[R/CC_analysis_functions_additive_model.R:17:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L17) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
calculate.llk.grid_scaled_additive <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:27:25:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L27) *style:* **Commas should always have a space after.**
```r
    op <- array(to.fill,c(length(prior$b.grid)))
                        ^
```
[R/CC_analysis_functions_additive_model.R:31:23:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                     ~^~
```
[R/CC_analysis_functions_additive_model.R:31:34:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                                ~^~
```
[R/CC_analysis_functions_additive_model.R:31:46:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                                            ~^~
```
[R/CC_analysis_functions_additive_model.R:35:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L35) *style:* **lines should not be more than 80 characters.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:35:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L35) *warning:* **no visible binding for global variable ‘cc_d.llk_additive’**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                       ^~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:35:59:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L35) *style:* **Put spaces around all infix operators.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                         ~^~
```
[R/CC_analysis_functions_additive_model.R:35:80:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L35) *style:* **Put spaces around all infix operators.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                              ~^~
```
[R/CC_analysis_functions_additive_model.R:35:96:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L35) *style:* **Put spaces around all infix operators.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                                ~^~
```
[R/CC_analysis_functions_additive_model.R:37:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L37) *style:* **lines should not be more than 80 characters.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:37:18:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L37) *warning:* **no visible global function definition for ‘cc_llk_additive’**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                 ^~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:37:36:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                  ~^~
```
[R/CC_analysis_functions_additive_model.R:37:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                ~^~
```
[R/CC_analysis_functions_additive_model.R:37:71:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                     ~^~
```
[R/CC_analysis_functions_additive_model.R:37:87:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                                ~^~
```
[R/CC_analysis_functions_additive_model.R:40:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                      ~^~
```
[R/CC_analysis_functions_additive_model.R:40:40:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                      ~^~
```
[R/CC_analysis_functions_additive_model.R:40:49:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                               ~^~
```
[R/CC_analysis_functions_additive_model.R:40:68:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                                                  ~^~
```
[R/CC_analysis_functions_additive_model.R:43:29:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L43) *style:* **Put spaces around all infix operators.**
```r
    if (scaled) op <- exp(op-mx);
                           ~^~
```
[R/CC_analysis_functions_additive_model.R:45:19:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L45) *style:* **Put spaces around all infix operators.**
```r
    return(list(op=op, b0.est=b0.est, lmx=mx));
                 ~^~
```
[R/CC_analysis_functions_additive_model.R:45:30:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L45) *style:* **Put spaces around all infix operators.**
```r
    return(list(op=op, b0.est=b0.est, lmx=mx));
                            ~^~
```
[R/CC_analysis_functions_additive_model.R:45:42:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L45) *style:* **Put spaces around all infix operators.**
```r
    return(list(op=op, b0.est=b0.est, lmx=mx));
                                        ~^~
```
[R/CC_analysis_functions_additive_model.R:60:31:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L60) *style:* **Put spaces around all infix operators.**
```r
    tmp1 <- (aff[1] + unaf[1])/(1 + exp(-b0))
                             ~^~
```
[R/CC_analysis_functions_additive_model.R:60:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L60) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp1 <- (aff[1] + unaf[1])/(1 + exp(-b0))
                               ^
```
[R/CC_analysis_functions_additive_model.R:61:31:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L61) *style:* **Put spaces around all infix operators.**
```r
    tmp2 <- (aff[2] + unaf[2])/(1 + exp(-(b0 + b1)))
                             ~^~
```
[R/CC_analysis_functions_additive_model.R:61:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L61) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp2 <- (aff[2] + unaf[2])/(1 + exp(-(b0 + b1)))
                               ^
```
[R/CC_analysis_functions_additive_model.R:61:42:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L61) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp2 <- (aff[2] + unaf[2])/(1 + exp(-(b0 + b1)))
                                         ^
```
[R/CC_analysis_functions_additive_model.R:62:31:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L62) *style:* **Put spaces around all infix operators.**
```r
    tmp3 <- (aff[3] + unaf[3])/(1 + exp(-(b0 + 2*b1)))
                             ~^~
```
[R/CC_analysis_functions_additive_model.R:62:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L62) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp3 <- (aff[3] + unaf[3])/(1 + exp(-(b0 + 2*b1)))
                               ^
```
