str_detect(variable, 'chrsofas_currscore_fu|chrsofas_currscore12mo_fu') ~ 'Melissa Kerr',
             str_detect(variable, 'psychs|sips|caarms|psychosis|dsm_schizo|first_degree_relative|drop30_sofas|premorbid_less90|conversion_date|sofas_premorbid') ~ 'Scott Woods',
             variable == 'sofas_oneyearago' | variable == 'sofas_pasyear' | variable == 'sofas_pastmonth' ~ 'Scott Woods',
             str_detect(variable, 'nsipr') ~ 'Greg Strauss',
             str_detect(variable, 'promis') ~ 'Jean Addington',
             str_detect(variable, 'pgi') ~ 'Jean Addington',
             str_detect(variable, 'promis') ~ 'Jean Addington',
             str_detect(variable, 'cssrs') ~ 'Cheryl Corcoran',
             str_detect(variable, 'chrpps') ~ 'Dominic Oliver',
             str_detect(variable, 'tobac|alco|cannab|cocaine|ampheta|inhalant|sedative|halluc|opiod|other') ~ 'Melissa Kerr',
             str_detect(variable, 'chrpred') ~ 'Jean Addington',
             str_detect(variable, 'childhood_subtotal|adolescence_sub|adulthood_sub|only_childhood|upto_') ~ 'Jean Addington'))%>%
  mutate(Notes = 
           case_when(variable == "psychs_pos_tot"                          ~ 'chrpsychs_scr_1d1+chrpsychs_scr_2d1+chrpsychs_scr_3d1+chrpsychs_scr_4d5+chrpsychs_scr_5d1+chrpsychs_scr_6d1+chrpsychs_scr_7d1+chrpsychs_scr_8d1+chrpsychs_scr_9d1+chrpsychs_scr_10d1+chrpsychs_scr_11d1+chrpsychs_scr_12d1+chrpsychs_scr_13d1+chrpsychs_scr_14d1+chrpsychs_scr_15d1',
                     variable == "psychs_sips_p1"                          ~ 'Maximum of chrpsychs_scr_1d1, chrpsychs_scr_3d1, chrpsychs_scr_4d1, chrpsychs_scr_5d1, chrpsychs_scr_6d1',
                     variable == "psychs_sips_p3"                          ~ 'Maximum of chrpsychs_scr_7d1, chrpsychs_scr_8d1',
                     variable == "psychs_sips_p4"                          ~ 'Maximum of chrpsychs_scr_9d1, chrpsychs_scr_10d1, chrpsychs_scr_11d1, chrpsychs_scr_12d1, chrpsychs_scr_13d1, chrpsychs_scr_14d1',
                     variable == "sips_pos_tot"                            ~ 'if screening: psychs_sips_p1+chrpsychs_scr_2d1+psychs_sips_p3+psychs_sips_p4+chrpsychs_scr_15d1, elseif: redcap_event_name != screening and network == pronet and studygroup == hc: psychs_sips_p1+hcpsychs_fu_2d1+psychs_sips_p3+psychs_sips_p4+hcpsychs_fu_15d1, else: psychs_sips_p1+chrpsychs_fu_2d1+psychs_sips_p3+psychs_sips_p4+chrpsychs_fu_15d1',
                     variable == "psychs_caarms_p1"                        ~ 'chrpsychs_scr_1d1*chrpsychs_scr_1d2',
                     variable == "psychs_caarms_p2"                        ~ 'Maximum of (chrpsychs_scr_2d1*chrpsychs_scr_2d2),(chrpsychs_scr_3d1*chrpsychs_scr_3d2),(chrpsychs_scr_4d1*chrpsychs_scr_4d2),(chrpsychs_scr_5d1*chrpsychs_scr_5d2),(chrpsychs_scr_6d1*chrpsychs_scr_6d2),(chrpsychs_scr_7d1*chrpsychs_scr_7d2),(chrpsychs_scr_8d1*chrpsychs_scr_8d2)',
                     variable == "psychs_caarms_p3"                        ~ 'Maximum of (chrpsychs_scr_9d1*chrpsychs_scr_9d2),(chrpsychs_scr_10d1*chrpsychs_scr_10d2),(chrpsychs_scr_11d1*chrpsychs_scr_11d2),(chrpsychs_scr_12d1*chrpsychs_scr_12d2),(chrpsychs_scr_13d1*chrpsychs_scr_13d2),(chrpsychs_scr_14d1*chrpsychs_scr_14d2)',
                     variable == "psychs_caarms_p4"                        ~ 'chrpsychs_scr_15d1*chrpsychs_scr_15d2',
                     variable == "caarms_pos_tot"                          ~ 'psychs_caarms_p1+psychs_caarms_p2+psychs_caarms_p3+psychs_caarms_p4',
                     variable == "psychosis_onset_date"                    ~ 'Minimum of chrpsychs_scr_1a6_on,chrpsychs_scr_2a6_on,chrpsychs_scr_3a6_on,chrpsychs_scr_4a6_on,chrpsychs_scr_5a6_on,chrpsychs_scr_6a6_on,chrpsychs_scr_7a6_on,chrpsychs_scr_8a6_on,chrpsychs_scr_9a6_on,chrpsychs_scr_10a6_on,chrpsychs_scr_11a6_on,chrpsychs_scr_12a6_on,chrpsychs_scr_13a6_on,chrpsychs_scr_14a6_on,chrpsychs_scr_15a6_on',
                     variable == "conversion_date"                         ~ 'if network == pronet and studygroup == hc and any of (hcpsychs_fu_1c6,hcpsychs_fu_2c6,hcpsychs_fu_3c6,hcpsychs_fu_4c6,hcpsychs_fu_5c6,hcpsychs_fu_6c6,hcpsychs_fu_7c6,hcpsychs_fu_8c6,hcpsychs_fu_9c6,hcpsychs_fu_10c6,hcpsychs_fu_11c6,hcpsychs_fu_12c6,hcpsychs_fu_13c6,hcpsychs_fu_14c6,hcpsychs_fu_15c6 == 1): min(hcpsychs_fu_1c6_on,hcpsychs_fu_2c6_on,hcpsychs_fu_3c6_on,hcpsychs_fu_4c6_on,hcpsychs_fu_5c6_on,hcpsychs_fu_6c6_on,hcpsychs_fu_7c6_on,hcpsychs_fu_8c6_on,hcpsychs_fu_9c6_on,hcpsychs_fu_10c6_on,hcpsychs_fu_11c6_on,hcpsychs_fu_12c6_on,hcpsychs_fu_13c6_on,hcpsychs_fu_14c6_on,hcpsychs_fu_15c6_on), elseif network == pronet and studygroup == hc: 1903-03-03, elseif: any of (chrpsychs_fu_1c6,chrpsychs_fu_2c6,chrpsychs_fu_3c6,chrpsychs_fu_4c6,chrpsychs_fu_5c6,chrpsychs_fu_6c6,chrpsychs_fu_7c6,chrpsychs_fu_8c6,chrpsychs_fu_9c6,chrpsychs_fu_10c6,chrpsychs_fu_11c6,chrpsychs_fu_12c6,chrpsychs_fu_13c6,chrpsychs_fu_14c6,chrpsychs_fu_15c6) == 1: min(chrpsychs_fu_1c6_on,chrpsychs_fu_2c6_on,chrpsychs_fu_3c6_on,chrpsychs_fu_4c6_on,chrpsychs_fu_5c6_on,chrpsychs_fu_6c6_on,chrpsychs_fu_7c6_on,chrpsychs_fu_8c6_on,chrpsychs_fu_9c6_on,chrpsychs_fu_10c6_on,chrpsychs_fu_11c6_on,chrpsychs_fu_12c6_on,chrpsychs_fu_13c6_on,chrpsychs_fu_14c6_on,chrpsychs_fu_15c6_on), else: 1903-03-03',
                     variable == "psychosis"                               ~ 'Redcap variable',
                     variable == "dsm_schizotypal_lifetime"                ~ 'Redcap variable',
                     variable == "first_degree_relative"                   ~ 'Redcap variable',                   
                     variable == "sips_grd_lifetime"                       ~ 'Redcap variable',
                     variable == "caarms_vulnerability_pastyear"           ~ 'Redcap variable',
                     variable == "drop30_sofas_pastmonth"                  ~ 'Redcap variable',
                     variable == "sips_grd_progression_pastmonth"          ~ 'Redcap variable',
                     variable == "sofas_curr_premorbid_less90"             ~ 'Redcap variable',
                     variable == "sips_grd_persistence_pastmonth"          ~ 'Redcap variable',
                     variable == "sips_grd_partial_remission_pastmonth"    ~ 'Redcap variable',
                     variable == "sips_grd_full_remission_pastmonth"       ~ 'Redcap variable',
                     variable == "caarms_blips"                            ~ 'Redcap variable',
                     variable == "caarms_aps_subthreshold_frequency"       ~ 'Redcap variable',
                     variable == "caarms_aps_subthreshold_intensity"       ~ 'Redcap variable',
