Merge pull request #101 from aim-rsf/go-back

Allow re-do of last categorisation & reduce number of autos

R/domain_mapping.R

@@ -60,7 +60,7 @@ domain_mapping <- function(json_file = NULL, domain_file = NULL, look_up_file =
   ## Present domains plots panel for user's reference ----
   colnames(domains)[1] = "Domain Name"
   graphics::plot.new()
-  domains_extend <- rbind(c("*NO MATCH / UNSURE*"), c("*METADATA*"), c("*ALF ID*"), c("*OTHER ID*"), c("*DEMOGRAPHICS*"), domains)
+  domains_extend <- rbind(c("*NO MATCH / UNSURE*"), c("*METADATA*"), c("*ID*"), c("*DEMOGRAPHICS*"), domains)
   Code <- data.frame(Code = 0:(nrow(domains_extend) - 1))
   Domain_table <- tableGrob(cbind(Code,domains_extend),rows = NULL,theme = ttheme_default())
   grid.arrange(Domain_table,nrow=1,ncol=1)

R/user_categorisation.R

@@ -12,25 +12,39 @@
 
 user_categorisation <- function(data_element,data_desc,data_type) {
 
-  # print text to R console
-  cat(paste(
-    "\nDATA ELEMENT -----> ", data_element,
-    "\n\nDESCRIPTION -----> ", data_desc,
-    "\n\nDATA TYPE -----> ", data_type, "\n"
-  ))
-
-  # ask user for categorisation
-
-  decision <- ""
-  cat("\n \n")
-  while (decision == "") {
-    decision <- readline("Categorise this data element into one or more domains, e.g. 5 or 5,8: ")
-  }
+  first_run = TRUE
+  go_back = ''
 
-  # ask user for note on categorisation
-  cat("\n \n")
-  decision_note <- readline("Optional note to explain decision (or press enter to continue): ")
+  while (go_back == "Y" | go_back == "y" | first_run == TRUE) {
 
-  return(list(decision = decision,decision_note = decision_note))
+    go_back = ''
+    # print text to R console
+    cat(paste(
+      "\nDATA ELEMENT -----> ", data_element,
+      "\n\nDESCRIPTION -----> ", data_desc,
+      "\n\nDATA TYPE -----> ", data_type, "\n"
+    ))
+
+    # ask user for categorisation
+
+    decision <- ""
+    cat("\n \n")
+    while (decision == "") {
+      decision <- readline("Categorise data element into domain(s). E.g. 3 or 3,4: ")
+    }
+
+    # ask user for note on categorisation
+    cat("\n \n")
+    decision_note <- readline("Categorisation note (or press enter to continue): ")
 
+    while (go_back != "Y" & go_back != "y" & go_back != "N" & go_back != "n") {
+      cat("\n \n")
+      go_back <- readline(prompt = "Re-do last categorisation? (y/n): ")
+    }
+
+    first_run = FALSE
   }
+
+  return(list(decision = decision,decision_note = decision_note))
+
+}

README.md

@@ -88,21 +88,20 @@ Take note of the **Plots** tab in R Studio which should show a table of domains
 
 - [0] *NO MATCH / UNSURE*
 - [1] *METADATA*
-- [2] *ALF ID*
-- [3] *OTHER ID*
-- [4] *DEMOGRAPHICS*
-- [5] Socioeconomic info 
-- [6] Location info 
-- [7] Education info
-- [8] Health info
+- [2] *ID*
+- [3] *DEMOGRAPHICS*
+- [4] Socioeconomic info 
+- [5] Location info 
+- [6] Education info
+- [7] Health info
 
-Reference this Plots tab throughout the demo run. You will be asked to label data elements with one (or more) of these numbers [0-8].
+Reference this Plots tab throughout the demo run. You will be asked to label data elements with one (or more) of these numbers [0-7].
 
-Here we have very simple domains [5-8] for the demo run. 
+Here we have very simple domains [4-7] for the demo run. 
 
 For a research study, your domains are likely to be much more specific e.g. 'Prenatal, antenatal, neonatal and birth' or 'Health behaviours and diet'.
 
-The 5 default domains are always included [0-4], appended on to any domain list given.
+The 4 default domains are always included [0-3], appended on to any domain list given.
 
 ``` 
 ✔ Running domain_mapping in demo mode using package data files
@@ -219,17 +218,26 @@ DESCRIPTION ----->  APGAR 1 score. This is a measure of a baby's physical state
 
 DATA TYPE ----->  CHARACTER 
 
-Categorise this data element into one or more domains, e.g. 5 or 5,8: 8
+Categorise data element into domain(s). E.g. 3 or 3,4: 7
+
+Categorisation note (or press enter to continue): your note here 
 
-Optional note to explain decision (or press enter to continue): 
 ```
 
-We chose to respond with '8' because that corresponds to the 'Health' domain in the table. More than one domain can be chosen. 
+We chose to respond with '7' because that corresponds to the 'Health info' domain in the table. More than one domain can be chosen. 
 
 A note can be included to explain why a categorisation has been made. Or press enter for no note. 
 
+You have the option to re-do the categorisation you just made, by replying 'y' to the question:
+
+```
+Re-do last categorisation? (y/n): y
+```
+
 After completing 20, it will then ask you to review the auto-categorisations it made. 
 