[R/CC_analysis_functions_additive_model.R:62:42:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L62) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp3 <- (aff[3] + unaf[3])/(1 + exp(-(b0 + 2*b1)))
                                         ^
```
[R/CC_analysis_functions_additive_model.R:62:49:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L62) *style:* **Put spaces around all infix operators.**
```r
    tmp3 <- (aff[3] + unaf[3])/(1 + exp(-(b0 + 2*b1)))
                                               ~^~
```
[R/CC_analysis_functions_additive_model.R:65:16:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L65) *style:* **Put spaces around all infix operators.**
```r
    return(tmp1+tmp2+tmp3+tmp4)
              ~^~
```
[R/CC_analysis_functions_additive_model.R:65:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L65) *style:* **Put spaces around all infix operators.**
```r
    return(tmp1+tmp2+tmp3+tmp4)
                   ~^~
```
[R/CC_analysis_functions_additive_model.R:65:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L65) *style:* **Put spaces around all infix operators.**
```r
    return(tmp1+tmp2+tmp3+tmp4)
                        ~^~
```
[R/CC_analysis_functions_additive_model.R:82:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L82) *style:* **Put spaces around all infix operators.**
```r
        2*b1)))
        ~^~
```
[R/CC_analysis_functions_additive_model.R:94:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L94) *style:* **lines should not be more than 80 characters.**
```r
calculate.integrated.llk_scaled_additive <- function(prior, llk.surf, scaled = TRUE) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:94:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L94) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
calculate.integrated.llk_scaled_additive <- function(prior, llk.surf, scaled = TRUE) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:126:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L126) *style:* **lines should not be more than 80 characters.**
```r
get.posterior.node_additive <- function(forward, backward, prior, id = 1, plot = FALSE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:126:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L126) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
get.posterior.node_additive <- function(forward, backward, prior, id = 1, plot = FALSE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:129:15:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L129) *style:* **Put spaces around all infix operators.**
```r
    tmp <- tmp/sum(tmp)
             ~^~
```
[R/CC_analysis_functions_additive_model.R:130:22:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L130) *warning:* **no visible binding for global variable ‘null.id’**
```r
    post.null <- tmp[null.id[1]]
                     ^~~~~~~
```
[R/CC_analysis_functions_additive_model.R:132:9:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L132) *warning:* **no visible binding for global variable ‘null.id’**
```r
    tmp[null.id[1]] <- 0
        ^~~~~~~
```
[R/CC_analysis_functions_additive_model.R:133:15:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L133) *style:* **Put spaces around all infix operators.**
```r
    tmp <- tmp/sum(tmp)
             ~^~
```
[R/CC_analysis_functions_additive_model.R:157:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L157) *style:* **Put spaces around all infix operators.**
```r
    spac <- abs(prior$b.grid[2]-prior$b.grid[1])
                              ~^~
```
[R/CC_analysis_functions_additive_model.R:163:35:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L163) *style:* **Put spaces around all infix operators.**
```r
        b1_ci_lhs = rg.1[1] - spac/2,
                                 ~^~
```
[R/CC_analysis_functions_additive_model.R:164:35:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L164) *style:* **Put spaces around all infix operators.**
```r
        b1_ci_rhs = rg.1[2] + spac/2,
                                 ~^~
```
[R/CC_analysis_functions.R:20:5:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L20) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    NODE.COUNT.LIMIT=10,
    ^~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:21:5:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L21) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    NUM.CASES.MIN=10
    ^~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:28:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L28) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(nrow(samples) != nrow(phens)) {
      ^
```
[R/CC_analysis_functions.R:32:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L32) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!all(samples$ID == phens$ID)) {
      ^
```
[R/CC_analysis_functions.R:36:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L36) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if( NODE.COUNT.LIMIT < NUM.CASES.MIN )
      ^
```
[R/CC_analysis_functions.R:36:9:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L36) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    if( NODE.COUNT.LIMIT < NUM.CASES.MIN )
        ^~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:36:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L36) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    if( NODE.COUNT.LIMIT < NUM.CASES.MIN )
                           ^~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:37:9:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L37) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
        NODE.COUNT.LIMIT <- NUM.CASES.MIN
        ^~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:37:29:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L37) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
        NODE.COUNT.LIMIT <- NUM.CASES.MIN
                            ^~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:42:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L42) *style:* **Commas should always have a space after.**
```r
    t <- t[!t$coding %in% 99999,]
                                ^
```
[R/CC_analysis_functions.R:45:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L45) *style:* **Commas should always have a space after.**
