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skills/graphpad-prism-skill/reference/syntax_and_basics.md

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+# GraphPad Prism Scripting - Syntax & Basics Summary
+
+## Script Syntax
+
+### Punctuation Rules
+- Command name followed by space, then arguments
+- Separate arguments with spaces or commas
+- Case-insensitive
+- Extra spaces allowed for readability
+
+### Documentation Notation
+- Required arguments: `[like this]`
+- Optional arguments: `<like this>`
+- Lowercase: value to enter
+- UPPERCASE: exact word to type
+
+## Comments
+
+### Syntax
+```
+// single line comment
+
+/*
+ multiple lines
+ of comments
+*/
+```
+
+## Row and Column Numbering
+
+### Columns
+- Row Title column: -1
+- X Column: 0
+- Column A: 1
+- Column B: 2, etc.
+
+### Rows
+- Column Title row: 0 or -1
+- First data row: 1 (not 0)
+- Subcolumn titles: not accessible via script
+
+## General Commands
+
+### GoTo Command
+Navigate between sheets and sections.
+
+**Syntax:**
+- `GoTo <section: D, I, R, G, or L>, <sheet#>, V<tab#>`
+- `GoTo +` (next sheet)
+- `GoTo -` (previous sheet)
+
+**Examples:**
+- `GoTo G` - go to graphs section, most recent graph
+- `GoTo 3` - third sheet of current section
+- `GoTo G, 3` - third graph
+- `GoTo V2` - second analysis tab of current results
+- `GoTo R, 3, V2` - second tab of third results sheet
+
+**Notes:**
+- Sheet numbering starts at 1 (not 0)
+- Space required between results and view: `R4V2` fails, use `R, 4, V2`
+
+## Loops and Simulations
+
+### Loop Commands
+- `ForEach [# of loops]` - loop specified number of times
+- `ForEach [filespec]` - loop over files (e.g., `ForEach *.CSV` or `ForEach "C:\data\DR*.txt"`)
+- `ForEachSheet` - loop over all sheets in current section
+- `Next` - end loop statement
+- `Regenerate` - regenerate random numbers (for Monte Carlo simulations)
+
+**Notes:**
+- Cannot nest loops
+- Used for simulations and repeated file imports
+
+### Monte Carlo Pattern
+1. Create Prism file with "Simulate data with random scatter" analysis
+2. Link simulated data to another analysis (e.g., nonlinear regression)
+3. In loop: GoTo simulation analysis → Regenerate → GoTo results → write output → Next
+
+## Variables for Text Output
+
+Available in any command that exports text, primarily useful in loops:
+
+- `%F` - file name (before period)
+- `%X` - file extension (without period)
+- `%S` - current sheet name (works inside or outside loops)
+- `%N` - loop number
+- `%%` - literal percent symbol (%)
+
+Variables can be preceded/followed by other text. Additional variables available when writing text files.
+
+## File Path Management
+
+### SetPath Command
+**Syntax:** `SetPath ["drive and folder path"]`
+
+Sets default path for file read/write commands unless overridden in individual commands.
+
+**Windows Examples:**
+```
+SetPath "C:\Users\(current user)\Documents\007\goldfinger\oddjob"
+SetPath "(local drive):\DataFiles\August2005\"
+SetPath "\\LabServer\DDrive\PrismFiles"
+```
+
+**Mac Example:**
+```
+SetPath "Hard Drive:Prism 4:Data:June21"
+```
+
+**Network drives:** Use `\\ServerName\DriveName\path` format without "C:" notation.
+
+Individual commands can specify full paths to override SetPath.