                     variable == "caarms_aps"                              ~ 'Redcap variable',
                     variable == "caarms_vulnerability"                    ~ 'Redcap variable',
                     variable == "caarms_uhr"                              ~ 'Redcap variable',
                     variable == "sips_bips_progression"                   ~ 'Redcap variable',
                     variable == "sips_bips_persistence"                   ~ 'Redcap variable',
                     variable == "sips_bips_partial_remission"             ~ 'Redcap variable',
                     variable == "sips_bips_full_remission"                ~ 'Redcap variable',
                     variable == "sips_apss_progression"                   ~ 'Redcap variable',
                     variable == "sips_apss_persistence"                   ~ 'Redcap variable',
                     variable == "sips_apss_partial_remission"             ~ 'Redcap variable',
                     variable == "sips_apss_full_remission"                ~ 'Redcap variable',
                     variable == "sips_grd_progression"                    ~ 'Redcap variable',
                     variable == "sips_grd_persistence"                    ~ 'Redcap variable',
                     variable == "sips_grd_partial_remission"              ~ 'Redcap variable',
                     variable == "sips_grd_full_remission"                 ~ 'Redcap variable',
                     variable == "sips_chr_progression"                    ~ 'Redcap variable',
                     variable == "sips_chr_persistence"                    ~ 'Redcap variable',
                     variable == "sips_chr_partial_remission"              ~ 'Redcap variable',
                     variable == "sips_chr_full_remission"                 ~ 'Redcap variable',
                     variable == "sips_current_status"                     ~ 'Redcap variable',
                     variable == "dsm5_attenuated_psychosis"               ~ 'Redcap variable',
                     variable == "psychosis_current"                       ~ 'Redcap variable',
                     variable == "psychosis_previous"                      ~ 'Redcap variable',
                     variable == "psychosis_first"                         ~ 'Redcap variable',
                     variable == "psychosis_conversion"                    ~ 'Redcap variable',
                     variable == "sofas_premorbid"                         ~ 'Redcap variable',
                     variable == "sofas_oneyearago"                        ~ 'Redcap variable',
                     variable == "sofas_pasyear"                           ~ 'Redcap variable',
                     variable == "sofas_pasyear"                           ~ 'Redcap variable',                           
                     variable == "sofas_pastmonth"                         ~ 'Redcap variable',
                     variable == "drop30_sofas_sincelastvisit"             ~ 'Redcap variable',             
                     variable == "sips_grd_new"                            ~ 'Redcap variable',
                     variable == "sips_grd_remain"                         ~ 'Redcap variable',                         
                     variable == "chrpps_sum1"                             ~ 'chrpps_sum1 = 2 if (24<chrdemo_age_yrs_chr<36 and chrguid_sex_chr==1) else chrpps_sum1 = 0',
                     variable == "chrpps_sum2"                             ~ 'chrpps_sum2 = 2 if (chrpps_writing+chrpps_throwing+chrpps_toothbrush+chrpps_spoon)<16 else chrpps_sum2 = 0',                             
                     variable == "chrpps_sum7"                             ~ 'chrpps_sum7 = 3.5 if chrpps_fage - chrpps_chrdemo_age_yrs_chr >45 else if chrpps_fage- chrpps_chrdemo_age_yrs_chr>35 chrpps_sum7=0.5 else chrpps_sum7=-0.5',
                     variable == "chrpps_sum8"                             ~ 'chrpps_sum8=1 if chrpps_focc>6 else chrpps_sum8=0',                             
                     variable == "chrpps_sum9"                             ~ 'chrpps_sum9 = 5.5 if at least one of the following variables is scored as a 3: chrfigs_mother_ddx chrfigs_mother_mdx chrfigs_mother_pdx chrfigs_mother_napdx chrfigs_mother_apdx chrfigs_father_ddx chrfigs_father_mdx chrfigs_father_pdx chrfigs_father_napdx chrfigs_father_apdx else chrpps_sum9=-2',
                     variable == "chrpps_sum10"                            ~ 'chrpps_sum10=5.5 if chrpps_sixmo>1 else chrpps_sum10=-2',
                     variable == "chrpps_sum11"                            ~ 'chrpps_sum11=3 if chrassist_whoassist_often1=6 else chrpps_sum=-0.5',
                     variable == "chrpps_sum12"                            ~ 'chrpps_sum12=7 if chrassist_whoassist_often3 > 3 else chrpps_sum12=0',                            
                     variable == "chrpps_sum13"                            ~ 'chrpps_sum13=4 if sum(chrpps_lazy chrpps_born, chrpps_hate, chrpps_hurt, chrpps_emoab, chrpps_doc, chrpps_bruise, chrpps_belt, chrpps_physab,  chrpps_beat, chrpps_touch, chrpps_threat, chrpps_sexual, chrpps_molest, chrpps_sexab, chrpps_loved(R), chrpps_special(R), chrpps_care(R), chrpps_closefam(R), chrpps_support(R), chrpps_hunger, chrpps_protect(R), chrpps_pardrunk, chrpps_dirty, chrpps_docr(R)) >55 else chrpps_sum13=-0.5',
                     variable == "chrpps_sum14"                            ~ 'chrpps_sum14=6.5 sum(chrpps_excite chrpps_taste chrpps_restaur (R) chrpps_roller chrpps_holiday chrpps_tasty chrpps_pleasure chrpps_lookfwd chrpps_menu chrpps_actor chrpps_crackle chrpps_rain chrpps_grass chrpps_air chrpps_coffee chrpps_hair chrpps_yawn chrpps_snow) >35 else chrpps_sum14=0',                            
                     variable == "chrassist_tobacco"                                 ~ 'chrassist_whoassist_often1 + chrassist_whoassist_urge1 + chrassist_whoassist_prob1 + chrassist_whoassist_fail1 +  chrassist_whoassist_concern1 + chrassist_whoassist_control1',
                     variable == "chrassist_alcohol"                                 ~ 'chrassist_whoassist_often2 + chrassist_whoassist_urge2 + chrassist_whoassist_prob2 + chrassist_whoassist_fail2 +  chrassist_whoassist_concern2 + chrassist_whoassist_control2',                                 
                     variable == "chrassist_cannabis"                                ~ 'chrassist_whoassist_often3 + chrassist_whoassist_urge3 + chrassist_whoassist_prob3 + chrassist_whoassist_fail3 +  chrassist_whoassist_concern3 + chrassist_whoassist_control3',