```r
    top.nodes <- t[ ! t$parent_id %in% t$node_id,,drop=F]
                                                 ^
```
[R/CC_analysis_functions.R:45:55:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L45) *style:* **Put spaces around all infix operators.**
```r
    top.nodes <- t[ ! t$parent_id %in% t$node_id,,drop=F]
                                                     ~^~
```
[R/CC_analysis_functions.R:47:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L47) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(nrow(top.nodes) > 1 ) {
      ^
```
[R/CC_analysis_functions.R:55:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L55) *style:* **Only use double-quotes.**
```r
            selectable = 'N'
                         ^~~
```
[R/CC_analysis_functions.R:59:31:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L59) *style:* **Only use double-quotes.**
```r
        t[t$parent_id %in% 0, 'parent_id'] <- '99999'
                              ^~~~~~~~~~~
```
[R/CC_analysis_functions.R:59:47:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L59) *style:* **Only use double-quotes.**
```r
        t[t$parent_id %in% 0, 'parent_id'] <- '99999'
                                              ^~~~~~~
```
[R/CC_analysis_functions.R:62:22:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L62) *style:* **Commas should always have a space after.**
```r
        t <- rbind(t,top.node)
                     ^
```
[R/CC_analysis_functions.R:64:58:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L64) *style:* **Commas should always have a space after.**
```r
        t <- rbind(t[ ! t$node_id %in% top.nodes$node_id,],
                                                         ^
```
[R/CC_analysis_functions.R:68:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L68) *style:* **Commas should always have a space after.**
```r
    map <- match(t$coding,colnames(phens))
                          ^
```
[R/CC_analysis_functions.R:77:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L77) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if( length(dummy) > 0 ) {
      ^
```
[R/CC_analysis_functions.R:79:12:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L79) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for( i in 1:length(dummy) ) {
           ^
```
[R/CC_analysis_functions.R:80:20:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L80) *style:* **Use <-, not =, for assignment.**
```r
            node.id=t[dummy[i],'node_id']
                   ^
```
[R/CC_analysis_functions.R:80:20:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L80) *style:* **Put spaces around all infix operators.**
```r
            node.id=t[dummy[i],'node_id']
                  ~^~
```
[R/CC_analysis_functions.R:80:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L80) *style:* **Only use double-quotes.**
```r
            node.id=t[dummy[i],'node_id']
                               ^~~~~~~~~
```
[R/CC_analysis_functions.R:80:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L80) *style:* **Commas should always have a space after.**
```r
            node.id=t[dummy[i],'node_id']
                               ^
```
[R/CC_analysis_functions.R:81:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L81) *style:* **Use <-, not =, for assignment.**
```r
            node.cod=t[dummy[i],'coding']
                    ^
```
[R/CC_analysis_functions.R:81:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L81) *style:* **Put spaces around all infix operators.**
```r
            node.cod=t[dummy[i],'coding']
                   ~^~
```
[R/CC_analysis_functions.R:81:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L81) *style:* **Only use double-quotes.**
```r
            node.cod=t[dummy[i],'coding']
                                ^~~~~~~~
```
[R/CC_analysis_functions.R:81:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L81) *style:* **Commas should always have a space after.**
```r
            node.cod=t[dummy[i],'coding']
                                ^
```
[R/CC_analysis_functions.R:82:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L82) *style:* **Use <-, not =, for assignment.**
```r
            node.mea=t[dummy[i],'meaning']
                    ^
```
[R/CC_analysis_functions.R:82:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L82) *style:* **Put spaces around all infix operators.**
```r
            node.mea=t[dummy[i],'meaning']
                   ~^~
```
[R/CC_analysis_functions.R:82:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L82) *style:* **Only use double-quotes.**
```r
            node.mea=t[dummy[i],'meaning']
                                ^~~~~~~~~
```
[R/CC_analysis_functions.R:82:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L82) *style:* **Commas should always have a space after.**
```r
            node.mea=t[dummy[i],'meaning']
                                ^
```
[R/CC_analysis_functions.R:83:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L83) *style:* **Use <-, not =, for assignment.**
```r
            node.counts=t[dummy[i],'counts']
                       ^
```
[R/CC_analysis_functions.R:83:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L83) *style:* **Put spaces around all infix operators.**
```r
            node.counts=t[dummy[i],'counts']
                      ~^~
```
[R/CC_analysis_functions.R:83:36:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L83) *style:* **Only use double-quotes.**
```r
            node.counts=t[dummy[i],'counts']
                                   ^~~~~~~~
```
[R/CC_analysis_functions.R:83:36:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L83) *style:* **Commas should always have a space after.**
```r
            node.counts=t[dummy[i],'counts']
                                   ^
```
[R/CC_analysis_functions.R:88:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L88) *style:* **Only use double-quotes.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                        ^~~~~~~~
```
[R/CC_analysis_functions.R:88:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L88) *style:* **Commas should always have a space after.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                        ^
```
