[R/CC_analysis_functions_additive_model.R:17:1:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L27) *style:* **Commas should always have a space after.**
```r
    op <- array(to.fill,c(length(prior$b.grid)))
                        ^
```
[R/CC_analysis_functions_additive_model.R:31:23:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                     ~^~
```
[R/CC_analysis_functions_additive_model.R:31:34:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                                ~^~
```
[R/CC_analysis_functions_additive_model.R:31:46:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                                            ~^~
```
[R/CC_analysis_functions_additive_model.R:35:1:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L35) *style:* **lines should not be more than 80 characters.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$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/2b8869ded781cb652ec696413c26455525e54dcd/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$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                       ^~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:35:59:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L35) *style:* **Put spaces around all infix operators.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$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/2b8869ded781cb652ec696413c26455525e54dcd/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$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                              ~^~
```
[R/CC_analysis_functions_additive_model.R:35:96:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L35) *style:* **Put spaces around all infix operators.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$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/2b8869ded781cb652ec696413c26455525e54dcd/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$b.grid[i], aff=data[4:6], unaf=data[1:3]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:37:18:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L37) *warning:* **no visible global function definition for ‘cc_llk_additive’**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$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/2b8869ded781cb652ec696413c26455525e54dcd/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$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                  ~^~
```
[R/CC_analysis_functions_additive_model.R:37:50:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$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/2b8869ded781cb652ec696413c26455525e54dcd/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$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                     ~^~
```
[R/CC_analysis_functions_additive_model.R:37:87:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$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/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                      ~^~
```
[R/CC_analysis_functions_additive_model.R:40:40:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                      ~^~
```
[R/CC_analysis_functions_additive_model.R:40:49:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                               ~^~
```
[R/CC_analysis_functions_additive_model.R:40:68:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                                                  ~^~
```
[R/CC_analysis_functions_additive_model.R:43:29:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L42) *style:* **Commas should always have a space after.**
```r
    t <- t[!t$coding %in% 99999,]
                                ^
```
[R/CC_analysis_functions.R:45:50:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L45) *style:* **Commas should always have a space after.**
```r
    top.nodes <- t[ ! t$parent_id %in% t$node_id,,drop=F]
                                                 ^
```
[R/CC_analysis_functions.R:45:55:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L45) *style:* **Put spaces around all infix operators.**
```r
    top.nodes <- t[ ! t$parent_id %in% t$node_id,,drop=F]
                                                     ~^~
```
[R/CC_analysis_functions.R:47:7:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L47) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(nrow(top.nodes) > 1 ) {
      ^
```
[R/CC_analysis_functions.R:55:26:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L55) *style:* **Only use double-quotes.**
```r
            selectable = 'N'
                         ^~~
```
[R/CC_analysis_functions.R:59:31:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L59) *style:* **Only use double-quotes.**
```r
        t[t$parent_id %in% 0, 'parent_id'] <- '99999'
                              ^~~~~~~~~~~
```
[R/CC_analysis_functions.R:59:47:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L59) *style:* **Only use double-quotes.**
```r
        t[t$parent_id %in% 0, 'parent_id'] <- '99999'
                                              ^~~~~~~
```
[R/CC_analysis_functions.R:62:22:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L62) *style:* **Commas should always have a space after.**
```r
        t <- rbind(t,top.node)
                     ^
```
[R/CC_analysis_functions.R:64:58:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L64) *style:* **Commas should always have a space after.**
```r
        t <- rbind(t[ ! t$node_id %in% top.nodes$node_id,],
                                                         ^
```
[R/CC_analysis_functions.R:68:27:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L68) *style:* **Commas should always have a space after.**
```r
    map <- match(t$coding,colnames(phens))
                          ^
```
[R/CC_analysis_functions.R:77:7:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L104) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                 ^
```