                     variable == "chrassist_cocaine"                                 ~ 'chrassist_whoassist_often4 + chrassist_whoassist_urge4 + chrassist_whoassist_prob4 + chrassist_whoassist_fail4 +  chrassist_whoassist_concern4 + chrassist_whoassist_control4',                                 
                     variable == "chrassist_amphetamines"                            ~ 'chrassist_whoassist_often5 + chrassist_whoassist_urge5 + chrassist_whoassist_prob5 + chrassist_whoassist_fail5 +  chrassist_whoassist_concern5 + chrassist_whoassist_control5',
                     variable == "chrassist_inhalants"                               ~ 'chrassist_whoassist_often6 + chrassist_whoassist_urge6 + chrassist_whoassist_prob6 + chrassist_whoassist_fail6 +  chrassist_whoassist_concern6 + chrassist_whoassist_control6',                               
                     variable == "chrassist_sedatives"                               ~ 'chrassist_whoassist_often7 + chrassist_whoassist_urge7 + chrassist_whoassist_prob7 + chrassist_whoassist_fail7 +  chrassist_whoassist_concern7 + chrassist_whoassist_control7',
                     variable == "chrassist_hallucinogens"                           ~ 'chrassist_whoassist_often8 + chrassist_whoassist_urge8 + chrassist_whoassist_prob8 + chrassist_whoassist_fail8 +  chrassist_whoassist_concern8 + chrassist_whoassist_control8',
                     variable == "chrassist_opiods"                                  ~ 'chrassist_whoassist_often9 + chrassist_whoassist_urge9 + chrassist_whoassist_prob9 + chrassist_whoassist_fail9 +  chrassist_whoassist_concern9 + chrassist_whoassist_control9',
                     variable == "chrassist_other"                                   ~ 'chrassist_whoassist_often10 + chrassist_whoassist_urge10 + chrassist_whoassist_prob10 + chrassist_whoassist_fail10 +  chrassist_whoassist_concern10 + chrassist_whoassist_control10',                                   
                     variable == "chrpas_childhood_subtotal"                      ~ '(chrpas_pmod_child1+chrpas_pmod_child2+chrpas_pmod_child3+chrpas_pmod_child4)/24',
                     variable == "chrpas_early_adolescence_subtotal"              ~ '(chrpas_pmod_adol_early1+chrpas_pmod_adol_early2+chrpas_pmod_adol_early3+chrpas_pmod_adol_early4+chrpas_pmod_adol_early5)/30',              
                     variable == "chrpas_late_adolescence_subtotal"               ~ '(chrpas_pmod_adol_late1+chrpas_pmod_adol_late2+chrpas_pmod_adol_late3+chrpas_pmod_adol_late4+chrpas_pmod_adol_late5)/30',
                     variable == "chrpas_adulthood_subtotal"                      ~ '(chrpas_pmod_adult1+chrpas_pmod_adult2+(chrpas_pmod_adult3v1 or + chrpas_pmod_adult3v3))/18',                      
                     variable == "chrpas_total_score_only_childhood"              ~ 'Childhood subtotal',
                     variable == "chrpas_total_score_upto_early_adolescence"      ~ '(Childhood subtotal +Early Adolescence subtotal)/2',      
                     variable == "chrpas_total_score_upto_late_adolescence"       ~ '(Childhood subtotal +Early Adolescence subtotal+Late Adolescence subtotal)/3',
                     variable == "chrpas_total_score_upto_adulthood"              ~ '(Childhood subtotal +Early Adolescence subtotal+Late Adolescence subtotal+Adulthood subtotal)/4',              
                     variable == "chrcssrs_intensity_lifetime"                ~ 'chrcssrsb_sidfrql + chrcssrsb_siddurl + chrcssrsb_sidctrl + chrcssrs_siddtrl + chrcssrsb_sidrsnl',
                     variable == "chrcssrs_intensity_pastmonth"               ~ 'chrcssrsb_css_sipmfreq + chrcssrsb_css_sipmdur + chrcssrsb_css_sipmctrl + chrcssrsb_css_sipmdet + chrcssrsb_css_sipmreas',               
                     variable == "chrpred_transition"                      ~ 'Redcap variable',
                     variable == "chrpred_experience"                      ~ 'Redcap variable',                      
                     variable == "chrpgi_2"                                ~ 'Redcap variable',
                     variable == "chrpromis_total"                            ~ 'chrpromis_sleep109+chrpromis_sleep116+(6-chrpromis_sleep20)+(6-chrpromis_sleep44)+(6-chrpromise_sleep108)+(6-chrpromis_sleep72)+(6-chrpromis_sleep67)+chrpromis_sleep115',                            
                     variable == "chrgfrs_decline_in_global_role_functioning"      ~ 'chrgfr_gf_role_high-chrgfr_gf_role_scole',
                     variable == "chrgfss_decline_in_global_social_functioning"    ~ 'chrgfs_gf_social_high-chrgfs_gf_social_scale ',    
                     variable == "chrnsipr_motivation_and_pleasure_dimension" ~ '(chrnsipr_item1 + chrnsipr_item2 + chrnsipr_item3 + chrnsipr_item4 + chrnsipr_item5 + chrnsipr_item6 + chrnsipr_item7)/7',
                     variable == "chrnsipr_diminished_expression_dimension"   ~ '(chrnsipr_item8 + chrnsipr_item9 + chrnsipr_item10 + chrnsipr_item11)/4',   
                     variable == "chrnsipr_avolition_domain"                  ~ '(chrnsipr_item1 + chrnsipr_item2)/2',
                     variable == "chrnsipr_asociality_domain"                 ~ '(chrnsipr_item3 + chrnsipr_item4 + chrnsipr_item5)/3',                 
                     variable == "chrnsipr_anhedonia_domain"                  ~ '(chrnsipr_item6 + chrnsipr_item7)/2',
                     variable == "chrnsipr_blunted_affect_domain"             ~ '(chrnsipr_item8 + chrnsipr_item9 + chrnsipr_item10)/3',             
                     variable == "chrnsipr_item11_rating"                  ~ 'Redcap variable',
                     variable == "chrsofas_premorbid"                      ~ 'Redcap variable',                      
                     variable == "chrsofas_currscore12mo"                  ~ 'Redcap variable',
                     variable == "chrsofas_currscore"                      ~ 'Redcap variable',        
                     variable == "chrsofas_lowscore"                       ~ 'Redcap variable',
                     variable == "chrsofas_currscore_fu"                   ~ 'Redcap variable',        
                     variable == "chrsofas_currscore12mo_fu"               ~ 'Redcap variable',
                     variable == "chrpds_total_score_female_sex"              ~ 'if female: chrpds_pds_1_p + chrpds_pds_2_p + chrpds_pds_3_p + chrpds_pds_f4_p + chrpds_pds_f5b_p, if male: -300',                     
                     variable == "chrpds_total_score_male_sex"                ~ 'if female: -300 if male: chrpds_pds_1_p + chrpds_pds_2_p + chrpds_pds_3_p + chrpds_pds_m4_p + chrpds_pds_m5_p',                     
