[R/data_description.r:11:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L11) *style:* **Lines should not be more than 80 characters.**
```r
  title(main = "Forces from posture #1", sub = paste("Adept x:", adept_x_val, "Adept y:",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:16:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L16) *style:* **Lines should not be more than 80 characters.**
```r
plot_muscle_forces_over_time <- function(forces, minimum_tendon_force, maximum_tendon_force,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:21:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L21) *style:* **Lines should not be more than 80 characters.**
```r
  lapply(list(do.call("rbind", forces[indices_of_interest])), function(force_ts) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:23:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L23) *style:* **Lines should not be more than 80 characters.**
```r
      "M1", "M2", "M3", "M4", "M5", "M6"), ylim = c(minimum_tendon_force, maximum_tendon_force))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:28:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L28) *style:* **Lines should not be more than 80 characters.**
```r
plot_jr3_force_over_time <- function(forces, minimum_tendon_force, maximum_tendon_force,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:42:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L42) *style:* **Lines should not be more than 80 characters.**
```r
##' @param wrench_vector a vector of six forces & torques, as numeric values in N or N*m
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:42:2:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L42) *style:* **Commented code should be removed.**
```r
##' @param wrench_vector a vector of six forces & torques, as numeric values in N or N*m
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:46:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L46) *style:* **Lines should not be more than 80 characters.**
```r
    "FZ =", wrench_vector[3], ", ", "MX =", wrench_vector[4], ", ", "MY =", wrench_vector[5],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:52:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L52) *style:* **Lines should not be more than 80 characters.**
```r
##' a Map is a Muscle Activation Pattern, which is, given N muscles, the map is a vector of N tensions.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:56:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L56) *style:* **Lines should not be more than 80 characters.**
```r
  muscle_activation_patterns <- rbind(unique(timeseries_df$reference_M0), unique(timeseries_df$reference_M1),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:57:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L57) *style:* **Lines should not be more than 80 characters.**
```r
    unique(timeseries_df$reference_M2), unique(timeseries_df$reference_M3), unique(timeseries_df$reference_M4),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:60:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L60) *style:* **Lines should not be more than 80 characters.**
```r
  colnames(muscle_activation_patterns) <- LETTERS[1:length(unique(timeseries_df$reference_M6))]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:65:2:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L65) *style:* **Commented code should be removed.**
```r
##' Plot wrench text for forces & torques
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:69:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L69) *style:* **Lines should not be more than 80 characters.**
```r
##' @param prepend_string empty, by default. Useful when you want to add "SD: " to the front
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:87:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L87) *style:* **Lines should not be more than 80 characters.**
```r
  p_raw <- ggparcoord(dataframe_of_observations, scale = "globalminmax", alpha = 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:89:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L89) *style:* **Lines should not be more than 80 characters.**
```r
  p <- p_raw + theme_bw() + theme(panel.grid.major.x = element_line(color = "black",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:111:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L111) *style:* **Lines should not be more than 80 characters.**
```r
  plot(NA, xlim = xlim, ylim = ylim, main = paste("Norm of w = ", norm_vec(wrench)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:112:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L112) *style:* **Lines should not be more than 80 characters.**
```r
    xlab = paste("Fx is ", wrench[1]), ylab = paste("Fy is ", wrench[2]), asp = 1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:116:3:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L116) *warning:* **local variable ‘x_sd’ assigned but may not be used**
```r
  x_sd <- wrench_sd[1]
  ^~~~
```
[R/data_description.r:117:3:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L117) *warning:* **local variable ‘y_sd’ assigned but may not be used**
```r
  y_sd <- wrench_sd[2]
  ^~~~
```
[R/data_description.r:118:3:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L118) *warning:* **local variable ‘z_sd’ assigned but may not be used**
```r
  z_sd <- wrench_sd[3]  #unused as of yet
  ^~~~
```
[R/data_description.r:128:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L128) *style:* **Lines should not be more than 80 characters.**
```r
##' By default, if the diameter is positive, then the circle_color is made green, but if negative, it will make the circle black.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:140:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L140) *style:* **Lines should not be more than 80 characters.**
```r
  draw.circle(x, y, diameter, border = "black", col = circle_color, lty = 1, lwd = 1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:143:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L143) *style:* **Lines should not be more than 80 characters.**
```r
##' @param list_of_wrenches list object, each element a list of numeric values of 3 forces in N and 3 torques in Nm
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:144:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L144) *style:* **Lines should not be more than 80 characters.**
```r
##' @param list_of_sd_for_wrenches list object, each element a list of numeric values of 3 forces in N and 3 torques in Nm
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:148:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L148) *style:* **Lines should not be more than 80 characters.**
```r
plot_endpoint_force_vectors <- function(list_of_wrenches, list_of_sd_for_wrenches,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:153:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L153) *style:* **Lines should not be more than 80 characters.**
```r
    plot_output_wrench_fx_fy(list_of_wrenches[[x]], list_of_sd_for_wrenches[[x]],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:159:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L159) *style:* **Lines should not be more than 80 characters.**
```r
##' Get the mean of the last n force values for each of the force signals, for the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:161:2:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L161) *style:* **Commented code should be removed.**
```r
##' ramp&hold time series dataframes force_column_names is a vecotr of character
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:162:2:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L162) *style:* **Commented code should be removed.**
```r
##' strings relating to the columns of forces[[i]] that contain force recordings
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:164:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L164) *style:* **Lines should not be more than 80 characters.**
```r
##' @param indices_of_interest the elements within the forces that will be included in the analysis
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:165:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L165) *style:* **Lines should not be more than 80 characters.**
```r
##' @param n number of last observations that will be extracted for this computation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:167:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L167) *style:* **Lines should not be more than 80 characters.**
```r
##' @return list_of_tail_wrench_means computed means of the last n milliseconds of the force columns
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:168:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L168) *style:* **Lines should not be more than 80 characters.**
```r
list_of_mean_of_last_n_observations <- function(forces, indices_of_interest, n, force_column_names) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:168:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L168) *style:* **Variable and function names should not be longer than 30 characters.**
```r
list_of_mean_of_last_n_observations <- function(forces, indices_of_interest, n, force_column_names) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:178:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L178) *style:* **Lines should not be more than 80 characters.**
```r
sd_of_last_n_observations <- function(forces, indices_of_interest, n = 100, force_column_names) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:187:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L187) *style:* **Variable and function names should not be longer than 30 characters.**
```r
plot_porcupine_of_endpoint_wrenches <- function(forces) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:188:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L188) *style:* **Lines should not be more than 80 characters.**
```r
  wrench_observation_df <- do.call("rbind", forces)  #only grab the first posture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:193:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L193) *style:* **Lines should not be more than 80 characters.**
```r
  scatterplot3d(wrench_observation_df[, 1], wrench_observation_df[, 2], wrench_observation_df[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:194:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L194) *style:* **Lines should not be more than 80 characters.**
```r
    3], pch = 16, xlim = force_ranges[, 1], ylim = force_ranges[, 2], zlim = force_ranges[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:198:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L198) *style:* **Lines should not be more than 80 characters.**
```r
  scatterplot3d(wrench_observation_df[, 4], wrench_observation_df[, 5], wrench_observation_df[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:199:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L199) *style:* **Lines should not be more than 80 characters.**
```r
    6], pch = 16, xlim = force_ranges[, 4], ylim = force_ranges[, 5], zlim = force_ranges[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:207:3:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L207) *warning:* **no visible binding for global variable ‘gradient_colors’**
```r
  gradient_colors < c("blue", "yellow")
  ^~~~~~~~~~~~~~~
```
[R/data_description.r:208:58:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L208) *warning:* **no visible binding for global variable ‘gradient_colors’**
```r
  z_colors <- color_gradient(wrench_observation_df[, 3], gradient_colors)
                                                         ^~~~~~~~~~~~~~~
