From aeba122b0c34271040842390aa678f2dfa0dda13 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Viktor=20Rogn=C3=A5s?= <viktor.rognas@gmail.com>
Date: Thu, 12 Sep 2024 20:04:19 +0200
Subject: [PATCH] Update snippets.json

---
 snippets/snippets.json | 76 ++++++++++++++++++++++--------------------
 1 file changed, 39 insertions(+), 37 deletions(-)

diff --git a/snippets/snippets.json b/snippets/snippets.json
index 13a6ea8..50ca54b 100644
--- a/snippets/snippets.json
+++ b/snippets/snippets.json
@@ -26,7 +26,7 @@
     "prefix": "section",
     "body": [
       ";; -----------------------------------------------------------------------------",
-      ";; ${1:Section name}",
+      ";; ${1:Section}",
       ";; -----------------------------------------------------------------------------",
       ""
     ],
@@ -195,8 +195,8 @@
     "prefix": ["mu_reference"],
     "body": [
       "\n",
-      "MU_$1 = THETA($2) ; use theta on log-scale, not log(thetha)",
-      "TV$3 = MU_$4 + ETA($5)",
+      "MU_$1 = THETA($1) ; use theta on log-scale, not log(thetha)",
+      "TV$2 = MU_$1 + ETA($3)",
       "\n$0"
     ],
     "description": "MU referencing\n"
@@ -222,7 +222,7 @@
       "\tOBASE = EXP(ODV) ; observed baseline response at time 0",
       "ENDIF",
       "IBASE = OBASE * EXP(ETA($1) * THETA($2)) ; observed baseline response, acknowledging the uncertainty with the same magnitude as RUV",
-      "A_0(X) = IBASE ; compartment initialization",
+      "A_0($3) = IBASE ; compartment initialization",
       "\\$THETA (0, 0.3) ; RUV magnitude (sd)",
       "\\$OMEGA 1 FIX ; IIV IBASE"
     ],
@@ -242,13 +242,14 @@
       "BRV = EXP(ETA($4) * W * IIVW)",
       "IBASE = (BPOP * RVW + OBASE * IIVW) * BRV ; individual baseline",
       "A_0($5) = IBASE ; compartment initialization",
-      "$0",
+      "",
       "; PUT BELOW IN \\$ERROR",
       "IF (TIME == 0) THEN",
       "\tIPRED = LOG(BPOP) + ETA($6) * IIV ; individual predicted baseline included to get an estimate of BPOP which is then used in the eq for IBASE",
       "ELSE",
       "\tIPRED = LOG(A(1))",
-      "ENDIF"
+      "ENDIF",
+      "$0"
     ],
     "description": "Baseline as a covariate.\nSimilar to ”Gold standard” (B1).\nNo assumption about size of IIV vs RV (B3)\n"
   },
@@ -261,9 +262,10 @@
       ";-----Baseline model-----------",
       "IF (TIME == 0) IBASE = EXP(DV) ; observed baseline response",
       "A_0($1) = IBASE ; compartment initialization",
-      "$0",
+      "",
       "; PUT BELOW IN \\$ERROR",
-      "IPRED = LOG(A(1) / IBASE) ; the observations subsequent to the baseline observation are normalized by the baseline value."