[R/CC_analysis_functions.R:88:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L88) *style:* **Commas should always have a space after.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                                 ^
```
[R/CC_analysis_functions.R:88:53:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L88) *style:* **Put spaces around all infix operators.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                                   ~^~
```
[R/CC_analysis_functions.R:88:54:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L88) *style:* **Only use double-quotes.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                                     ^~
```
[R/CC_analysis_functions.R:93:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L93) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                       ^~~~~~~~
```
[R/CC_analysis_functions.R:93:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L93) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                       ^
```
[R/CC_analysis_functions.R:93:52:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L93) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                                                   ^
```
[R/CC_analysis_functions.R:93:59:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L93) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                                                          ^
```
[R/CC_analysis_functions.R:93:62:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L93) *style:* **Put spaces around all infix operators.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                                                            ~^~
```
[R/CC_analysis_functions.R:93:63:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L93) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                                                              ^~
```
[R/CC_analysis_functions.R:94:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L94) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                       ^~~~~~~~~
```
[R/CC_analysis_functions.R:94:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L94) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                       ^
```
[R/CC_analysis_functions.R:94:53:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L94) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                                                    ^
```
[R/CC_analysis_functions.R:94:60:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L94) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                                                           ^
```
[R/CC_analysis_functions.R:94:63:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L94) *style:* **Put spaces around all infix operators.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                                                             ~^~
```
[R/CC_analysis_functions.R:94:64:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L94) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                                                               ^~
```
[R/CC_analysis_functions.R:95:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L95) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'selectable'] <- "N"
                       ^~~~~~~~~~~~
```
[R/CC_analysis_functions.R:95:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L95) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'selectable'] <- "N"
                       ^
```
[R/CC_analysis_functions.R:96:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L96) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'counts'] <- NA
                       ^~~~~~~~
```
[R/CC_analysis_functions.R:96:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L96) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'counts'] <- NA
                       ^
```
[R/CC_analysis_functions.R:98:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L98) *style:* **Commas should always have a space after.**
```r
            t <- rbind(t,new.node)
                         ^
```
[R/CC_analysis_functions.R:104:34:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L104) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                 ^
```
[R/CC_analysis_functions.R:104:45:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L104) *style:* **Only use double-quotes.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^~~~
```
[R/CC_analysis_functions.R:104:45:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L104) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^
```
[R/CC_analysis_functions.R:106:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L106) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                          ^~~~
```
[R/CC_analysis_functions.R:106:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L106) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                          ^
```
[R/CC_analysis_functions.R:106:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L106) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                        ^~~~~
```
[R/CC_analysis_functions.R:106:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L106) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                        ^
```
[R/CC_analysis_functions.R:106:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L106) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                                 ^~~~
```
[R/CC_analysis_functions.R:106:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L106) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                                 ^
```
[R/CC_analysis_functions.R:107:25:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L107) *style:* **Only use double-quotes.**
```r
    i.par <- setdiff(t[,'ID'], i.ter);
                        ^~~~
```
[R/CC_analysis_functions.R:107:25:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L107) *style:* **Commas should always have a space after.**
```r
    i.par <- setdiff(t[,'ID'], i.ter);
                        ^
```
[R/CC_analysis_functions.R:110:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L110) *style:* **Commas should always have a space after.**