```
[R/data_description.r:211:3:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L211) *warning:* **local variable ‘z_range_midpoint’ assigned but may not be used**
```r
  z_range_midpoint <- z_range_distance/2 + z_range[1]
  ^~~~~~~~~~~~~~~~
```
[R/data_description.r:211:39:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L211) *style:* **Put spaces around all infix operators.**
```r
  z_range_midpoint <- z_range_distance/2 + z_range[1]
                                     ~^~
```
[R/data_description.r:215:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L215) *style:* **Lines should not be more than 80 characters.**
```r
  segments(origin_points, origin_points, wrench_observation_df[, 1], wrench_observation_df[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:217:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L217) *style:* **Lines should not be more than 80 characters.**
```r
  points(wrench_observation_df[, 1], wrench_observation_df[, 2], xlim = c(force_ranges[1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:222:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L222) *style:* **Lines should not be more than 80 characters.**
```r
  legend_image <- as.raster(matrix(colorRampPalette(gradient_colors)(100), ncol = 1))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:222:53:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L222) *warning:* **no visible binding for global variable ‘gradient_colors’**
```r
  legend_image <- as.raster(matrix(colorRampPalette(gradient_colors)(100), ncol = 1))
                                                    ^~~~~~~~~~~~~~~
```
[R/data_description.r:225:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L225) *style:* **Lines should not be more than 80 characters.**
```r
  text(x = -1, y = seq(1, 3, l = length(values_to_label_on_legend)), labels = signif(values_to_label_on_legend,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:231:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L231) *style:* **Lines should not be more than 80 characters.**
```r
##' @param colors list of string colors that are desired in the gradient. c("blue", "yellow") by default
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:231:2:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L231) *style:* **Commented code should be removed.**
```r
##' @param colors list of string colors that are desired in the gradient. c("blue", "yellow") by default
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:233:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L233) *style:* **Lines should not be more than 80 characters.**
```r
##' @return color_gradient returns a function that takes an integer argument (the required number of colors) and returns a character vector of colors (see ‘rgb’) interpolating the given sequence (similar to ‘heat.colors’ or ‘terrain.colors’.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:239:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L239) *style:* **Lines should not be more than 80 characters.**
```r
data_description_analysis <- function(first_data_chunk, minimum_tendon_force, maximum_tendon_force,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:242:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L242) *style:* **Lines should not be more than 80 characters.**
```r
  forces <- unlist(lapply(postures, split_by_reference_force), recursive = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:245:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L245) *style:* **Lines should not be more than 80 characters.**
```r
  muscle_activation_patterns <- do.call("rbind", lapply(forces[indices_of_interest],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:247:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L247) *style:* **Lines should not be more than 80 characters.**
```r
  row.names(muscle_activation_patterns) <- LETTERS[1:length(indices_of_interest)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:253:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L253) *style:* **Lines should not be more than 80 characters.**
```r
  plot(plot_muscle_forces_over_time(forces, minimum_tendon_force, maximum_tendon_force,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:258:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L258) *style:* **Lines should not be more than 80 characters.**
```r
  plot(plot_jr3_force_over_time(forces, minimum_tendon_force, maximum_tendon_force,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:262:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L262) *style:* **Lines should not be more than 80 characters.**
```r
  list_of_tail_wrench_mean <- list_of_mean_of_last_n_observations(forces, indices_of_interest,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:264:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L264) *style:* **Lines should not be more than 80 characters.**
```r
  list_of_tail_wrench_SD <- sd_of_last_n_observations(forces, indices_of_interest,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:264:3:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L264) *style:* **Variable or function name should be snake_case.**
```r
  list_of_tail_wrench_SD <- sd_of_last_n_observations(forces, indices_of_interest,
  ^~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:270:8:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L270) *style:* **Use <-, not =, for assignment.**
```r
  xlim = range(lapply(list_of_wrenches, function(x) {
       ^
```
[R/data_description.r:273:8:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L273) *style:* **Use <-, not =, for assignment.**
```r
  ylim = range(lapply(list_of_wrenches, function(x) {
       ^
```
[R/data_description.r:276:8:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L276) *style:* **Use <-, not =, for assignment.**
```r
  zlim = range(lapply(list_of_wrenches, function(x) {
       ^
```
[R/data_description.r:280:11:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L280) *style:* **Use <-, not =, for assignment.**
```r
  xlim[1] = xlim[1] - max(abs(zlim))
          ^
```
[R/data_description.r:282:11:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L282) *style:* **Use <-, not =, for assignment.**
```r
  xlim[2] = max(c(xlim[2] + max(abs(zlim)), 0))
          ^
```
[R/data_description.r:287:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L287) *style:* **Lines should not be more than 80 characters.**
```r
  indices_of_correctly_lengthed_forces <- which(lapply(forces, force_ts_len_is_acceptable) ==
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:287:3:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L287) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  indices_of_correctly_lengthed_forces <- which(lapply(forces, force_ts_len_is_acceptable) ==
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:290:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L290) *style:* **Lines should not be more than 80 characters.**
```r
  force_extended_list <- list_of_mean_of_last_n_observations(forces, indices_of_interest = 1:length(forces),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:292:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L292) *style:* **Lines should not be more than 80 characters.**
```r
  posture_1_viable_forces <- force_extended_list[indices_of_correctly_lengthed_forces]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:296:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L296) *style:* **Lines should not be more than 80 characters.**
```r
  elapsed_trial_times <- plot_force_trial_elapsed_time_distribution(forces[indices_of_correctly_lengthed_forces])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:296:3:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L296) *warning:* **local variable ‘elapsed_trial_times’ assigned but may not be used**
```r
  elapsed_trial_times <- plot_force_trial_elapsed_time_distribution(forces[indices_of_correctly_lengthed_forces])
  ^~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:298:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L298) *style:* **Variable and function names should not be longer than 30 characters.**
```r
plot_force_trial_elapsed_time_distribution <- function(forces) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/data_description.r:300:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/data_description.r#L300) *style:* **Lines should not be more than 80 characters.**
```r
  hist(vector_of_times, breaks = 10, xlab = "Time per force trial (ms)", ylab = "Number of force trials",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:3:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L3) *style:* **Lines should not be more than 80 characters.**
```r
##' @param last_n_milliseconds the number of tail milliseconds from which we should calculate the settled standard deviation.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:5:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L5) *style:* **Lines should not be more than 80 characters.**
```r
##' @return reference_standard_deviation df with reference (desired) muscle tension, variance, maximum residual
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:6:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L6) *style:* **Lines should not be more than 80 characters.**
```r
get_reference_to_variance_relationship_df <- function(force_list, last_n_milliseconds,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:6:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L6) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_reference_to_variance_relationship_df <- function(force_list, last_n_milliseconds,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:19:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L19) *style:* **Lines should not be more than 80 characters.**
```r
##' @param last_n_milliseconds the number of tail milliseconds from which we should calculate the settled standard deviation.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:22:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L22) *style:* **Lines should not be more than 80 characters.**
```r
force_trial_to_stable_metrics <- function(force_trial, last_n_milliseconds, muscle) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:26:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L26) *style:* **Lines should not be more than 80 characters.**
```r
  vec_row <- data.frame(last_n_milliseconds = last_n_milliseconds, reference = ref,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:32:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L32) *style:* **Lines should not be more than 80 characters.**
```r
##' @param last_n_milliseconds the number of tail milliseconds from which we should calculate the settled standard deviation.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:34:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L34) *style:* **Lines should not be more than 80 characters.**
```r
##' @return stability_df_rows df with reference (desired) muscle tension, variance, maximum residual
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:35:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L35) *style:* **Lines should not be more than 80 characters.**
```r
ft_list_to_stability_df_rows <- function(list_of_force_trials, last_n_milliseconds,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:37:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L37) *style:* **Lines should not be more than 80 characters.**
```r