                     variable == "chrpds_pds_f5b_p"                        ~ 'Redcap variable',
                     variable == "chrbprs_bprs_total"                      ~ 'Redcap variable',                              
                     variable == "chrbprs_affect_subscale"                    ~ 'chrbprs_bprs_depr+chrbprs_bprs_suic+chrbprs_depr_guil',
                     variable == "chrbprs_positive_symptom_subscale"          ~ 'chrbprs_bprs_unus+chrbprs_bprs_hall+chrbprs_bprs_susp',          
                     variable == "chrbprs_negative_symptom_subscale"          ~ 'chrbprs_bprs_blun+chrbprs_bprs_motr+chrbprs_bprs_emot',
                     variable == "chrbprs_activation_subscale"                ~ 'chrbprs_bprs_exci+chrbprs_bprs_mohy+chrbprs_bprs_elat ',
                     variable == "chrbprs_disorganization_subscale"           ~ 'chrbprs_bprs_diso+chrbprs_bprs_conc+chrbprs_bprs_self',
                     variable == "chroasis_total"                             ~ 'chroasis_oasis_1+chroasis_oasis_2+chroasis_oasis_3+chroasis_oasis_4+chroasis_oasis_5',                             
                     variable == "chrpds_perceived_discrimination_total"          ~ 'chrdim_dim_yesno_q1_1+chrdim_dim_yesno_q1_2+chrdlm_dim_sex+chrdlm_dim_yesno_age+chrdlm_dim_yesno_q4_1+chrdlm_dim_yesno_q5+chrdlm_dim_yesno_q3+chrdlm_dim_yesno_q6+chrdlm_dim_yesno_other',
                     variable == "chrcdss_total"                              ~ 'chrcdss_calg1 + chrcdss_calg2+chrcdss_calg3+chrcdss_calg4+chrcdss_calg5+chrcdss_calg6+chrcdss_calg7+chrcdss_calg8+chrcdss_calg9',                              
                     variable == "chrpss_perceived_stress_scale_total"            ~ 'chrpss_pssp1_1+chrpss_pssp1_2+chrpss_pssp1_3+(4-chrpss_pssp2_1)+(4-chrpss_pssp2_2)+chrpss_pssp2_3+(4-chrpss_pssp2_4)+(4-chrpss_pssp2_5)+chrpss_pssp3_1+chrpss_pssp3_4'))%>%
  mutate(Notes = case_when(is.na(Notes) ~ 'Redcap variable', 
                           TRUE ~ Notes))%>%
  mutate(original_calculation_adapted_np_or_comment = 
           case_when(variable == "psychs_pos_tot"        ~ '',
                     variable == "psychs_sips_p1"        ~ '',
                     variable == "psychs_sips_p2"        ~ '',
                     variable == "psychs_sips_p3"        ~ '',
                     variable == "psychs_sips_p4"        ~ '',
                     variable == "psychs_sips_p5"        ~ '',
                     variable == "sips_pos_tot"          ~ '',
                     variable == "psychs_caarms_p1"      ~ '',
                     variable == "psychs_caarms_p2"      ~ '',
                     variable == "psychs_caarms_p3"      ~ '',
                     variable == "psychs_caarms_p4"      ~ '',
                     variable == "caarms_pos_tot" ~ '',
                     variable == "psychosis_onset_date"  ~ '',
                     variable == "psychosis"             ~ '',
                     variable == "dsm_schizotypal_lifetime" ~ '',
                     variable == "first_degree_relative"    ~ '',                   
                     variable == "sips_grd_lifetime"        ~ '',
                     variable == "caarms_vulnerability_pastyear" ~ '',
                     variable == "drop30_sofas_pastmonth" ~ '',
                     variable == "sips_grd_progression_pastmonth" ~ '',
                     variable == "sofas_curr_premorbid_less90" ~ '',
                     variable == "sips_grd_persistence_pastmonth" ~ '',
                     variable == "sips_grd_partial_remission_pastmonth" ~ '',
                     variable == "sips_grd_full_remission_pastmonth" ~ '',
                     variable == "caarms_blips" ~ '',
                     variable == "caarms_aps_subthreshold_frequency" ~ '',
                     variable == "caarms_aps_subthreshold_intensity" ~ '',
                     variable == "caarms_aps" ~ '',
                     variable == "caarms_vulnerability" ~ '',
                     variable == "caarms_uhr" ~ '',
                     variable == "sips_bips_progression" ~ '',
                     variable == "sips_bips_persistence" ~ '',
                     variable == "sips_bips_partial_remission" ~ '',
                     variable == "sips_bips_full_remission" ~ '',
                     variable == "sips_apss_progression" ~ '',
                     variable == "sips_apss_persistence" ~ '',
                     variable == "sips_apss_partial_remission" ~ '',
                     variable == "sips_apss_full_remission" ~ '',
                     variable == "sips_grd_progression" ~ '',
                     variable == "sips_grd_persistence" ~ '',
                     variable == "sips_grd_partial_remission" ~ '',
                     variable == "sips_grd_full_remission" ~ '',
                     variable == "sips_chr_progression" ~ '',
                     variable == "sips_chr_persistence" ~ '',
                     variable == "sips_chr_partial_remission" ~ '',
                     variable == "sips_chr_full_remission" ~ '',
                     variable == "sips_current_status" ~ '',
                     variable == "dsm5_attenuated_psychosis" ~ '',
                     variable == "conversion_date" ~ '',
                     variable == "psychosis_current" ~ '',
                     variable == "psychosis_previous" ~ '',
                     variable == "psychosis_first" ~ '',
                     variable == "psychosis_conversion" ~ '',
                     variable == "sofas_premorbid" ~ '',
                     variable == "sofas_oneyearago" ~ '',
                     variable == "sofas_pasyear" ~ '',
                     variable == "sofas_pasyear" ~ '',                           
                     variable == "sofas_pastmonth" ~ '',
                     variable == "drop30_sofas_sincelastvisit" ~ '',             
                     variable == "sips_grd_new" ~ '',
                     variable == "sips_grd_remain" ~ '',                         
                     variable == "chrpps_sum1" ~ '',
                     variable == "chrpps_sum2" ~ '',                             
                     variable == "chrpps_sum7" ~ '',
                     variable == "chrpps_sum8" ~ '',                             
                     variable == "chrpps_sum9" ~ '',
                     variable == "chrpps_sum10" ~ 'event number 15 is None of the above. Therefore, if subject fulfills only event number 15 still -2',                            
                     variable == "chrpps_sum11" ~ '',