```r
    t <- rbind(t[i.ter,],
                       ^
```
[R/CC_analysis_functions.R:111:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L111) *style:* **Commas should always have a space after.**
```r
                  t[i.par,])
                          ^
```
[R/CC_analysis_functions.R:112:15:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L112) *style:* **Only use double-quotes.**
```r
    t[nrow(t),'Par'] <- 0
              ^~~~~
```
[R/CC_analysis_functions.R:112:15:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L112) *style:* **Commas should always have a space after.**
```r
    t[nrow(t),'Par'] <- 0
              ^
```
[R/CC_analysis_functions.R:115:34:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L115) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                 ^
```
[R/CC_analysis_functions.R:115:45:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L115) *style:* **Only use double-quotes.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^~~~
```
[R/CC_analysis_functions.R:115:45:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L115) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^
```
[R/CC_analysis_functions.R:116:15:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L116) *style:* **Only use double-quotes.**
```r
    t[nrow(t),'Par'] <- 0
              ^~~~~
```
[R/CC_analysis_functions.R:116:15:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L116) *style:* **Commas should always have a space after.**
```r
    t[nrow(t),'Par'] <- 0
              ^
```
[R/CC_analysis_functions.R:117:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L117) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                          ^~~~
```
[R/CC_analysis_functions.R:117:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L117) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                          ^
```
[R/CC_analysis_functions.R:117:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L117) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                        ^~~~~
```
[R/CC_analysis_functions.R:117:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L117) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                        ^
```
[R/CC_analysis_functions.R:117:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L117) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                                 ^~~~
```
[R/CC_analysis_functions.R:117:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L117) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                                 ^
```
[R/CC_analysis_functions.R:118:25:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L118) *style:* **Only use double-quotes.**
```r
    i.par <- setdiff(t[,'ID'], i.ter);
                        ^~~~
```
[R/CC_analysis_functions.R:118:25:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L118) *style:* **Commas should always have a space after.**
```r
    i.par <- setdiff(t[,'ID'], i.ter);
                        ^
```
[R/CC_analysis_functions.R:121:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L121) *style:* **Commas should always have a space after.**
```r
    t.ter <- t[t$ID %in% i.ter,]
                               ^
```
[R/CC_analysis_functions.R:123:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L123) *style:* **Commas should always have a space after.**
```r
    t2 <- t[nrow(t),,drop=F]
                    ^
```
[R/CC_analysis_functions.R:123:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L123) *style:* **Put spaces around all infix operators.**
```r
    t2 <- t[nrow(t),,drop=F]
                        ~^~
```
[R/CC_analysis_functions.R:126:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L126) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    while(cont) {
         ^
```
[R/CC_analysis_functions.R:128:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L128) *style:* **Only use double-quotes.**
```r
        child.ids <- t[t$Par %in% t2$ID,'ID']
                                        ^~~~
```
[R/CC_analysis_functions.R:128:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L128) *style:* **Commas should always have a space after.**
```r
        child.ids <- t[t$Par %in% t2$ID,'ID']
                                        ^
```
[R/CC_analysis_functions.R:131:43:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L131) *style:* **Commas should always have a space after.**
```r
        t2 <- rbind(t[t$ID %in% child.ids,],
                                          ^
```
[R/CC_analysis_functions.R:135:11:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L135) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(nrow(t2) == nrow(t)) cont <- FALSE
          ^
```
[R/CC_analysis_functions.R:139:42:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L139) *style:* **Commas should always have a space after.**
```r
               t2[ ! t2$ID %in% t.ter$ID,])
                                         ^
```
[R/CC_analysis_functions.R:144:43:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L144) *style:* **Commas should always have a space after.**
```r
    tree$Par <- tree[match(tree$parent_id,tree$node_id),'ID']
                                          ^
```
[R/CC_analysis_functions.R:144:57:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L144) *style:* **Only use double-quotes.**
```r
    tree$Par <- tree[match(tree$parent_id,tree$node_id),'ID']
                                                        ^~~~
```
[R/CC_analysis_functions.R:144:57:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L144) *style:* **Commas should always have a space after.**
```r
    tree$Par <- tree[match(tree$parent_id,tree$node_id),'ID']
                                                        ^
```
[R/CC_analysis_functions.R:145:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L145) *style:* **Only use double-quotes.**
```r
    tree[nrow(tree),'Par'] <- 0
                    ^~~~~
```
[R/CC_analysis_functions.R:145:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L145) *style:* **Commas should always have a space after.**
```r
    tree[nrow(tree),'Par'] <- 0
                    ^
```