[R/CC_analysis_functions.R:104:45:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L104) *style:* **Only use double-quotes.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^~~~
```
[R/CC_analysis_functions.R:104:45:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L115) *style:* **Only use double-quotes.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^~~~
```
[R/CC_analysis_functions.R:115:45:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L115) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^
```
[R/CC_analysis_functions.R:116:15:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L121) *style:* **Commas should always have a space after.**
```r
    t.ter <- t[t$ID %in% i.ter,]
                               ^
```
[R/CC_analysis_functions.R:123:21:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L123) *style:* **Commas should always have a space after.**
```r
    t2 <- t[nrow(t),,drop=F]
                    ^
```
[R/CC_analysis_functions.R:123:26:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L123) *style:* **Put spaces around all infix operators.**
```r
    t2 <- t[nrow(t),,drop=F]
                        ~^~
```
[R/CC_analysis_functions.R:126:10:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L126) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    while(cont) {
         ^
```
[R/CC_analysis_functions.R:128:41:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L128) *style:* **Only use double-quotes.**
```r
        child.ids <- t[t$Par %in% t2$ID,'ID']
                                        ^~~~
```
[R/CC_analysis_functions.R:128:41:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L128) *style:* **Commas should always have a space after.**
```r
        child.ids <- t[t$Par %in% t2$ID,'ID']
                                        ^
```
[R/CC_analysis_functions.R:131:43:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L131) *style:* **Commas should always have a space after.**
```r
        t2 <- rbind(t[t$ID %in% child.ids,],
                                          ^
```
[R/CC_analysis_functions.R:135:11:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L144) *style:* **Commas should always have a space after.**
```r
    tree$Par <- tree[match(tree$parent_id,tree$node_id),'ID']
                                          ^
```
[R/CC_analysis_functions.R:144:57:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L144) *style:* **Only use double-quotes.**
```r
    tree$Par <- tree[match(tree$parent_id,tree$node_id),'ID']
                                                        ^~~~
```
[R/CC_analysis_functions.R:144:57:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L191) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.0.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:192:10:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L192) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.1.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:193:10:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L193) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.2.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:194:10:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L194) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.0.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:195:10:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L195) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.1.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:196:10:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/R/CC_analysis_functions.R#L196) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.2.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:199:19:](https://github.com/shajoezhu/TreeWAS/blob/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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/2b8869ded781cb652ec696413c26455525e54dcd/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",
                                                              ^
```


TeamCity Market :: INFRA :: Graphouse :: Graphouse on change [Build 57](https://teamcity.yandex-team.ru/viewLog.html?buildId=8382342&buildTypeId=MarketInfra_Graphouse_GraphouseOnChangeOpensource) outcome was **SUCCESS**
Summary: Tests passed: 11 Build time: 00:00:37


@jimfulton you need to sign Plone Contributor Agreement in order to merge this pull request.

Learn about the Plone Contributor Agreement: http://docs.plone.org/develop/coredev/docs/contributors_agreement_explained.html


Can you give the steps necessary to re-produce this, I will check it out then.


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/59e715fc-1922-44e4-8188-940bfd079c0e "xynazog"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/7f35ebd7-57d7-488c-922e-e7a49cfc3ba4 "xynazog") deployed [XynazogBluemix](https://github.com/xynazog/XynazogBluemix/releases/tag/deploy-ibm-yp-us-south-NYU-DevOps-test-20170412-133530 "deploy-ibm-yp-us-south-NYU-DevOps-test-20170412-133530") to [test](https://console.ng.bluemix.net/apps/bd2cb29b-7122-42d7-a245-a9493595fa6b "ibm:yp:us-south:NYU DevOps:test"), including this commit


Shouldn't these keys match the ones in the map below?


Wat. You're declaring it here and [here](https://github.com/dirajrk/GuessingGame/commit/141b8559d1d30db8e326a10a3acfe5478e269bb1#diff-1163d646d923063af8fcec326d0b87e2R70) too.


Fulfilled the code convention.


@lmaurel - we should try to remove these `import *` statements where possible.  Also, no need for the `import unittest`


delete comments


Type in `message`.


![image](https://cloud.githubusercontent.com/assets/18514793/24960123/76a4fcce-1f9d-11e7-8f5f-4110ae8214da.png)
It appears when in Derived class isn't overriden one or more pure virtual functions of an abstract Base class
But I've override them all, so why it fails?


seems redundant since it is already defined in ./src/main/target/common_fc_pre.h


Imo, it will not work with other schemas such as ftp://


Added new subfolders


Tried this on dev preview, still fails.