                     variable == "chrpps_sum12" ~ '',                            
                     variable == "chrpps_sum13" ~ '',
                     variable == "chrpps_sum14" ~ 'here, the code has to be the other way around. If the score is below 36 (<36) there is a higher risk (=6.5) and if the score is higher than 35 (>35) there is a lower risk (=0) ',                            
                     variable == "chrassist_tobacco" ~ 'Additionally, to the sum we consider whether individual ever consumed the substance. If not this score is 0',
                     variable == "chrassist_alcohol" ~ 'Additionally, to the sum we consider whether individual ever consumed the substance. If not this score is 0',                                 
                     variable == "chrassist_cannabis" ~ 'Additionally, to the sum we consider whether individual ever consumed the substance. If not this score is 0',
                     variable == "chrassist_cocaine" ~ 'Additionally, to the sum we consider whether individual ever consumed the substance. If not this score is 0',                                 
                     variable == "chrassist_amphetamines" ~ 'Additionally, to the sum we consider whether individual ever consumed the substance. If not this score is 0',
                     variable == "chrassist_inhalants" ~ 'Additionally, to the sum we consider whether individual ever consumed the substance. If not this score is 0',                               
                     variable == "chrassist_sedatives" ~ 'Additionally, to the sum we consider whether individual ever consumed the substance. If not this score is 0',
                     variable == "chrassist_hallucinogens" ~ 'Additionally, to the sum we consider whether individual ever consumed the substance. If not this score is 0',
                     variable == "chrassist_opiods" ~ 'Additionally, to the sum we consider whether individual ever consumed the substance. If not this score is 0',
                     variable == "chrassist_other" ~ 'Additionally, to the sum we consider whether individual ever consumed the substance. If not this score is 0',                                   
                     variable == "chrpas_childhood_subtotal" ~ '',
                     variable == "chrpas_early_adolescence_subtotal" ~ '',              
                     variable == "chrpas_late_adolescence_subtotal" ~ '',
                     variable == "chrpas_adulthood_subtotal" ~ '',                      
                     variable == "chrpas_total_score_only_childhood" ~ '',
                     variable == "chrpas_total_score_upto_early_adolescence" ~ '',      
                     variable == "chrpas_total_score_upto_late_adolescence" ~ '',
                     variable == "chrpas_total_score_upto_adulthood" ~ '',              
                     variable == "chrcssrs_intensity_lifetime" ~ 'Before the sum score calculation: if someone never had suicidal thoughts in a lifetime (chrcssrsb_si1l and chrcssrsb_si2l == 0), cssrs intensity for lifetime and past month should be zero.',
                     variable == "chrcssrs_intensity_pastmonth" ~ 'Before the sum score calculation: if someone never had suicidal thoughts in a lifetime (chrcssrsb_si1l and chrcssrsb_si2l == 0) or in the past month (chrcssrsb_css_sim1 and chrcssrsb_css_sim1 == 0), cssrs intensity for lifetime and past month should be zero.',               
                     variable == "chrpred_transition" ~ '',
                     variable == "chrpred_experience" ~ '',                      
                     variable == "chrpgi_2" ~ '',
                     variable == "chrpromis_total" ~ '',                            
                     variable == "chrgfrs_decline_in_global_role_functioning" ~ '',
                     variable == "chrgfss_decline_in_global_social_functioning" ~ '',    
                     variable == "chrnsipr_motivation_and_pleasure_dimension" ~ '',
                     variable == "chrnsipr_diminished_expression_dimension" ~ '',   
                     variable == "chrnsipr_avolition_domain" ~ '',
                     variable == "chrnsipr_asociality_domain" ~ '',                 
                     variable == "chrnsipr_anhedonia_domain" ~ '',
                     variable == "chrnsipr_blunted_affect_domain" ~ '',             
                     variable == "chrnsipr_item11_rating" ~ '',
                     variable == "chrsofas_premorbid" ~ '',                      
                     variable == "chrsofas_currscore12mo" ~ '',
                     variable == "chrsofas_currscore" ~ '',        
                     variable == "chrsofas_lowscore" ~ '',
                     variable == "chrsofas_currscore_fu" ~ '',        
                     variable == "chrsofas_currscore12mo_fu" ~ '',
                     variable == "chrpds_total_score_sex" ~ 'Other than in the outcome calculation we have only one score instead of female/male. Depending on which sex the individual was assigned at birth. We then calculate the score based on the originally provided calculations.',                     
                     variable == "chrpds_pds_f5b_p" ~ '',
                     variable == "chrbprs_bprs_total" ~ '',                              
                     variable == "chrbprs_affect_subscale" ~ '',
                     variable == "chrbprs_positive_symptom_subscale" ~ '',          
                     variable == "chrbprs_negative_symptom_subscale" ~ '',
                     variable == "chrbprs_activation_subscale" ~ '',
                     variable == "chrbprs_disorganization_subscale" ~ '',
                     variable == "chroasis_total" ~ '',                             
                     variable == "chrpds_perceived_discrimination_total" ~ '',
                     variable == "chrcdss_total" ~ '',                              
                     variable == "chrpss_perceived_stress_scale_total" ~ '4 of the scores have to be reversed: (4-xxx) [chrpss_pssp2_1, chrpss_pssp2_2, chrpss_pssp2_4, chrpss_pssp2_5]'))%>%
  mutate(Expert_Name = 'Expert: ',
         Calculation = ', Calculation: ',
         #Calculation = 'Calculation: ',
         Adaptation  = ', adapted by AMP-SCZ staff: ')%>%
  mutate(distinct_values_new = case_when(
    variable == 'psychosis_onset_date'|variable == 'conversion_date' ~ 
      '',
      TRUE ~ ';-900;-300'))%>%
  mutate(value_range = case_when( variable == "psychs_pos_tot"             ~ '0::90',
                                  variable == "psychs_sips_p1"             ~ '0::6',