+      "IPRED = LOG(A(1) / IBASE) ; the observations subsequent to the baseline observation are normalized by the baseline value.",
+      "$0"
     ],
     "description": "Subtracting baseline (B4)\nLargest bias and imprecision.\nWith this method the baseline observation is subtracted from all subsequent measurements, alternatively all subsequent measurements are divided with the baseline observation.\nThe error in the baseline observations will be carried on to all subsequent observations.\nThe performance of this method will be better the smaller the residual error of the baseline observations\n"
   },
@@ -309,21 +311,21 @@
   "Boc-Cox transformation": {
     "prefix": ["boxcox"],
     "body": [
-      "BXPAR = THETA(2) ; Shape parameter",
-      "PHI = EXP(ETA(2)) ; Exponential transformation",
-      "ETATR = (PHI**BXPAR-1)/BXPAR ; Transformed eta",
-      "CL = TVCL*EXP(ETATR) ; Individual parameter"
+      "BXPAR = THETA($1) ; Shape parameter",
+      "PHI = EXP(ETA($2)) ; Exponential transformation",
+      "ETATR = (PHI**BXPAR - 1) / BXPAR ; Transformed eta",
+      "CL = TVCL * EXP(ETATR) ; Individual parameter"
     ],
     "description": "Box-Cox transformation"
   },
   "t-distribution transformation": {
     "prefix": ["tdist"],
     "body": [
-      "DF = THETA(2) ; Degrees of freedom, t-distribution",
+      "DF = THETA($1) ; Degrees of freedom, t-distribution",
       "; t-distribution transformed ETA",
-      "ETATR = ETA(1) * (1 + ((ETA(1)**2 + 1) / (4 * DF)) + &",
-      "((5 * ETA(1)**4 + 16 * ETA(1)**2 + 3) / (96 * DF**2)) + &",
-      "((3 * ETA(1)**6 + 19 * ETA(1)**4 + 17 * ETA(1)**2 - 15)/(384 * DF**3)))",
+      "ETATR = ETA($2) * (1 + ((ETA($2)**2 + 1) / (4 * DF)) + &",
+      "((5 * ETA($2)**4 + 16 * ETA($2)**2 + 3) / (96 * DF**2)) + &",
+      "((3 * ETA($2)**6 + 19 * ETA($2)**4 + 17 * ETA($2)**2 - 15)/(384 * DF**3)))",
       "CL = TVCL * EXP(ETATR) ; Individual parameter"
     ],
     "description": "t-distribution transformation"
@@ -332,10 +334,10 @@
     "prefix": ["uniformdist"],
     "body": [
       "; A uniform parameter distribution between estimated values x and x+y",
-      "P_UNIF=THETA(1)+THETA(2)*PHI(ETA(1))",
-      "$THETA x ; 1",
-      "$THETA (0, y) ; 2",
-      "$OMEGA 1 FIX ; 1"
+      "P_UNIF=THETA($1)+THETA($2)*PHI(ETA($3))",
+      "\\$THETA x ; 1",
+      "\\$THETA (0, y) ; 2",
+      "\\$OMEGA 1 FIX ; 1"
     ],
     "description": "uniform-distribution transformation"
   },
@@ -343,7 +345,7 @@
     "prefix": ["hazard_exponential"],
     "body": [
       "DADT($1) = SCALE",
-      "SUR = EXP(-A($2))"
+      "SUR = EXP(-A($1))"
     ],
     "description": "Exponential hazard function\n"
   },
@@ -353,7 +355,7 @@
       "DEL = 1E-12",
       "TIM = T + DEL",
       "DADT($1) = SCALE * SHAPE * (SCALE * TIM)**(SHAPE - 1)",
-      "SUR = EXP(-A($2))"
+      "SUR = EXP(-A($1))"
     ],
     "description": "Weibull hazard function\n"
   },
@@ -363,7 +365,7 @@
       "DEL = 1E-12",
       "TIM = T + DEL",
       "DADT($1) = SCALE * EXP(SHAPE * TIM)",
-      "SUR = EXP(-A($2))"
+      "SUR = EXP(-A($1))"
     ],
     "description": "Gompertz hazard function\n"
   },
@@ -378,7 +380,7 @@
       "X1 = (LNT - MU) / SIGM",
       "PDF = EXP(-0.5 * (X1**2)) / SQRT(2 * PI)",
       "DADT($3)=1 / (TIM * SIGM) * PDF / (1 - PHI(X1))",
-      "SUR = EXP(-A($4))"
+      "SUR = EXP(-A($3))"
     ],
     "description": "Log-normal hazard function\n"
   },
@@ -497,7 +499,7 @@
       "ENDIF",
       "",
       "\\$SIMULATION (12345) (678910 UNIFORM)",