Typo in "need"


I disagree since the resource directory was already created. Please check again the absolute file path app/src/main/res/xml/settings_main.xml . The steps for the necessary modifications are explained in the 4th slide of the "Preferences" section.


I would suggest not only checking for the existence of subscriptions, but also count them and check if it's for the right components. In this case it would actually be added to all subscriptions because `subscription` is used instead of `components`.

https://github.com/CachetHQ/Cachet/blob/2.3/app/Http/Controllers/Api/SubscriberController.php#L55


It might be just the p. But considering the bad shape this commit is in (illegal identation, NameErrors) I just reverted it.

IMO, We need a proper testcase to allow such changes back in.


@cekees @lmaurel  - in the most recent version of master (merged moments ago), there is now a new test class called `AirWaterVVTest`.  We should try migrating these tests to inherit from this class.  Eg. this line should read something like
`class TestDambreakUbbinkTetgen(TestTools.AirWaterVVTest):`.
This way, functionality common to all AirWaterVVTests can be placed in `TestTools` so that it does not need to be duplicated throughout the library.


leave the newline :sweat:


Specifically, for acoustics acquisition.


Remove this pref.


Wrong issue.... Correct issue https://github.com/zammad/zammad/issues/245


Ehh, live and learn. :) Done: https://github.com/fabiangreffrath/crispy-doom/pull/184


@pliu On which platform?

If this is Unix/Linux, the fix is maybe on IntelliJ side (I don't have IntelliJ to verify): if they want programs that run in their console to run like in a console, they have to make it behave like a console which means to run them in a PTY.


Bluemix [toolchain](https://dev-console.stage1.ng.bluemix.net/devops/toolchains/ccdfbb00-a390-4bd9-825e-8da3da79e74e "simple-toolchain-20170412134056730"): [Delivery Pipeline](https://dev-console.stage1.ng.bluemix.net/devops/pipelines/0cc25c65-6fe6-4dda-b5b9-05e2f63c5685 "simple-toolchain-20170412134056730") deployed [simple-toolchain-20170412134056730](https://github.com/jerome-lanneluc/simple-toolchain-20170412134056730/releases/tag/deploy-ibm-yp-eu-gb-jerome_lanneluc-fr.ibm.com-dev-20170412-134623 "deploy-ibm-yp-eu-gb-jerome_lanneluc-fr.ibm.com-dev-20170412-134623") to [dev](https://console.eu-gb.bluemix.net/apps/5072e6d9-8fcf-428f-9177-b11844211c36 "ibm:yp:eu-gb:jerome_lanneluc@fr.ibm.com:dev"), including this commit


Also, change TF-IDF
 * Add threegramms
 * Add max_features=2000000


Second


So the version bump is just to be aligned with graphite?


I agree, it shouldn't have passed the test. Also there's pathlib for these things.


sir can i contact u via email please?

gamingonline001@gmail.com @m3kgin3er


你好，感谢阅读，我重新把代码改了一下，你用新的code来练习。
再有问题随时提出。


Second commit


oh yes I forgot this one and the sluice gate


Ok I'll try it.


1. 应该改成np.array(shape[1],dtype='float32'))
2. 0.12版本后的tensorflow是改变了初始化指令
3. 是初始化的问题，最初的初始化方法很不容易训练，应该是由于后面会提到的局部最小值问题。较好的初始化方式可以解决。
4. 可以post你想实现的想法。tensorflow不仅仅可以做深度学习，还可以用于实现其他的算法。


Hello World


Fixed with this commit 3d0bfee0f2b5106e73ad2dbeb01cb07f7a92ca96

-Michael


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/e53faf7e-9ab7-49a9-8ea0-e0faceb2c8b3 "HRFinance"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/1fa107af-7894-46fe-9f68-d997b1aff229 "HRFinance") deployed [HRFinance](https://github.com/nsonwane/HRFinance/releases/tag/deploy-ibm-yp-us-south-perfectsolutions-dev-20170412-135558 "deploy-ibm-yp-us-south-perfectsolutions-dev-20170412-135558") to [dev](https://console.ng.bluemix.net/apps/49ac065a-e686-4b03-973f-5fa4536dbbe1 "ibm:yp:us-south:perfectsolutions:dev"), including this commit


Thank's! 👍


Hey Kiran - I got your message on my ser-222 repo. I'm glad you found it helpful, but hopefully in a way in keeping with academic integrity. :) To be honest, my intention wasn't to store my stuff on here as a reference, but because I work on two computers and needed a central place to store my work. I really should have deleted my repos when I was done with each class, lest it be mistaken as an attempt at academic dishonesty. Though, I will say that if anyone's concerned about students sharing their work here, they should be providing private accounts.