                                  variable == "psychs_sips_p2"             ~ '0::6',
                                  variable == "psychs_sips_p3"             ~ '0::6',
                                  variable == "psychs_sips_p4"             ~ '0::6',
                                  variable == "psychs_sips_p5"             ~ '0::6',
                                  variable == "sips_pos_tot"               ~ '0::30',
                                  variable == "psychs_caarms_p1"           ~ '0::36',
                                  variable == "psychs_caarms_p2"           ~ '0::36',
                                  variable == "psychs_caarms_p3"           ~ '0::36',
                                  variable == "psychs_caarms_p4"           ~ '0::36',
                                  variable == "caarms_pos_tot"             ~ '0::144',
                                  variable == "psychosis_onset_date"       ~ '',
                                  variable == "chrpsychs_scr_ac1"          ~ '0;1',
                                  variable == "chrpsychs_scr_ac2"          ~ '0;1',
                                  variable == "chrpsychs_scr_ac3"          ~ '0;1',
                                  variable == "chrpsychs_scr_ac4"          ~ '0;1',
                                  variable == "chrpsychs_scr_ac5"          ~ '0;1',
                                  variable == "chrpsychs_scr_ac6"          ~ '0;1',
                                  variable == "chrpsychs_scr_ac7"          ~ '0;1',
                                  variable == "chrpsychs_scr_ac9"          ~ '0;1',
                                  variable == "chrpsychs_scr_ac10"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac11"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac12"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac15"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac16"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac17"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac18"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac21"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac22"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac23"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac24"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac27"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac28"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac29"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac30"         ~ '0;1',
                                  variable == "chrpsychs_scr_ac31"         ~ '1::5',
                                  variable == "chrpsychs_scr_ac32"         ~ '0;1',
                                  variable == "conversion_date"            ~ '',
                                  variable == "hcpsychs_fu_ac1"              ~ '0;1',
                                  variable == "hcpsychs_fu_ac1_curr"         ~ '0;1',
                                  variable == "hcpsychs_fu_ac1_prev"         ~ '0;1',
                                  variable == "hcpsychs_fu_ac1_first"        ~ '0;1',
                                  variable == "hcpsychs_fu_ac1_conv"         ~ '0;1',
                                  variable == "hcpsychs_fu_ac9"              ~ '0;1',
                                  variable == "hcpsychs_fu_ac10"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac11"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac12"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac15"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac16"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac17"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac18"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac21"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac22"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac23"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac24"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac27"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac28"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac29"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac30"             ~ '0;1',
                                  variable == "hcpsychs_fu_ac31"             ~ '1::5',
                                  variable == "hcpsychs_fu_ac32"             ~ '0;1',
                                  variable == "chrpsychs_fu_ac1"              ~'0;1',
                                  variable == "chrpsychs_fu_ac1_curr"         ~'0;1',
                                  variable == "chrpsychs_fu_ac1_prev"         ~'0;1',
                                  variable == "chrpsychs_fu_ac1_first"        ~'0;1',
                                  variable == "chrpsychs_fu_ac1_conv"         ~'0;1',
                                  variable == "chrpsychs_fu_ac9"              ~'0;1',
                                  variable == "chrpsychs_fu_ac10"             ~'0;1',
                                  variable == "chrpsychs_fu_ac11"             ~'0;1',
                                  variable == "chrpsychs_fu_ac12"             ~'0;1',
                                  variable == "chrpsychs_fu_ac15"             ~'0;1',
                                  variable == "chrpsychs_fu_ac16"             ~'0;1',
                                  variable == "chrpsychs_fu_ac17"             ~'0;1',
                                  variable == "chrpsychs_fu_ac18"             ~'0;1',
                                  variable == "chrpsychs_fu_ac21"             ~'0;1',
                                  variable == "chrpsychs_fu_ac22"             ~'0;1',
                                  variable == "chrpsychs_fu_ac23"             ~'0;1',
                                  variable == "chrpsychs_fu_ac24"             ~'0;1',
                                  variable == "chrpsychs_fu_ac27"             ~'0;1',
                                  variable == "chrpsychs_fu_ac28"             ~'0;1',
                                  variable == "chrpsychs_fu_ac29"             ~'0;1',
                                  variable == "chrpsychs_fu_ac30"             ~'0;1',
                                  variable == "chrpsychs_fu_ac31"             ~'1::5',
                                  variable == "chrpsychs_fu_ac32"             ~'0;1',
                                  variable == "psychosis_current"           ~  '0;1',
                                  variable == "psychosis_previous"          ~  '0;1',
                                  variable == "psychosis_first"             ~  '0;1',