  reference_df_rows <- lapply(list_of_force_trials, force_trial_to_stable_metrics,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:44:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L44) *style:* **Lines should not be more than 80 characters.**
```r
##' Produces a plot of remaining fraction as a function of increasing err threshold. Draws a hardcoded line for the 99%
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:45:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L45) *style:* **Lines should not be more than 80 characters.**
```r
##' @param force_trials a list of raw force timeseries_DFs. has_settled has not been applied yet
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:46:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L46) *style:* **Lines should not be more than 80 characters.**
```r
##' @param err_lenout integer, the resolution along the X axis by which diff err thresholds will be evaluated
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:48:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L48) *style:* **Variable and function names should not be longer than 30 characters.**
```r
try_different_stability_thresholds <- function(force_trials, err_lenout = 20) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:50:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L50) *style:* **Lines should not be more than 80 characters.**
```r
  num_remaining_force_trials <- unlist(mclapply(different_errors, function(err) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:53:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L53) *style:* **Lines should not be more than 80 characters.**
```r
  plot_remaining_force_trial_fraction_as_function_of_err(different_errors, num_remaining_force_trials,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:61:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L61) *style:* **Lines should not be more than 80 characters.**
```r
indices_from_posture_df_row <- function(posture_df_row) c(posture_df_row[["initial"]],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:65:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L65) *style:* **Lines should not be more than 80 characters.**
```r
##' Turn a dataframe of collected observations, with square input to reference, into formal ForceTrial objects
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:66:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L66) *style:* **Lines should not be more than 80 characters.**
```r
##' Works with stabilized or nonstabilized force trials. It will add attributes of stabilization only for those that meet the err criteria
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:68:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L68) *style:* **Lines should not be more than 80 characters.**
```r
##' @param df_row dataframe with 1 row with columns including the initial and final indices in reference to a posture collected.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:72:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L72) *style:* **Lines should not be more than 80 characters.**
```r
##' @param err max allowable residual from reference force for muscle of interest
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:73:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L73) *style:* **Lines should not be more than 80 characters.**
```r
save_ForceTrials_to_rds <- function(df_row, column_to_separate_forces, data_location,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:73:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L73) *style:* **Variable or function name should be snake_case.**
```r
save_ForceTrials_to_rds <- function(df_row, column_to_separate_forces, data_location,
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:76:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L76) *style:* **Lines should not be more than 80 characters.**
```r
  force_trial_file_string_with_posture <- paste0("force_trial_adept_x_", df_row[["adept_x"]],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:76:3:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L76) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  force_trial_file_string_with_posture <- paste0("force_trial_adept_x_", df_row[["adept_x"]],
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:80:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L80) *style:* **Lines should not be more than 80 characters.**
```r
  force_trials_list <- lapply(force_list, ForceTrial, data_location, full_df, err)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:87:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L87) *style:* **Lines should not be more than 80 characters.**
```r
##' Turn a dataframe of collected observations, with square input to reference, into formal ForceTrial objects
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:88:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L88) *style:* **Lines should not be more than 80 characters.**
```r
##' Works with stabilized or nonstabilized force trials. It will add attributes of stabilization only for those that meet the err criteria
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:90:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L90) *style:* **Lines should not be more than 80 characters.**
```r
##' @param df_of_postures dataframe with columns including the initial and final indices in reference to each posture group collected.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:91:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L91) *style:* **Lines should not be more than 80 characters.**
```r
##' @param full_df dataframe object of the full dataset collected, from which the indices will extract the sections.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:93:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L93) *style:* **Lines should not be more than 80 characters.**
```r
posture_start_finish_indices_to_L_of_ForceTrials <- function(df_of_postures, full_df,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:93:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L93) *style:* **Variable and function names should not be longer than 30 characters.**
```r
posture_start_finish_indices_to_L_of_ForceTrials <- function(df_of_postures, full_df,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:93:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L93) *style:* **Variable or function name should be snake_case.**
```r
posture_start_finish_indices_to_L_of_ForceTrials <- function(df_of_postures, full_df,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:95:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L95) *style:* **Lines should not be more than 80 characters.**
```r
  lapply(df_to_list_of_rows(df_of_postures), save_ForceTrials_to_rds, column_to_separate_forces = "measured_M0",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:104:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L104) *style:* **Lines should not be more than 80 characters.**
```r
  max_residuals_and_sd <- lapply(posture, ForceTrial_to_signed_max_residual_and_sd)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:105:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L105) *style:* **Lines should not be more than 80 characters.**
```r
  stability <- cbind(ForceTrials_to_stability_info_df(posture), ForceTrials_to_stability_df(posture))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:107:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L107) *style:* **Lines should not be more than 80 characters.**
```r
  posture_and_residual_sd <- dcrb(lapply(max_residuals_and_sd, add_posture_to_max_residual_and_sd,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:113:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L113) *style:* **Lines should not be more than 80 characters.**
```r
##' @param rds_postures list of full filepaths to each rds Posture, each with a list of ForceTrials
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:114:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L114) *style:* **Lines should not be more than 80 characters.**
```r
##' @return stability_df data.frame with all stabiliyt information observations at postures. Includes adept xy coordinates
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:115:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L115) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_stability_df_for_all_postures <- function(rds_postures) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:123:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L123) *style:* **Lines should not be more than 80 characters.**
```r
##' @param stability_df dataframe with adept_x and adept_y column, sd, and signed_max_residual
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:126:13:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L126) *style:* **Use <-, not =, for assignment.**
```r
  my_breaks = c(1, 10, 100, 1000, 10000, 1e+05)
            ^
```
[R/force_trial_stability.r:127:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L127) *style:* **Lines should not be more than 80 characters.**
```r
  ggplot(stability_df, aes(sd, signed_max_residual)) + theme_bw() + stat_binhex(bins = 100) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:128:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L128) *style:* **Lines should not be more than 80 characters.**
```r
    scale_fill_gradient(name = "count", trans = "log", breaks = my_breaks, labels = my_breaks) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:133:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L133) *style:* **Lines should not be more than 80 characters.**
```r
##' @param list_of_stability_dfs dataframes with adept_x and adept_y column, sd, and signed_max_residual. first is fix_x_sdres
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:134:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L134) *style:* **Lines should not be more than 80 characters.**
```r
##' @param adept_dimension_that_changes either 'adept_x' or 'adept_y', describing the one that is changing
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:136:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L136) *style:* **Lines should not be more than 80 characters.**
```r
sd_residual_plot_scatter_posture <- function(stability_df, adept_dimension_that_changes,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:136:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L136) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sd_residual_plot_scatter_posture <- function(stability_df, adept_dimension_that_changes,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:138:3:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L138) *warning:* **local variable ‘my_breaks’ assigned but may not be used**
```r
  my_breaks = c(1, 10, 100, 1000, 10000, 1e+05)
  ^~~~~~~~~
```
[R/force_trial_stability.r:138:13:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L138) *style:* **Use <-, not =, for assignment.**
```r
  my_breaks = c(1, 10, 100, 1000, 10000, 1e+05)
            ^
```
[R/force_trial_stability.r:139:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L139) *style:* **Lines should not be more than 80 characters.**
```r
  p <- ggplot(stability_df, aes(sd, signed_max_residual)) + geom_point(size = size) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:140:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L140) *style:* **Lines should not be more than 80 characters.**
```r
    theme_bw() + xlab(paste("sd of last 100ms,", adept_dimension_that_changes)) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:146:2:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L146) *style:* **Commented code should be removed.**