[R/CC_analysis_functions.R:146:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L146) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                ^~~~
```
[R/CC_analysis_functions.R:146:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L146) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                ^
```
[R/CC_analysis_functions.R:146:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L146) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                 ^~~~~
```
[R/CC_analysis_functions.R:146:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L146) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                 ^
```
[R/CC_analysis_functions.R:146:59:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L146) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                          ^~~~
```
[R/CC_analysis_functions.R:146:59:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L146) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                          ^
```
[R/CC_analysis_functions.R:147:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L147) *style:* **Only use double-quotes.**
```r
    i.par <- setdiff(tree[,'ID'], i.ter);
                           ^~~~
```
[R/CC_analysis_functions.R:147:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L147) *style:* **Commas should always have a space after.**
```r
    i.par <- setdiff(tree[,'ID'], i.ter);
                           ^
```
[R/CC_analysis_functions.R:152:8:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L152) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(i in 1:length(i.ter) ) {
       ^
```
[R/CC_analysis_functions.R:153:11:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L153) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(is.na(tree[i.ter[i],'counts'])) {
          ^
```
[R/CC_analysis_functions.R:153:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L153) *style:* **Only use double-quotes.**
```r
        if(is.na(tree[i.ter[i],'counts'])) {
                               ^~~~~~~~
```
[R/CC_analysis_functions.R:153:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L153) *style:* **Commas should always have a space after.**
```r
        if(is.na(tree[i.ter[i],'counts'])) {
                               ^
```
[R/CC_analysis_functions.R:154:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L154) *style:* **Only use double-quotes.**
```r
            tree[i.ter[i],'REMOVE'] <- TRUE
                          ^~~~~~~~
```
[R/CC_analysis_functions.R:154:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L154) *style:* **Commas should always have a space after.**
```r
            tree[i.ter[i],'REMOVE'] <- TRUE
                          ^
```
[R/CC_analysis_functions.R:155:18:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L155) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        } else if(tree[i.ter[i],'counts'] <= NODE.COUNT.LIMIT) {
                 ^
```
[R/CC_analysis_functions.R:155:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L155) *style:* **Only use double-quotes.**
```r
        } else if(tree[i.ter[i],'counts'] <= NODE.COUNT.LIMIT) {
                                ^~~~~~~~
```
[R/CC_analysis_functions.R:155:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L155) *style:* **Commas should always have a space after.**
```r
        } else if(tree[i.ter[i],'counts'] <= NODE.COUNT.LIMIT) {
                                ^
```
[R/CC_analysis_functions.R:155:46:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L155) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
        } else if(tree[i.ter[i],'counts'] <= NODE.COUNT.LIMIT) {
                                             ^~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:156:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L156) *style:* **Only use double-quotes.**
```r
            tree[i.ter[i],'REMOVE'] <- TRUE
                          ^~~~~~~~
```
[R/CC_analysis_functions.R:156:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L156) *style:* **Commas should always have a space after.**
```r
            tree[i.ter[i],'REMOVE'] <- TRUE
                          ^
```
[R/CC_analysis_functions.R:160:8:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L160) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(i in 1:length(i.par) ) {
       ^
```
[R/CC_analysis_functions.R:161:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L161) *style:* **Only use double-quotes.**
```r
        w.d <- which(tree[,'Par'] == i.par[i])
                           ^~~~~
```
[R/CC_analysis_functions.R:161:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L161) *style:* **Commas should always have a space after.**
```r
        w.d <- which(tree[,'Par'] == i.par[i])
                           ^
```
[R/CC_analysis_functions.R:163:11:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L163) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if( all(tree[w.d,'REMOVE']) ) {
          ^
```
[R/CC_analysis_functions.R:163:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L163) *style:* **Only use double-quotes.**
```r
        if( all(tree[w.d,'REMOVE']) ) {
                         ^~~~~~~~
```
[R/CC_analysis_functions.R:163:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L163) *style:* **Commas should always have a space after.**
```r
        if( all(tree[w.d,'REMOVE']) ) {
                         ^
```
[R/CC_analysis_functions.R:164:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L164) *style:* **Only use double-quotes.**
```r
            tree[i.par[i],'REMOVE'] <- TRUE
                          ^~~~~~~~
```
[R/CC_analysis_functions.R:164:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L164) *style:* **Commas should always have a space after.**
```r
            tree[i.par[i],'REMOVE'] <- TRUE
                          ^
```
[R/CC_analysis_functions.R:168:31:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L168) *style:* **Commas should always have a space after.**
```r
    tree <- tree[!tree$REMOVE,]
                              ^
```
[R/CC_analysis_functions.R:170:40:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L170) *style:* **Commas should always have a space after.**
```r
    tree.par <- tree.id[match(tree$Par,tree$ID)]