                                  variable == "psychosis_conversion"        ~  '0;1',
                                  variable == "chrpps_sum1" ~ '0;2',
                                  variable == "chrpps_sum2" ~ '0;2',                             
                                  variable == "chrpps_sum7" ~ '0;5',
                                  variable == "chrpps_sum8" ~  '0;1',                             
                                  variable == "chrpps_sum9" ~  '0;5.5',
                                  variable == "chrpps_sum10" ~ '0;5.5',                            
                                  variable == "chrpps_sum11" ~ '0;5',
                                  variable == "chrpps_sum12" ~ '0;7',                            
                                  variable == "chrpps_sum13" ~ '0;5',
                                  variable == "chrpps_sum14" ~ '0;6.5',                            
                                  variable == "chrassist_tobacco"       ~ '0::39',
                                  variable == "chrassist_alcohol"       ~ '0::39',                                 
                                  variable == "chrassist_cannabis"      ~ '0::39',
                                  variable == "chrassist_cocaine"       ~ '0::39',                                 
                                  variable == "chrassist_amphetamines"  ~ '0::39',
                                  variable == "chrassist_inhalants"     ~ '0::39',                               
                                  variable == "chrassist_sedatives"     ~ '0::39',
                                  variable == "chrassist_hallucinogens" ~ '0::39',
                                  variable == "chrassist_opiods"        ~ '0::39',
                                  variable == "chrassist_other"         ~ '0::39',                                   
                                  variable == "chrpas_childhood_subtotal"                 ~ '0::24',
                                  variable == "chrpas_early_adolescence_subtotal"         ~ '0::30',              
                                  variable == "chrpas_late_adolescence_subtotal"          ~ '0::30',
                                  variable == "chrpas_adulthood_subtotal"                 ~ '0::18',                      
                                  variable == "chrpas_total_score_only_childhood"         ~ '0::24',
                                  variable == "chrpas_total_score_upto_early_adolescence" ~ '0::27',      
                                  variable == "chrpas_total_score_upto_late_adolescence"  ~ '0::28',
                                  variable == "chrpas_total_score_upto_adulthood"         ~ '0::26',              
                                  variable == "chrcssrs_intensity_lifetime"           ~ '0::25',
                                  variable == "chrcssrs_intensity_pastmonth"          ~ '0::25',               
                                  variable == "chrpred_transition"                 ~ '0;1',
                                  variable == "chrpred_experience"                 ~ '1::240',                      
                                  variable == "chrpgi_2"                           ~ '1::5',
                                  variable == "chrpromis_total"                       ~ '7::35',                            
                                  variable == "chrgfrs_decline_in_global_role_functioning" ~ '0::10',
                                  variable == "chrgfss_decline_in_global_social_functioning" ~ '0::10',    
                                  variable == "chrnsipr_motivation_and_pleasure_dimension" ~ '0::5',
                                  variable == "chrnsipr_diminished_expression_dimension" ~ '0::5',  
                                  variable == "chrnsipr_avolition_domain" ~ '0::5',
                                  variable == "chrnsipr_asociality_domain" ~ '0::5',                 
                                  variable == "chrnsipr_anhedonia_domain" ~ '0::5',
                                  variable == "chrnsipr_blunted_affect_domain" ~ '0::5',             
                                  variable == "chrnsipr_item11_rating" ~ '0::5',
                                  variable == "chrsofas_premorbid" ~            '0::100', 
                                  variable == "chrsofas_currscore12mo" ~        '0::100',
                                  variable == "chrsofas_currscore" ~            '0::100',
                                  variable == "chrsofas_lowscore" ~             '0::100',
                                  variable == "chrsofas_currscore_fu" ~         '0::100',
                                  variable == "chrsofas_currscore12mo_fu" ~     '0::100',
                                  variable == "chrpds_total_score_female_sex" ~ '5::20',                     
                                  variable == "chrpds_total_score_male_sex" ~   '5::20',                     
                                  variable == "chrpds_pds_f5b_p" ~           '1;4',
                                  variable == "chrbprs_bprs_total" ~             '24::168',                              
                                  variable == "chrbprs_affect_subscale" ~           '3::21',
                                  variable == "chrbprs_positive_symptom_subscale" ~ '3::21',          
                                  variable == "chrbprs_negative_symptom_subscale" ~ '3::21',
                                  variable == "chrbprs_activation_subscale" ~       '3::21',
                                  variable == "chrbprs_disorganization_subscale" ~  '3::21',
                                  variable == "chroasis_total" ~ '0::20',                             
                                  variable == "chrpds_perceived_discrimination_total" ~ '0::9',
                                  variable == "chrcdss_total" ~ '0::27',                              
                                  variable == "chrpss_perceived_stress_scale_total" ~ '0::40'))%>%
  mutate_all(~ case_when(is.na(.) ~ "", TRUE ~ .))%>%
  mutate(Notes_for_Calc = Notes)%>%
  unite('Notes', c(Expert_Name, Experts, Calculation, Notes, Adaptation, original_calculation_adapted_np_or_comment), sep = '')%>%
  #unite('Notes', c(Calculation, Notes), sep = '')%>%
  unite('VALUE_RANGE', c(value_range, distinct_values_new), sep = '')%>%
  dplyr::select(variable, VALUE_RANGE, min_value, max_value, data_type, description, Notes, csv_names, distinct_values, diverging_expert_variable_name, Notes_for_Calc)%>%