```r
##' the length of the whiskers =  1.5 the IQR
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:147:2:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L147) *style:* **Commented code should be removed.**
```r
##' @param stability_df dataframe with adept_* and y variable to respond
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:148:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L148) *style:* **Lines should not be more than 80 characters.**
```r
##' @param adept_dimension_that_changes either 'adept_x' or 'adept_y', describing the one that is changing
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:151:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L151) *style:* **Lines should not be more than 80 characters.**
```r
adept_boxplots <- function(stability_df, adept_dimension_that_changes, response_variable) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:153:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L153) *style:* **Lines should not be more than 80 characters.**
```r
  min_distance_between_adept_postures <- abs(min(diff(unique(stability_df[[adept_dimension_that_changes]])))) *
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:153:3:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L153) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  min_distance_between_adept_postures <- abs(min(diff(unique(stability_df[[adept_dimension_that_changes]])))) *
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:155:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L155) *style:* **Lines should not be more than 80 characters.**
```r
  p <- ggplot(stability_df, aes_string(y = response_variable, group = adept_dimension_that_changes))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:155:8:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L155) *warning:* **no visible global function definition for ‘ggplot’, Did you mean 'biplot'?**
```r
  p <- ggplot(stability_df, aes_string(y = response_variable, group = adept_dimension_that_changes))
       ^~~~~~
```
[R/force_trial_stability.r:155:29:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L155) *warning:* **no visible global function definition for ‘aes_string’**
```r
  p <- ggplot(stability_df, aes_string(y = response_variable, group = adept_dimension_that_changes))
                            ^~~~~~~~~~
```
[R/force_trial_stability.r:156:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L156) *style:* **Lines should not be more than 80 characters.**
```r
  p <- p + geom_boxplot(aes_string(cut_width(stability_df[[adept_dimension_that_changes]],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:157:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L157) *style:* **Lines should not be more than 80 characters.**
```r
    min_distance_between_adept_postures)), outlier.alpha = 0.2, outlier.size = 0.1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:159:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L159) *style:* **Lines should not be more than 80 characters.**
```r
  p <- p + theme_bw() + xlab(paste(adept_dimension_that_changes, "postures from", adept_range[1], "to", adept_range[2]))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:159:12:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L159) *warning:* **no visible global function definition for ‘theme_bw’**
```r
  p <- p + theme_bw() + xlab(paste(adept_dimension_that_changes, "postures from", adept_range[1], "to", adept_range[2]))
           ^~~~~~~~
```
[R/force_trial_stability.r:159:25:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L159) *warning:* **no visible global function definition for ‘xlab’, Did you mean 'lag'?**
```r
  p <- p + theme_bw() + xlab(paste(adept_dimension_that_changes, "postures from", adept_range[1], "to", adept_range[2]))
                        ^~~~
```
[R/force_trial_stability.r:160:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L160) *style:* **Lines should not be more than 80 characters.**
```r
  p <- p + theme(panel.background = element_rect(fill = "white", colour = "grey50"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:160:12:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L160) *warning:* **no visible global function definition for ‘theme’, Did you mean 'time'?**
```r
  p <- p + theme(panel.background = element_rect(fill = "white", colour = "grey50"))
           ^~~~~
```
[R/force_trial_stability.r:160:37:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L160) *warning:* **no visible global function definition for ‘element_rect’**
```r
  p <- p + theme(panel.background = element_rect(fill = "white", colour = "grey50"))
                                    ^~~~~~~~~~~~
```
[R/force_trial_stability.r:166:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L166) *style:* **Lines should not be more than 80 characters.**
```r
##' Relationship between adept posture and signed max residual in scatter plot form
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:167:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L167) *style:* **Lines should not be more than 80 characters.**
```r
##' @param stability_df dataframe with adept_x and adept_y column, sd, and signed_max_residual
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:168:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L168) *style:* **Lines should not be more than 80 characters.**
```r
##' @param adept_dimension_that_changes either 'adept_x' or 'adept_y', describing the one that is changing (the one that's not fixed)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:170:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L170) *style:* **Lines should not be more than 80 characters.**
```r
signed_max_residual_vs_posture <- function(stability_df, adept_dimension_that_changes) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:171:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L171) *style:* **Lines should not be more than 80 characters.**
```r
  p <- ggplot(stability_df, aes_string(adept_dimension_that_changes, "signed_max_residual"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:171:8:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L171) *warning:* **no visible global function definition for ‘ggplot’, Did you mean 'biplot'?**
```r
  p <- ggplot(stability_df, aes_string(adept_dimension_that_changes, "signed_max_residual"))
       ^~~~~~
```
[R/force_trial_stability.r:171:29:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L171) *warning:* **no visible global function definition for ‘aes_string’**
```r
  p <- ggplot(stability_df, aes_string(adept_dimension_that_changes, "signed_max_residual"))
                            ^~~~~~~~~~
```
[R/force_trial_stability.r:172:12:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L172) *warning:* **no visible global function definition for ‘geom_point’**
```r
  p <- p + geom_point(size = 0.1) + theme_bw()
           ^~~~~~~~~~
```
[R/force_trial_stability.r:172:37:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L172) *warning:* **no visible global function definition for ‘theme_bw’**
```r
  p <- p + geom_point(size = 0.1) + theme_bw()
                                    ^~~~~~~~
```
[R/force_trial_stability.r:177:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L177) *style:* **Lines should not be more than 80 characters.**
```r
##' @param stability_df dataframe with adept_x and adept_y column, sd, and signed_max_residual
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:178:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L178) *style:* **Lines should not be more than 80 characters.**
```r
##' @param adept_dimension_that_changes either 'adept_x' or 'adept_y', describing the one that is changing (the one that's not fixed)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:180:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L180) *style:* **Lines should not be more than 80 characters.**
```r
produce_stability_plots <- function(stability_df, adept_dimension_that_changes) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:182:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L182) *style:* **Lines should not be more than 80 characters.**
```r
  p_max_residual <- signed_max_residual_vs_posture(stability_df, adept_dimension_that_changes)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/force_trial_stability.r:183:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/force_trial_stability.r#L183) *style:* **Lines should not be more than 80 characters.**
```r
  p_sdres_adept <- sd_residual_plot_scatter_posture(stability_df, adept_dimension_that_changes)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ForceTrial.r:3:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/ForceTrial.r#L3) *style:* **Lines should not be more than 80 characters.**
```r
##' experiments it appeared to have a representative response for the other muscles
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ForceTrial.r:4:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/ForceTrial.r#L4) *style:* **Lines should not be more than 80 characters.**
```r
##' if any observations were recorded when the robot was initalized or moving, those rows were removed.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ForceTrial.r:5:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/ForceTrial.r#L5) *style:* **Lines should not be more than 80 characters.**
```r
##' we remove the angle and adept columns because they are unused and redundant, respectively
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ForceTrial.r:10:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/ForceTrial.r#L10) *style:* **Lines should not be more than 80 characters.**
```r
##' @param last_n_milliseconds number of milliseconds to base the stability metrics off.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ForceTrial.r:11:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/ForceTrial.r#L11) *style:* **Lines should not be more than 80 characters.**
```r
##' @return forcetrial_structure_object the object with all relevant attributes and stability metrics
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ForceTrial.r:12:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/ForceTrial.r#L12) *style:* **Lines should not be more than 80 characters.**
```r
ForceTrial <- function(timeseries_df, full_df_path, full_df, err, last_n_milliseconds = 100,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ForceTrial.r:12:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/ForceTrial.r#L12) *style:* **Variable or function name should be snake_case.**
```r
ForceTrial <- function(timeseries_df, full_df_path, full_df, err, last_n_milliseconds = 100,
^~~~~~~~~~
```
[R/ForceTrial.r:24:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/ForceTrial.r#L24) *style:* **Lines should not be more than 80 characters.**
```r
  all_muscles_stabilized_by_last_val <- all_muscles_stabilized(timeseries_df, err)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ForceTrial.r:24:3:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/ForceTrial.r#L24) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  all_muscles_stabilized_by_last_val <- all_muscles_stabilized(timeseries_df, err)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ForceTrial.r:25:1:](https://github.com/bc/frontiers2017/blob/5179d60f553b7b229240e4df07355632340e9d44/R/ForceTrial.r#L25) *style:* **Lines should not be more than 80 characters.**
```r
  ForceTrialObj <- structure(rm_encoder_and_adept_cols(timeseries_df), adept_coordinates = adept_coordinates(timeseries_df),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