+These auto-categorisations are based on the mappings included in the [data-raw/look_up.csv](data-raw/look_up.csv). This look-up file can be changed (see the section 'Using your own input files' below). ALF refers to 'Anonymous Linking Field' - this field is used within datasets that have been anonymised and encrypted for inclusion within SAIL Databank. 
+
 ```
 ! Please check the auto categorised data elements are accurate for table CHILD:
 
@@ -238,7 +246,7 @@ After completing 20, it will then ask you to review the auto-categorisations it
 2    ALF_MTCH_PCT   2            AUTO CATEGORISED
 3    ALF_STS_CD     2            AUTO CATEGORISED
 6    AVAIL_FROM_DT  1            AUTO CATEGORISED  
-19   GNDR_CD        4            AUTO CATEGORISED
+19   GNDR_CD        3            AUTO CATEGORISED
 
 ℹ Press enter to accept the auto categorisations for table CHILD or enter each row you'd like to edit:
 
@@ -251,21 +259,21 @@ Press enter for now. It will then ask you if you want to review the categorisati
 Would you like to review your categorisations? (y/n): y
 
       DataElement             Domain_code Note
-4     APGAR_1                 8
-5     APGAR_2                 8
-7     BIRTH_ORDER             8           10% missingness
-8     BIRTH_TM                1,8         20% missingness 
-9     BIRTH_WEIGHT            8
-10    BIRTH_WEIGHT_DEC        8
-11    BREASTFEED_8_WKS_FLG    8
-12    BREASTFEED_BIRTH_FLG    8
-13    CHILD_ID_E              3
-14    CURR_LHB_CD_BIRTH       6,8         Place of birth
-15    DEL_CD                  8
-16    DOD                     4,8
-17    ETHNIC_GRP_CD           4
-18    GEST_AGE                4,8
-20    HEALTH_VISITOR_CD_E     3
+4     APGAR_1                 7
+5     APGAR_2                 7
+7     BIRTH_ORDER             7           10% missingness
+8     BIRTH_TM                1,7         20% missingness 
+9     BIRTH_WEIGHT            7
+10    BIRTH_WEIGHT_DEC        7
+11    BREASTFEED_8_WKS_FLG    7
+12    BREASTFEED_BIRTH_FLG    7
+13    CHILD_ID_E              2
+14    CURR_LHB_CD_BIRTH       5,7         Place of birth
+15    DEL_CD                  7
+16    DOD                     3,7
+17    ETHNIC_GRP_CD           3
+18    GEST_AGE                3,7
+20    HEALTH_VISITOR_CD_E     2
 
 ℹ Press enter to accept your categorisations for table CHILD, or enter each row number you'd like to edit:
 
@@ -325,9 +333,9 @@ The json file:
 
 The domain_file:	
 
-- a csv file created by the user, with each domain listed on a separate line
+- a csv file created by the user, with each domain listed on a separate line, no header
 - see [data-raw/domain_list_demo.csv](data-raw/domain_list_demo.csv) for a template
-- the first 5 domains will be auto populated (see demo above)
+- the first 4 domains will be auto populated (see demo above)
 
 The lookup file:
 

data-raw/look_up.csv

@@ -1,28 +1,28 @@
 DataElement,DomainLabel,DomainCode
 NA,No Match / Unsure,0
 AVAIL_FROM_DT,Metadata,1
-ALF_E,ALF ID,2
-MOTHER_ALF_E,ALF ID,2
-CHILD_ALF_E,ALF ID,2
-RALF,ALF ID,2
-ALF_STS_CD,ALF ID,2
-MOTHER_ALF_STS_CD,ALF ID,2
-CHILD_ALF_STS_CD,ALF ID,2
-ALF_MTCH_PCT,ALF ID,2
-MOTHER_ALF_MTCH_PCT,ALF ID,2
-CHILD_ALF_MTCH_PCT,ALF ID,2
-SERVICE_USER_LOCAL_ID_E,OTHER ID,3
-MAT_SERVICE_USER_LOCAL_ID_E,OTHER ID,3
-CLIENT_ID_E,OTHER ID,3
-AGE,Demographics,4
-MAT_AGE,Demographics,4
-MAT_AGE_AT_ASS,Demographics,4
-CONTACT_AGE,Demographics,4
-WOB,Demographics,4
-MAT_WOB,Demographics,4
-SEX,Demographics,4
-SERVICE_USER_SEX_CD,Demographics,4
-NENONATE_SEX_CD,Demographics,4
-GENDER,Demographics,4
-GNDR,Demographics,4
-GNDR_CD,Demographics,4
+ALF_E,ID,2
+MOTHER_ALF_E,ID,2
+CHILD_ALF_E,ID,2
+RALF,ID,2
+ALF_STS_CD,ID,2
+MOTHER_ALF_STS_CD,ID,2
+CHILD_ALF_STS_CD,ID,2
+ALF_MTCH_PCT,ID,2
+MOTHER_ALF_MTCH_PCT,ID,2
+CHILD_ALF_MTCH_PCT,ID,2
+SERVICE_USER_LOCAL_ID_E,ID,2
+MAT_SERVICE_USER_LOCAL_ID_E,ID,2
+CLIENT_ID_E,ID,2
+AGE,Demographics,3
+MAT_AGE,Demographics,3
+MAT_AGE_AT_ASS,Demographics,3
+CONTACT_AGE,Demographics,3
+WOB,Demographics,3
+MAT_WOB,Demographics,3
+SEX,Demographics,3
+SERVICE_USER_SEX_CD,Demographics,3
+NENONATE_SEX_CD,Demographics,3
+GENDER,Demographics,3
+GNDR,Demographics,3
+GNDR_CD,Demographics,3