-      "\n$0"
+      "$0"
     ],
     "description": "Simulation from binary models"
   },
@@ -507,7 +509,7 @@
       "\n",
       "\\$ESTIMATION METHOD=CONDITIONAL INTERACTION NOABORT MAXEVALS=99999 PRINT=1",
       "            NSIG=3 MCETA=0 RANMETHOD=4P SEED=1337 MSFO=$TM_FILENAME_BASE.msf",
-      "\n$0"
+      "$0"
     ],
     "description": "FOCEI with sane defaults"
   },
@@ -517,7 +519,7 @@
       "\n",
       "\\$ESTIMATION METHOD=IMP INTERACTION ISAMPLES=10000 NITER=10 PRINT=1",
       "            EONLY=1 RANMETHOD=3S2P SEED=1337",
-      "\n$0"
+      "$0"
     ],
     "description": "IMP for OFV evaluation"
   },
@@ -529,7 +531,7 @@
       "            ISAMPLE=1000 CTYPE=3 NITER=500 STDOBJ=10",
       "            ISAMPEND=10000 NOPRIOR=1 CITER=10 CINTERVAL=0",
       "            CALPHA=0.05 EONLY=0",
-      "\n$0"
+      "$0"
     ],
     "description": "Options when setting AUTO=1 for DIRECT"
   },
@@ -545,7 +547,7 @@
       "            PSAMPLE_M1=1 PSAMPLE_M2=-1 PSAMPLE_M3=1 OSAMPLE_M1=-1",
       "            OSAMPLE_M2=-1 OACCEPT=0.5 ISAMPLE_M1=2 ISAMPLE_M1A=0",
       "            ISAMPLE_M2=2 ISAMPLE_M3=3 ISAMPLE_M1B=2 MCETA=0",
-      "\n$0"
+      "$0"
     ],
     "description": "Options when setting AUTO=1 for BAYES"
   },
@@ -654,30 +656,30 @@
       "",
       "\\$TABLE ID TIME EVID MDV IPRED IRES IWRES CWRES",
       "VARCALC=1",
-      "NOPRINT ONEHEADER FILE=sdtab$1 ; Standard table file",
+      "NOPRINT ONEHEADER FILE=sdtab${1:runno} ; Standard table file",
       "",
       "\\$TABLE ID CL V KA ETAS(1:LAST)",
       "VARCALC=1",
-      "NOPRINT ONEHEADER FILE=patab$2 ; Model parameters - THETAs, ETAs and EPSes",
+      "NOPRINT ONEHEADER FILE=patab${1:runno} ; Model parameters - THETAs, ETAs and EPSes",
       "",
       "\\$TABLE ID AGE WT",
-      "NOPRINT ONEHEADER FILE=cotab$3 ; Continuous covariates",
+      "NOPRINT ONEHEADER FILE=cotab${1:runno} ; Continuous covariates",
       "",
       "\\$TABLE ID SEX",
-      "NOPRINT ONEHEADER FILE=catab$4 ; Categorical covariates",
+      "NOPRINT ONEHEADER FILE=catab${1:runno} ; Categorical covariates",
       "\n$0"
     ],
     "description": "Xpose-compatible TABLE records"
   },
   "csv": {
     "prefix": ["format_csv"],
-    "body": ["FORMAT=,1PE15.8$0"],
+    "body": ["FORMAT=,1PE15.8"],
     "description": "Format the NONMEM output into a comma separated file\nThe default is s1PE12.5.\nFirst character specifies delimiter (, s for space, or t for tab)\n1PE15.8 means E field notation, 15 total characters allotted to number, 8 digits beyond decimal point, 1 digits before decimal point"
   },
   "theta": {
     "prefix": ["$THETA"],
     "body": [
-      "\\$THETA (${1:-Inf}, ${2:0}, ${3:Inf}) ${4:FIX }; TV ${5:Description}",
+      "\\$THETA (${1:-Inf}, ${2:1}, ${3:Inf}) ${4:FIX} ; TV ${5:Description}",
       "$0"
     ],
     "description": "New THETA record"
@@ -685,7 +687,7 @@
   "omega": {
     "prefix": ["$OMEGA"],
     "body": [
-      "\\$OMEGA (${1:-Inf}, ${2:0}, ${3:Inf}) ${4:FIX }; IIV ${5:Description}",
+      "\\$OMEGA (${1:-Inf}, ${2:0.9}, ${3:Inf}) ${4:FIX} ; IIV ${5:Description}",
       "$0"
     ],
     "description": "New OMEGA record"
@@ -693,7 +695,7 @@
   "sigma": {
     "prefix": ["$SIGMA"],
     "body": [
-      "\\$SIGMA (${1:-Inf}, ${2:0}, ${3:Inf}) ${4:FIX }; RUV ${5:Description}",
+      "\\$SIGMA (${1:-Inf}, ${2:0.9}, ${3:Inf}) ${4:FIX} ; RUV ${5:Description}",
       "$0"
     ],
     "description": "New SIGMA record"