                                       ^
```
[R/CC_analysis_functions.R:173:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L173) *style:* **Only use double-quotes.**
```r
    tree[nrow(tree),'Par'] <- 0
                    ^~~~~
```
[R/CC_analysis_functions.R:173:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L173) *style:* **Commas should always have a space after.**
```r
    tree[nrow(tree),'Par'] <- 0
                    ^
```
[R/CC_analysis_functions.R:175:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L175) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                ^~~~
```
[R/CC_analysis_functions.R:175:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L175) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                ^
```
[R/CC_analysis_functions.R:175:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L175) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                 ^~~~~
```
[R/CC_analysis_functions.R:175:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L175) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                 ^
```
[R/CC_analysis_functions.R:175:59:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L175) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                          ^~~~
```
[R/CC_analysis_functions.R:175:59:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L175) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                          ^
```
[R/CC_analysis_functions.R:176:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L176) *style:* **Only use double-quotes.**
```r
    i.par <- setdiff(tree[,'ID'], i.ter);
                           ^~~~
```
[R/CC_analysis_functions.R:176:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L176) *style:* **Commas should always have a space after.**
```r
    i.par <- setdiff(tree[,'ID'], i.ter);
                           ^
```
[R/CC_analysis_functions.R:180:5:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L180) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    expected.node.ids <- 1:NUM.NODES
    ^~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:182:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L182) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!all(tree[,'ID'] == expected.node.ids)) {
      ^
```
[R/CC_analysis_functions.R:182:19:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L182) *style:* **Only use double-quotes.**
```r
    if(!all(tree[,'ID'] == expected.node.ids)) {
                  ^~~~
```
[R/CC_analysis_functions.R:182:19:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L182) *style:* **Commas should always have a space after.**
```r
    if(!all(tree[,'ID'] == expected.node.ids)) {
                  ^
```
[R/CC_analysis_functions.R:182:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L182) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    if(!all(tree[,'ID'] == expected.node.ids)) {
                           ^~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:183:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L183) *style:* **lines should not be more than 80 characters.**
```r
        stop("Node IDs are not compatible. Check that they are numeric and increasing bottom to top\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:186:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L186) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!all(i.ter == 1:length(i.ter))) {
      ^
```
[R/CC_analysis_functions.R:191:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L191) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.0.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:192:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L192) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.1.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:193:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L193) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.2.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:194:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L194) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.0.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:195:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L195) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.1.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:196:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L196) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.2.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:199:19:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                  ^
```
[R/CC_analysis_functions.R:199:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                         ^
```
[R/CC_analysis_functions.R:199:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                               ^
```
[R/CC_analysis_functions.R:199:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                                        ^
```
[R/CC_analysis_functions.R:199:51:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                                                  ^
```
[R/CC_analysis_functions.R:199:63:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                                                              ^
```


The default DB_PORT should be set to 3306. Will investigate this.


I can, but why?
It's not part of Graphite 1.0.0 release, I do not want to confuse people here.


@fabiangreffrath, sure, but excuse me, PR is an Git issue? Or commit?


the input should be accepted for return and enter, and any change canceled
if 'cancel' pressed. Up and down keys should not get us out of editor

On Wed, 12 Apr 2017 at 12:56 Michael Fuchs <notifications@github.com> wrote:

> The input is accepted when Return or Enter (Numpad) is pressed. Which
> other events should set the new text?
> Are there any checks about the validity of the text necessary?
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/QTodoTxt/QTodoTxt2/commit/d268c403fc7f7e5be9835910f8905da0308f89ff#commitcomment-21731422>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/ACcfzlOQRTzxyxwXc3bjzgJ7Z070SKqzks5rvK3agaJpZM4M7RBw>
> .
>


在 `options` 意义不大的情况下，template 直接写死为 `xxx.wxss` 之类的文件，然后通过 `fs.readFile` 来引入该文件，能提高该文件的可读性和可编辑性