That's Polish. Brasilien is PT_BR.


clean data names


let data become"long"


Bluemix [toolchain](https://console.bluemix.net/devops/toolchains/e0a5e767-f82f-47ec-a224-2fb3ae78f297 "simple-conversation-66185"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/d4cedbcf-440b-4e7a-a284-2468f250b8ce "simple-conversation-66185") deployed [simple-conversation-66185](https://github.com/JiaLu/simple-conversation-66185/releases/tag/deploy-ibm-yp-us-south-Moxin-dev-20171025-030006 "deploy-ibm-yp-us-south-Moxin-dev-20171025-030006") to [dev](https://console.bluemix.net/apps/6e453450-0e92-42f3-9442-266db888ae03?env_id=ibm:yp:us-south "ibm:yp:us-south:Moxin:dev"), including this commit


Created multidev environment [electronil#pr-setup](https://dashboard.pantheon.io/sites/17d8094e-ddfb-4032-83e4-771bdf4a36d2#pr-setup).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-setup-electronil.pantheonsite.io/)


getRating parameter is nullable


also nullable


nullable


Ah, I see... so I definitely won't go messing with trying to resize the primary data partition then...

I was looking around and saw `nand-part`, but I don't see `/dev/nand` to access with it... only individual partitions...

Do you know of any way to resize the data partition to take the extra ~64MB at the end of the end?


Penanganan Next(elmt terakhir) menjadi Next(P)


WOAH MAN


It must be enabled when we build shared libraries, so it is safe.  I usually leave it off when building executables from the static libraries since it does have a small cost in terms of performance and size.  So it is fine to enable it, but we should probably have some means of turning it off when not needed.


language: java


compile for 10.31

if(version >= 1031) {
-
+        enableFeature(Otc::GameEnhancedAnimations);
-    Proto::buildMessageModesMap(version);
+    }


Necesita revisión de redacción.


delete


I think I pulled on a few threads tracking down some potential issues and that made a few other things unravel so I think it best we make the current develop into master, then after that I will merge this branch into develop after I finish mending it and we can make it the 0.4 release in a week or so.


jdk:
  - oraclejdk8


Half deliberate, I think we should avoid them in kakrc files, they are nice for interactive use, but the more explicit name is better in saved files.

If there is strong demand to keep them highlighted, thats fine as well.


Penanganan ketika X ada di address awal List atau diakhir list.


descriptive information about the code


Esta es la página de bienvenida de la clase de Artes Visuales! 🙆♂


setwd("~/Computer Science Texts + Syllabus/BioInformatics/R Data")
read.csv("OverviewSelCoeff_BachelerFilter.csv") -> CSV
library("ggplot2", lib.loc="~/R/x86_64-pc-linux-gnu-library/3.4")
library("plyr", lib.loc="~/R/x86_64-pc-linux-gnu-library/3.4")
library(grid)

##SYN SITES (LEFT GRAPH)
#all green points for the left synonomous site grapha
a <- frequenciesOfSynAmutsNONCP <- CSV[which(((CSV$TypeOfSite == "syn"  )) & (CSV$WTnt == "a" & (CSV$bigAAChange == "0") &(CSV$makesCpG == "0"))),3]
c <- frequenciesOfSynAmutsNONCP <- CSV[which(((CSV$TypeOfSite == "syn"  )) & (CSV$WTnt == "t" & (CSV$bigAAChange == "0") &(CSV$makesCpG == "0"))),3]
e <- frequenciesOfSynAmutsNONCP <- CSV[which(((CSV$TypeOfSite == "syn"  )) & (CSV$WTnt == "c" & (CSV$bigAAChange == "0") &(CSV$makesCpG == "0"))),3]
f <- frequenciesOfSynAmutsNONCP <- CSV[which(((CSV$TypeOfSite == "syn"  )) & (CSV$WTnt == "g" & (CSV$bigAAChange == "0") &(CSV$makesCpG == "0"))),3]

#blue dots of left graph that show a CpG-forming mutation
b <- frequenciesOfSynAmutsCP <- CSV[which(((CSV$TypeOfSite == "syn"  )) & (CSV$WTnt == "a") & (CSV$bigAAChange == "0") & (CSV$makesCpG == "1")),3]
d <- frequenciesOfSynTmutsCP <- CSV[which(((CSV$TypeOfSite == "syn"  )) & (CSV$WTnt == "t") & (CSV$bigAAChange == "0") & (CSV$makesCpG == "1")),3]

#NON SYN SITES (RIGHT GRAPH)
#all green points for the right NON-synonomous site graph
g <- frequenciesOfNONSynAmutsNONCP <- CSV[which(((CSV$TypeOfSite == "nonsyn"  )) & (CSV$WTnt == "a" & (CSV$bigAAChange == "0") &(CSV$makesCpG == "0"))),3]
k <- frequenciesOfNONSynAmutsNONCP <- CSV[which(((CSV$TypeOfSite == "nonsyn"  )) & (CSV$WTnt == "t" & (CSV$bigAAChange == "0") &(CSV$makesCpG == "0"))),3]
o <- frequenciesOfNONSynAmutsNONCP <- CSV[which(((CSV$TypeOfSite == "nonsyn"  )) & (CSV$WTnt == "c" & (CSV$bigAAChange == "0") &(CSV$makesCpG == "0"))),3]
q <- frequenciesOfNONSynAmutsNONCP <- CSV[which(((CSV$TypeOfSite == "nonsyn"  )) & (CSV$WTnt == "g" & (CSV$bigAAChange == "0") &(CSV$makesCpG == "0"))),3]

#blue dots of right graph that show a CpG-forming mutation
h <- frequenciesOfNONSynAmutsCP <- CSV[which(((CSV$TypeOfSite == "nonsyn"  )) & (CSV$WTnt == "a") & (CSV$bigAAChange == "0") & (CSV$makesCpG == "1")),3]
l <- frequenciesOfNONSynTmutsCP <- CSV[which(((CSV$TypeOfSite == "nonsyn"  )) & (CSV$WTnt == "t") & (CSV$bigAAChange == "0") & (CSV$makesCpG == "1")),3]

#all yellow points for the right NON-SYN site graph
i <- frequenciesOfNONSynAmutsDRASTIC <- CSV[which(((CSV$TypeOfSite == "nonsyn"  )) & (CSV$WTnt == "a" & (CSV$bigAAChange == "1") &(CSV$makesCpG == "0"))),3]
m <- frequenciesOfNONSynTmutsDRASTIC <- CSV[which(((CSV$TypeOfSite == "nonsyn"  )) & (CSV$WTnt == "t" & (CSV$bigAAChange == "1") &(CSV$makesCpG == "0"))),3]
p <- frequenciesOfNONSynGmutsDRASTIC <- CSV[which(((CSV$TypeOfSite == "nonsyn"  )) & (CSV$WTnt == "c" & (CSV$bigAAChange == "1") &(CSV$makesCpG == "0"))),3]
r <- frequenciesOfNONSynCmutsDRASTIC <- CSV[which(((CSV$TypeOfSite == "nonsyn"  )) & (CSV$WTnt == "g" & (CSV$bigAAChange == "1") &(CSV$makesCpG == "0"))),3]

#red points on the right
j <- frequenciesOfNONSynAmutsCPDRASTIC <- CSV[which(((CSV$TypeOfSite == "nonsyn"  )) & (CSV$WTnt == "a" & (CSV$bigAAChange == "1") &(CSV$makesCpG == "1"))),3]
n <- frequenciesOfNONSynTmutsCPDRASTIC <- CSV[which(((CSV$TypeOfSite == "nonsyn"  )) & (CSV$WTnt == "t" & (CSV$bigAAChange == "1") &(CSV$makesCpG == "1"))),3]

mylist <- list (a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r)
mylist

llngths<-lapply(mylist, function(x) length(x))
vlngths<-unlist(llngths)
maxlngth <- max(vlngths)

myfn<-function(x,maxlngth){
  length(x)<-maxlngth
  return (x)}
mtxmylst <-sapply(mylist, myfn, maxlngth)
mtxmylst

rm (mxstats)
means<-sapply(mylist, function(x) mean(x,na.rm = TRUE))
ucls<-sapply(mylist, function(x) (sd(x, na.rm = TRUE) + mean(x, na.rm = TRUE)))
lcls <- sapply (mylist, function(x)(mean(x, na.rm = TRUE) - sd(x, na.rm = TRUE)))
mxstats<-rbind(means,ucls)
mxstats<-rbind(mxstats,lcls)
mxstats

dfval<-data.frame(mtxmylst)
names<-c("means","ucls","lcls")
dfstats<-data.frame(mxstats,row.names = names)
dfstats

rename
dfval<-rename(dfval,c("X1"="val_a","X2"="val_b","X3"="val_c","X4"="val_d","X5"="val_e","X6"="val_f","X7"="val_g","X8"="val_h","X9"="val_i","X10"="val_j","X11"="val_k","X12"="val_l","X13"="val_m","X14"="val_n","X15"="val_o","X16"="val_p","X17"="val_q", "X18"= "val_r"))
dfstats<-rename(dfstats,c("X1"="mut_a","X2"="mut_b","X3"="mut_c","X4"="mut_d","X5"="mut_e","X6"="mut_f","X7"="mut_g","X8"="mut_h","X9"="mut_i","X10"="mut_j","X11"="mut_k","X12"="mut_l","X13"="mut_m","X14"="mut_n","X15"="mut_o","X16"="mut_p","X17"="mut_q", "X18"= "mut_r"))
dfval
dfstats
sink("Routput(sap).txt")
print(dfstats)
sink()

class(dfval[,2])
class(dfstats[,2])