Anyway, I'm happy to chat with you. My school email is rbeerma@asu.edu.
Thanks!


Hey @lgalke Feel free to send a PR when you think it is ready! 🥂


ok that makes sense why the game has bad graphical glitches when very far out in the world


How do I solve this error here?
Error:NDK not configured. C:\Users\pc\AppData\Local\Android\Sdk\ndk-bundle
Download it with SDK manager.

qual arquivo devo instalar para funciona???
How do I solve this error here?
Error:NDK not configured. C:\Users\pc\AppData\Local\Android\Sdk\ndk-bundle
Download it with SDK manager.

Which file should I install to work ???


Oh, this is handy to know :)


not bad


“• Предпочитайте функциям-членам функции, не являющиеся ни членами, ни друзьями класса. Это повышает степень инкапсуляции и расширяемости, а также гибкость «упаковки» функциональности.”

Excerpt From: Майерс, Скотт. “Эффективное использование C++. 55 верных способов улучшить структуру и код ваших программ.” iBooks.
This material may be protected by copyright.


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/d7e5d188-ea4e-46b4-ad6a-3243a7f6e66c "ruwebapp"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/03a31f7d-8098-4ab7-8353-3072ef7c4053 "ruwebapp") deployed [ruwebapp](https://github.com/gwmiller717/ruwebapp/releases/tag/deploy-ibm-yp-us-south-gwmiller-us.ibm.com-ruCommonSpace-20170412-135928 "deploy-ibm-yp-us-south-gwmiller-us.ibm.com-ruCommonSpace-20170412-135928") to [ruCommonSpace](https://console.ng.bluemix.net/apps/a8c6ad23-0892-4278-b375-2947f77f8ee3 "ibm:yp:us-south:gwmiller@us.ibm.com:ruCommonSpace"), including this commit


智向阳学长您好，我运行代码在选择第二种方法的时候遇到了bug，显示“未定义与 'double' 类型的输入参数相对应的函数 'pointCloud'“，请问怎么解决这个问题？


It didn’t compile. CLJS requires js/Object instead of plain Object so it’s a conditional anyways. I just decided not to do JS part because it got ignored anyways.


I did it on the supposition that the link would be an url on the web so http. Do you think someone would use this for other protocols too?


TeamCity OTA+ :: rvi_sota_server :: ci [Build 2387](http://teamcity.prod01.internal.advancedtelematic.com:8111/viewLog.html?buildId=28701&buildTypeId=ota_plus_RviSotaServer_Ci) is now running


Bug introduced in 5611ddebe4dd800410f0c413ee034735e1d9993c : [argv[i] replaced by argv[1]](https://github.com/slodki/systemd/commit/5611ddebe4dd800410f0c413ee034735e1d9993c#diff-100b1098e493e90c7ab92940bae5e1a0R948)


TeamCity OTA+ :: rvi_sota_server :: ci [Build 2388](http://teamcity.prod01.internal.advancedtelematic.com:8111/viewLog.html?buildId=28703&buildTypeId=ota_plus_RviSotaServer_Ci) is now running


accepted


@brunasmedeiros just pointing this out. I am going to try to gradually reduce our custom rules so that we can get as close to the airbnb standard as possible, but doing it all at once will require way too much fixing.

I'll update FRW with the new rules.


죄송. count 였어요!


`all its imported dependencies` would be clearer yes.


goob job!


Result still seems broken but it's larger (44K instead of 8K); `file` still reports it as being 8-bit/color RGBA.

![doom02](https://cloud.githubusercontent.com/assets/63694/24961727/a6398600-1f91-11e7-8d0d-6cd17ec39691.png)


it's need?