  dplyr::rename(ELEMENT_NAME = variable ,
                DATA_TYPE = data_type,
                DESCRIPTION = description,
                NOTES = Notes,
                ALIASES = diverging_expert_variable_name)%>%
  dplyr::select(ELEMENT_NAME, DATA_TYPE, DESCRIPTION,	VALUE_RANGE, NOTES,	csv_names, ALIASES, Notes_for_Calc)%>%
  mutate(real_calculation = case_when(ELEMENT_NAME == 'chrpps_sum10' ~                        'chrpps_sum10=5.5 if (chrpps_sixmo___1 == 1 or chrpps_sixmo___2 == 1 or chrpps_sixmo___3 == 1 or chrpps_sixmo___4 == 1 or chrpps_sixmo___5 == 1 or chrpps_sixmo___6 == 1 or chrpps_sixmo___7 == 1 or chrpps_sixmo___8 == 1 or chrpps_sixmo___9 == 1 or chrpps_sixmo___10 == 1 or chrpps_sixmo___11 == 1 or chrpps_sixmo___12 == 1 or chrpps_sixmo___13 == 1 or chrpps_sixmo___14 == 1) elif chrpps_sum10 = -2 (chrpps_sixmo___1 == 0 and chrpps_sixmo___2 == 0 and chrpps_sixmo___3 == 0 and chrpps_sixmo___4 == 0 and chrpps_sixmo___5 == 0 and chrpps_sixmo___6 == 0 and chrpps_sixmo___7 == 0 and chrpps_sixmo___8 == 0 and chrpps_sixmo___9 == 0 and chrpps_sixmo___10 == 0 and chrpps_sixmo___11 == 0 and chrpps_sixmo___12 == 0 and chrpps_sixmo___13 == 0 and chrpps_sixmo___14 == 0 and chrpps_sixmo___15 ==1)',
                                      ELEMENT_NAME == "chrpps_sum14" ~                        'chrpps_sum14=0 if sum(chrpps_excite, chrpps_taste,(7-chrpps_restaur),chrpps_roller, chrpps_holiday, chrpps_tasty, chrpps_pleasure, chrpps_lookfwd, chrpps_menu, chrpps_actor, chrpps_crackle, chrpps_rain, chrpps_grass, chrpps_air, chrpps_coffee, chrpps_hair, chrpps_yawn, chrpps_snow) >35 else chrpps_sum14=6.5',                            
                                      ELEMENT_NAME == "chrassist_tobacco" ~                   'chrassist_tobacco       = 0 if chrassist_whoassist_use1 == 0, else chrassist_whoassist_often1 + chrassist_whoassist_urge1 + chrassist_whoassist_prob1 + chrassist_whoassist_fail1 +  chrassist_whoassist_concern1 + chrassist_whoassist_control1',
                                      ELEMENT_NAME == "chrassist_alcohol" ~                   'chrassist_alcohol       = 0 if chrassist_whoassist_use2 == 0, else chrassist_whoassist_often2 + chrassist_whoassist_urge2 + chrassist_whoassist_prob2 + chrassist_whoassist_fail2 +  chrassist_whoassist_concern2 + chrassist_whoassist_control2',                                 
                                      ELEMENT_NAME == "chrassist_cannabis" ~                  'chrassist_cannabis      = 0 if chrassist_whoassist_use3 == 0, else chrassist_whoassist_often3 + chrassist_whoassist_urge3 + chrassist_whoassist_prob3 + chrassist_whoassist_fail3 +  chrassist_whoassist_concern3 + chrassist_whoassist_control3',
                                      ELEMENT_NAME == "chrassist_cocaine" ~                   'chrassist_cocaine       = 0 if chrassist_whoassist_use4 == 0, else chrassist_whoassist_often4 + chrassist_whoassist_urge4 + chrassist_whoassist_prob4 + chrassist_whoassist_fail4 +  chrassist_whoassist_concern4 + chrassist_whoassist_control4',                                 
                                      ELEMENT_NAME == "chrassist_amphetamines" ~              'chrassist_amphetamines  = 0 if chrassist_whoassist_use5 == 0, else chrassist_whoassist_often5 + chrassist_whoassist_urge5 + chrassist_whoassist_prob5 + chrassist_whoassist_fail5 +  chrassist_whoassist_concern5 + chrassist_whoassist_control5',
                                      ELEMENT_NAME == "chrassist_inhalants" ~                 'chrassist_inhalants     = 0 if chrassist_whoassist_use6 == 0, else chrassist_whoassist_often6 + chrassist_whoassist_urge6 + chrassist_whoassist_prob6 + chrassist_whoassist_fail6 +  chrassist_whoassist_concern6 + chrassist_whoassist_control6',                               
                                      ELEMENT_NAME == "chrassist_sedatives" ~                 'chrassist_sedatives     = 0 if chrassist_whoassist_use7 == 0, else chrassist_whoassist_often7 + chrassist_whoassist_urge7 + chrassist_whoassist_prob7 + chrassist_whoassist_fail7 +  chrassist_whoassist_concern7 + chrassist_whoassist_control7',
                                      ELEMENT_NAME == "chrassist_hallucinogens" ~             'chrassist_hallucinogens = 0 if chrassist_whoassist_use8 == 0, else chrassist_whoassist_often8 + chrassist_whoassist_urge8 + chrassist_whoassist_prob8 + chrassist_whoassist_fail8 +  chrassist_whoassist_concern8 + chrassist_whoassist_control8',
                                      ELEMENT_NAME == "chrassist_opiods" ~                    'chrassist_opiods        = 0 if chrassist_whoassist_use9 == 0, else chrassist_whoassist_often9 + chrassist_whoassist_urge9 + chrassist_whoassist_prob9 + chrassist_whoassist_fail9 +  chrassist_whoassist_concern9 + chrassist_whoassist_control9',
                                      ELEMENT_NAME == "chrassist_other" ~                     'chrassist_other         = 0 if chrassist_whoassist_use10 == 0, else chrassist_whoassist_often10 + chrassist_whoassist_urge10 + chrassist_whoassist_prob10 + chrassist_whoassist_fail10 +  chrassist_whoassist_concern10 + chrassist_whoassist_control10',                                   
                                      ELEMENT_NAME == "chrcssrs_intensity_lifetime" ~         'chrcssrs_intensity_lifetime = -300 if (chrcssrsb_si1l and chrcssrsb_si2l == 0) else chrcssrsb_sidfrql + chrcssrsb_siddurl + chrcssrsb_sidctrl + chrcssrs_siddtrl + chrcssrsb_sidrsnl',
                                      ELEMENT_NAME == "chrcssrs_intensity_pastmonth" ~        'chrcssrs_intensity_pastmonth = -300 if (chrcssrsb_si1l and chrcssrsb_si2l) or (chrcssrsb_css_sim1 and chrcssrsb_css_sim1 == 0) else chrcssrsb_css_sipmfreq + chrcssrsb_css_sipmdur + chrcssrsb_css_sipmctrl + chrcssrsb_css_sipmdet + chrcssrsb_css_sipmreas',               
                                      ELEMENT_NAME == "chrpss_perceived_stress_scale_total" ~ 'chrpss_pssp1_1+chrpss_pssp1_2+chrpss_pssp1_3+(4-chrpss_pssp2_1)+(4-chrpss_pssp2_2)+chrpss_pssp2_3+(4-chrpss_pssp2_4)+(4-chrpss_pssp2_5)+chrpss_pssp3_1+chrpss_pssp3_4',
                                      TRUE ~ Notes_for_Calc))%>%
  dplyr::select(-NOTES)%>%
  rename(NOTES = real_calculation)%>%
  dplyr::select(ELEMENT_NAME, DATA_TYPE, DESCRIPTION,	VALUE_RANGE, NOTES,	csv_names, ALIASES)

        
write.csv(variables_outcome, 'C:/Users/Nora/Documents/Harvard/U24/outcome_calculations/dictionary_outcomes_new.csv', row.names = FALSE)
#write.csv(variables_outcome, 'C:/Users/Nora/Documents/Harvard/U24/outcome_calculations/dictionary_outcomes.csv', row.names = FALSE)