Synplt <- ggplot() +

  geom_point( data = dfval, mapping = aes(x="a", y= val_a), colour = "green", size = 0.1) +xlab("Mutation Type") + ylab("Samples' Average Frequencies of Mutations") +
  geom_point(data = dfstats, mapping = aes (x = "a", y = dfstats["means","mut_a"]), colour = "green",size = 5.0) +
  #geom_errorbar(data = dfstats,aes(x = "a", ymin= dfstats["lcls","mut_a"], ymax= dfstats["ucls","mut_a"], color = "red",width=.5)) +

  annotate("text", x  = 1.5, y = 0.00001, label = "A -> G") +

  geom_point( data = dfval, mapping = aes(x="b", y= val_b), colour = "blue", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "b", y = dfstats["means","mut_b"]), colour = "blue",size = 5.0) +
  #  geom_errorbar(data = dfstats,aes(x = "b", ymin= dfstats["lcls","mut_b"], ymax= dfstats["ucls","mut_b"], color = "red",width=.5)) +

  geom_vline(aes(linetype=1, colour="black"),xintercept =c(2.5)) +

  geom_point( data = dfval, mapping = aes(x="c", y= val_c), colour = "green", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "c", y = dfstats["means","mut_c"]), colour = "green",size = 5.0) +
  # geom_errorbar(data = dfstats,aes(x = "c", ymin= dfstats["lcls","mut_c"], ymax= dfstats["ucls","mut_c"], color = "red",width=.5)) +

  annotate("text", x  = 3.5, y = 0.00001, label = "T -> C") +

  geom_point( data = dfval, mapping = aes(x="d", y= val_d), colour = "blue", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "d", y = dfstats["means","mut_d"]), colour = "blue",size = 5.0) +
  #  geom_errorbar(data = dfstats,aes(x = "d", ymin= dfstats["lcls","mut_d"], ymax= dfstats["ucls","mut_d"], color = "red",width=.5)) +

  geom_vline(aes(linetype=1, colour="black"),xintercept =c(4.5)) +

  geom_point( data = dfval, mapping = aes(x="e", y= val_e), colour = "green", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "e", y = dfstats["means","mut_e"]), colour = "green",size = 5.0) +
  # geom_errorbar(data = dfstats,aes(x = "e", ymin= dfstats["lcls","mut_e"], ymax= dfstats["ucls","mut_e"], color = "red",width=.5)) +

  geom_point(data = dfstats, mapping = aes (x = "e1", y = 0.0), colour = "red",size = 0.0) +

  annotate("text", x  = 5.5, y = 0.00001, label = "C -> T") +

  geom_vline(aes(linetype=1, colour="black"),xintercept =c(6.5)) +

  geom_point( data = dfval, mapping = aes(x="f", y= val_f), colour = "green", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "f", y = dfstats["means","mut_f"]), colour = "green",size = 5.0) +
  # geom_errorbar(data = dfstats,aes(x = "f", ymin= dfstats["lcls","mut_f"], ymax= dfstats["ucls","mut_f"], color = "red",width=.5)) +

  geom_point(data = dfstats, mapping = aes (x = "f1", y = 0.0), colour = "red",size = 0.0) +

  annotate("text", x  = 7.5, y = 0.00001, label = "G -> A") +

  scale_x_discrete(labels=c("a" = "", "b" = "", "c" = "", "d" = "","e" = "", "e1" = "","f" ="", "f1" = "")) +

  #ggtitle("HIV Genetic Mutations Study - Frequency vs Type") +
  scale_y_log10() +
  theme(legend.position="none") +
  expand_limits(y = c(0.00001, 0.1)) +
  theme(plot.margin = unit(c(1,1,2.5,1), "cm")) +
  theme (panel.border = element_rect(colour = "black", fill=NA, size=3),plot.title = element_text(hjust = 0.5))

NonSynplt <- ggplot() +

  geom_point( data = dfval, mapping = aes(x="g", y= val_g), colour = "green", size = 0.1) +xlab("Mutation Type") + ylab("Samples' Average Frequencies of Mutations") +
  geom_point(data = dfstats, mapping = aes (x = "g", y = dfstats["means","mut_g"]), colour = "green",size = 5.0) +
  geom_errorbar(data = dfstats,aes(x = "g", ymin= dfstats["lcls","mut_g"], ymax= dfstats["ucls","mut_g"], color = "red",width=.5)) +

  annotate("text", x  = 2.5, y = 0.00001, label = "A -> G") +

  geom_point( data = dfval, mapping = aes(x="h", y= val_h), colour = "blue", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "h", y = dfstats["means","mut_h"]), colour = "blue",size = 5.0) +
  #geom_errorbar(data = dfstats,aes(x = "h", ymin= dfstats["lcls","mut_h"], ymax= dfstats["ucls","mut_h"], color = "red",width=.5)) +

  geom_point( data = dfval, mapping = aes(x="i", y= val_i), colour = "yellow", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "i", y = dfstats["means","mut_i"]), colour = "yellow",size = 5.0) +
  # geom_errorbar(data = dfstats,aes(x = "i", ymin= dfstats["lcls","mut_i"], ymax= dfstats["ucls","mut_i"], color = "red",width=.5)) +

  geom_point( data = dfval, mapping = aes(x="j", y= val_j), colour = "red", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "j", y = dfstats["means","mut_j"]), colour = "red",size = 5.0) +
  #geom_errorbar(data = dfstats,aes(x = "j", ymin= dfstats["lcls","mut_j"], ymax= dfstats["ucls","mut_j"], color = "red",width=.5)) +

  geom_vline(aes(linetype=1, colour="black"),xintercept =c(4.5)) +

  annotate("text", x  = 6.5, y = 0.00001, label = "T -> C") +

  geom_point( data = dfval, mapping = aes(x="k", y= val_k), colour = "green", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "k", y = dfstats["means","mut_k"]), colour = "green",size = 5.0) +
  #geom_errorbar(data = dfstats,aes(x = "k", ymin= dfstats["lcls","mut_k"], ymax= dfstats["ucls","mut_k"], color = "red",width=.5)) +

  geom_point( data = dfval, mapping = aes(x="l", y= val_l), colour = "blue", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "l", y = dfstats["means","mut_l"]), colour = "blue",size = 5.0) +
 # geom_errorbar(data = dfstats,aes(x = "l", ymin= dfstats["lcls","mut_l"], ymax= dfstats["ucls","mut_l"], color = "red",width=.5)) +

  geom_vline(aes(linetype=1, colour="black"),xintercept =c(8.5)) +

  geom_point( data = dfval, mapping = aes(x="m", y= val_m), colour = "yellow", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "m", y = dfstats["means","mut_m"]), colour = "yellow",size = 5.0) +
#  geom_errorbar(data = dfstats,aes(x = "m", ymin= dfstats["lcls","mut_m"], ymax= dfstats["ucls","mut_m"], color = "red",width=.5)) +

  annotate("text", x  = 9.5, y = 0.00001, label = "C -> T") +

  geom_point( data = dfval, mapping = aes(x="n", y= val_n), colour = "red", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "n", y = dfstats["means","mut_n"]), colour = "red",size = 5.0) +
#  geom_errorbar(data = dfstats,aes(x = "n", ymin= dfstats["lcls","mut_n"], ymax= dfstats["ucls","mut_n"], color = "red",width=.5)) +

  geom_vline(aes(linetype=1, colour="black"),xintercept =c(10.5)) +

  geom_point( data = dfval, mapping = aes(x="o", y= val_o), colour = "green", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "o", y = dfstats["means","mut_o"]), colour = "green",size = 5.0) +
#  geom_errorbar(data = dfstats,aes(x = "o", ymin= dfstats["lcls","mut_o"], ymax= dfstats["ucls","mut_o"], color = "red",width=.5)) +

  annotate("text", x  = 11.5, y = 0.00001, label = "G -> A") +

  geom_point( data = dfval, mapping = aes(x="p", y= val_p), colour = "yellow", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "p", y = dfstats["means","mut_p"]), colour = "yellow",size = 5.0) +
#  geom_errorbar(data = dfstats,aes(x = "p", ymin= dfstats["lcls","mut_p"], ymax= dfstats["ucls","mut_p"], color = "red",width=.5)) +

  geom_point( data = dfval, mapping = aes(x="q", y= val_q), colour = "green", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "q", y = dfstats["means","mut_q"]), colour = "green",size = 5.0) +
 # geom_errorbar(data = dfstats,aes(x = "q", ymin= dfstats["lcls","mut_q"], ymax= dfstats["ucls","mut_q"], color = "red",width=.5)) +

  geom_point( data = dfval, mapping = aes(x="r", y= val_r), colour = "yellow", size = 0.1) +
  geom_point(data = dfstats, mapping = aes (x = "r", y = dfstats["means","mut_r"]), colour = "yellow",size = 5.0) +
#  geom_errorbar(data = dfstats,aes(x = "r", ymin= dfstats["lcls","mut_r"], ymax= dfstats["ucls","mut_r"], color = "red",width=.5)) +

  scale_x_discrete(labels=c("g" = "", "h" = "", "i" = "", "j" = "","k" = "","l" ="","m" ="", "n"="","o" = "","p" = "","q"="","r"="")) +

  #ggtitle("HIV Genetic Mutations Study - Frequency vs Type") +
  scale_y_log10() +
  theme(legend.position="none") +
  expand_limits(y = c(0.00001, 0.1)) +
  theme(plot.margin = unit(c(1,1,2.5,1), "cm")) +
  theme (panel.border = element_rect(colour = "black", fill=NA, size=3),plot.title = element_text(hjust = 0.5))

#, vp=viewport(width=1.0, height=0.97)
library("gridExtra", lib.loc="~/R/x86_64-pc-linux-gnu-library/3.4")
require(grid)
require(gridExtra)
title1=textGrob("
                Fig. 3: type of site vs frequency, highlighting mean and 1 sd range", gp=gpar(fontface="bold", fontsize = 16, cex = 1))
grid.arrange( top =title1,Synplt + ggtitle('Synonymous Plots'), NonSynplt + ggtitle('Non-synonymous Plots'),  nrow=1)

grid.text("
KEY GOES HERE",
          x = unit(3, "cm"), y = unit(1.00,"cm"), just = "left", vjust = unit(0.0,"cm"))

#sink("Routput(loop).txt")
#print(dfval)
#print(dfstats)
#class(dfstats)
#sink()


Created multidev environment [electronil#ci-22](https://dashboard.pantheon.io/sites/17d8094e-ddfb-4032-83e4-771bdf4a36d2#ci-22).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-22-electronil.pantheonsite.io/)


This is Doug.


[inst/examples/Wolf-Sheep-Predation/Wolf-Sheep-Predation.R:249:8:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/inst/examples/Wolf-Sheep-Predation/Wolf-Sheep-Predation.R#L249) *style:* **Place a space before left parenthesis, except in a function call.**
```r
while ((NLany(sheep) | NLany(wolves)) & time < maxTime) {
       ^
```
[inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.R:64:1:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.R#L64) *style:* **Variable or function name should be lowerCamelCase.**
```r
doEvent.WolfSheepPredation <- function(sim, eventTime, eventType, debug = FALSE) {
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.R:113:1:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.R#L113) *style:* **Variable or function name should be lowerCamelCase.**
```r
WolfSheepPredationInit <- function(sim) {
^~~~~~~~~~~~~~~~~~~~~~
```
[inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.R:185:1:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.R#L185) *style:* **Variable or function name should be lowerCamelCase.**
```r
WolfSheepPredationSave <- function(sim) {
^~~~~~~~~~~~~~~~~~~~~~
```
[inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.R:200:1:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.R#L200) *style:* **Variable or function name should be lowerCamelCase.**
```r
WolfSheepPredationPosition <- function(sim) {
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.R:220:1:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.R#L220) *style:* **Variable or function name should be lowerCamelCase.**
```r
WolfSheepPredationPopSize <- function(sim) {
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.R:243:1:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.R#L243) *style:* **Variable or function name should be lowerCamelCase.**
```r
WolfSheepPredationEvent <- function(sim){
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/agentMatrix-Class-methods.R:15:12:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/agentMatrix-Class-methods.R#L15) *style:* **Variable or function name should be lowerCamelCase.**
```r
  function(.Object="agentMatrix", coords, ..., levelsAM) {
           ^~~~~~~
```
[R/agentMatrix-Class-methods.R:16:5:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/agentMatrix-Class-methods.R#L16) *style:* **Variable or function name should be lowerCamelCase.**
```r
    Coords <- TRUE
    ^~~~~~
```
[R/agentMatrix-Class-methods.R:29:7:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/agentMatrix-Class-methods.R#L29) *style:* **Variable or function name should be lowerCamelCase.**
```r
      Coords <- FALSE
      ^~~~~~
```
[R/agentMatrix-Class-methods.R:99:11:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/agentMatrix-Class-methods.R#L99) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if ((is.matrix(dotCols[[1]]) & is.numeric(dotCols[[1]])) | is(dotCols[[1]], "agentMatrix"))
          ^
```
[R/agentMatrix-Class-methods.R:403:6:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/agentMatrix-Class-methods.R#L403) *style:* **Commented code should be removed.**
```r
    #charCols <- match(j, nam)
     ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/agentMatrix-Class-methods.R:404:6:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/agentMatrix-Class-methods.R#L404) *style:* **Commented code should be removed.**
```r
    #charCols <- match(nam, j)
     ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/agentMatrix-Class-methods.R:405:34:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/agentMatrix-Class-methods.R#L405) *style:* **Commented code should be removed.**
```r
    numCols <- which(!charCols) #colNums[!(colNums %in% charCols)]
                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/agentMatrix-Class-methods.R:412:8:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/agentMatrix-Class-methods.R#L412) *style:* **Commented code should be removed.**
```r
      #numColsJ <- which(colNums %in% numCols)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/agentMatrix-Class-methods.R:417:8:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/agentMatrix-Class-methods.R#L417) *style:* **Commented code should be removed.**
```r
      #charColsJ <- which(colNums %in% charCols)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/agentMatrix-Class-methods.R:624:1:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/agentMatrix-Class-methods.R#L624) *style:* **Variable or function name should be lowerCamelCase.**
```r
head.agentMatrix <- function(x, n = 6L, ...) {
^~~~~~~~~~~~~~~~
```
[R/agentMatrix-Class-methods.R:633:1:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/agentMatrix-Class-methods.R#L633) *style:* **Variable or function name should be lowerCamelCase.**
```r
tail.agentMatrix <- function(x, n = 6L, ...) {
^~~~~~~~~~~~~~~~
```
[R/agentMatrix-Class-methods.R:655:36:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/agentMatrix-Class-methods.R#L655) *style:* **Variable or function name should be lowerCamelCase.**
```r
cbind.agentMatrix <- function(..., deparse.level) {
                                   ^~~~~~~~~~~~~
```
[R/agentMatrix-Class-methods.R:680:36:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/agentMatrix-Class-methods.R#L680) *style:* **Variable or function name should be lowerCamelCase.**
```r
rbind.agentMatrix <- function(..., deparse.level = 1) {
                                   ^~~~~~~~~~~~~
```
[R/plot.R:37:3:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/plot.R#L37) *style:* **Variable or function name should be lowerCamelCase.**
```r
  Ras <- world2raster(x)
  ^~~
```
[R/plot.R:53:3:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/plot.R#L53) *style:* **Variable or function name should be lowerCamelCase.**
```r
  Ras <- world2raster(x)
  ^~~
```
[R/quickPlot.R:179:39:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/quickPlot.R#L179) *style:* **Commas should always have a space after.**
```r
    grobToPlot@.Data <- toPlot@.Data[,,sGrob@layerName];
                                      ^
```
[R/turtle-functions.R:93:32:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/turtle-functions.R#L93) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    coords <- cbind(xcor = rep(((maxPxcor(world) - minPxcor(world)) / 2) + minPxcor(world), n),
                               ^
```
[R/turtle-functions.R:93:33:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/turtle-functions.R#L93) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    coords <- cbind(xcor = rep(((maxPxcor(world) - minPxcor(world)) / 2) + minPxcor(world), n),
                                ^
```
[R/turtle-functions.R:94:32:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/turtle-functions.R#L94) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                    ycor = rep(((maxPycor(world) - minPycor(world)) / 2) + minPycor(world), n))
                               ^
```
[R/turtle-functions.R:94:33:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/turtle-functions.R#L94) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                    ycor = rep(((maxPycor(world) - minPycor(world)) / 2) + minPycor(world), n))
                                ^
```
[R/turtle-functions.R:454:35:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/turtle-functions.R#L454) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                          xcor = ((world@extent@xmax - world@extent@xmin) / 2) +
                                  ^
```
[R/turtle-functions.R:456:35:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/turtle-functions.R#L456) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                          ycor = ((world@extent@ymax - world@extent@ymin) / 2) +
                                  ^
```
[R/world-functions.R:527:25:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/world-functions.R#L527) *style:* **Put spaces around all infix operators.**
```r
          mid <- floor(n/2)
                       ~^~
```
[R/world-functions.R:544:9:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/world-functions.R#L544) *style:* **Commented code should be removed.**
```r
    #   cat("names       :", paste(ln, collapse=", "), "\n")
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/world-functions.R:548:28:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/world-functions.R#L548) *style:* **Commas should always have a space after.**
```r
    print(object@.Data[1:4,1:4,])
                           ^
```
[R/world-functions.R:548:32:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/world-functions.R#L548) *style:* **Commas should always have a space after.**
```r
    print(object@.Data[1:4,1:4,])
                               ^
```
[R/worldNLR-classes-methods.R:345:5:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/worldNLR-classes-methods.R#L345) *style:* **Variable or function name should be lowerCamelCase.**
```r
    NLwMs <- list(...)
    ^~~~~
```
[R/worldNLR-classes-methods.R:510:11:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/R/worldNLR-classes-methods.R#L510) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    floor((cellNum - 1) / b[2]) + seq.int(from = 1, to = prod(b),
          ^
```
[tests/testthat/test-plotting.R:6:3:](https://github.com/PredictiveEcology/NetLogoR/blob/a7c047d763019dfeac7ed394566858f7913af468/tests/testthat/test-plotting.R#L6) *style:* **Variable or function name should be lowerCamelCase.**
```r
  t1_0 <- createTurtles(n = 10, coords = cbind(rep(0, 10), rep(0, 10)))
  ^~~~
```


Web Browser XSS Protection Not Enabled

Web Browser XSS Protection is not enabled, or is disabled by the configuration of the 'X-XSS-Protection' HTTP response header on the web server

Solution: Ensure that the web browser's XSS filter is enabled, by setting the X-XSS-Protection HTTP response header to '1'.

X-Content-Type-Options Header Missing

The Anti-MIME-Sniffing header X-Content-Type-Options was not set to 'nosniff'. This allows older versions of Internet Explorer and Chrome to perform MIME-sniffing on the response body, potentially causing the response body to be interpreted and displayed as a content type other than the declared content type. Current (early 2014) and legacy versions of Firefox will use the declared content type (if one is set), rather than performing MIME-sniffing.

Solution: Ensure that the application/web server sets the Content-Type header appropriately, and that it sets the X-Content-Type-Options header to 'nosniff' for all web pages. If possible, ensure that the end user uses a standards-compliant and modern web browser that does not perform MIME-sniffing at all, or that can be directed by the web application/web server to not perform MIME-sniffing.

X-Frame-Options Header Not Set

X-Frame-Options header is not included in the HTTP response to protect against 'ClickJacking' attacks.

Solution: Most modern Web browsers support the X-Frame-Options HTTP header. Ensure it's set on all web pages returned by your site (if you expect the page to be framed only by pages on your server (e.g. it's part of a FRAMESET) then you'll want to use SAMEORIGIN, otherwise if you never expect the page to be framed, you should use DENY. ALLOW-FROM allows specific websites to frame the web page in supported web browsers).


@phlptp are you able to join on gitter? We can discuss these changes, merge to master and tag a release.


needs some more work!


This was meant to say fix lint for the commit message.


you might want to name this variable `song` to make clear that it is a "song" within a collection of "songs"


Version : 1


tis should be singular IMO


Yep, this broke the module for me too.


(define pi (* 4 (atan 1))) ; 3.14159...


I don't use (nor plan to use) `0` value in `disposition` anywhere. It is **known default** after zero filling of a struct. Then, real values are above `0`, so they are marked in `enum` with `= 1`. This is simple concept.

To define some `DEFAULT` constant as `0` is not meaningful (increasing of entities). This is step in defining all zeros everywhere to some `ZERO`, `DEFAULT`, `UNDEFINED`, `FALSE`, `MEMSET0` constants. Why name them? It is default value after `memset( ,0, )`. Let's name what have meaning.

Also, undefined `0` default would be checked as (!disposition) if ever need. But, if it's defined we should use `(disposition == CONTENT_DEFAULT)` to make previous definitions not worthless. We make `CONTENT_DEFAULT` non-transparent.

Let's define zero value only if it is set explicitly and (it's meaning is) non-default after struct initialization.


I really wish @puppetlabs would accept issues on their modules here rather than having to use the craptastic Jira....


支持回国功能


This still contains the bug:

```
Error: Could not retrieve catalog from remote server: Error 500 on SERVER: Server Error: no parameter named 'format' at /etc/puppetlabs/code/environments/update_puppet_modules/modules/concat/manifests/init.pp:94 on Concat_file[/root/.bash_profile]
```


👍  I wanted to talk over this specifically on thursday @mnichols. While I got it working with trial and error, I don't necessarily _get_ the syntax here. Could I theoretically put anything here? As in.... ng-repeat="`a singular item whose name I'm defining right now` in `an array of items that exists in this object I'm referencing`"?


was actually working through this: http://www.learn-angular.org/#!/lessons/repeaters as you were reviewing.


Special effects do not work when scaling.
subtitles - https://www.sendspace.com/file/popl5d
screenshot - https://i.imgur.com/gbwfQdQ.jpg
patch - https://sourceforge.net/p/mpcbe/code/3014/


Yeah so I noticed I had stuff I just never committed from a year ago lol. Actually scrapping this project and starting anew on a unity project soon


> set CONTENT_DEFAULT = 0 and then stay with the memset() (or maybe calloc())

This sounds **just wrong**. Why define constant and then don't use? Inconsistent. Who knows to what `memset()` will initialize, certainly not to semantically defined values.


啊啊


modify kernel to expose /dev/nand
working on it


no me gusta que agregues cosas sin permiso


oye muchas gracias por tu aporte , ha sido de maravilla


You've obviously been trying to read and write a full nand image using fel, but what about using `dd` with `/dev/nand`?

Couldn't you memboot a kernel that doesn't mount anything on nand to prevent corruption in either the backup or restored nand?


esta linea  me parece genial, muchas gracias


Executing the daily benchmark build, I will reply here when finished:

@nanosoldier `runbenchmarks(ALL, isdaily = true)`


@mnichols tested this out a bit. I think I better understand this now. Thx for highlighting


Cool, but the test could be better by directly using hamcrest.


Do you mean formatting of previous `if`? I split it because it was just blob, to be consistent with 'everything is on new line' style. Also, it's easier to see when [-2] [1] [2] values are checked (they now go in single column).

`buffer_appends(dst, "@...")` adds 8 html-entities-encoded bytes, `buffer_appends(dst, "@...")` adds 4 to plain text. Also, second one is not increase or decrease buffer size, so content-length could be calculated in advance.


Creator comments should be removed


minima


Ao testar o email eu estava usando email já cadastrado por isso falhava.


assertThat(CollectionUtils.isEmpty(null), is(true));


assertThat(CollectionUtils.isEmpty(emptyList()), is(true));


assertThat(CollectionUtils.isEmpty(singletonList("some str")), is(true));


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