Data Analytics GM Tables Practice

---

Site 1: Calico Basin

Site 2: Valley of Fire

table_transect_logistics <- gila_transect_data %>%
  select(
    site_id,
    detection,
    total_length_m,
    tran_time_min
  ) %>%
  tbl_summary(
    by = site_id,
    missing = "no",
    digits = all_continuous() ~ 1,
    statistic = list(all_continuous() ~ "{mean} ({sd})",
                     all_categorical() ~ "{n} ({p}%)"),
    label = list(
      detection ~ "Detections",
      tran_time_min ~ "Length of Time (min)",
      total_length_m ~ "Distance (m)")) %>%
  modify_caption("Table 1. Transect Logistics Data")

table_transect_logistics

Table 1. Transect Logistics Data

Characteristic	Calico Basin N = 1381	Valley of Fire N = 1491
Detections	7 (5.1%)	15 (10%)
Distance (m)	1,000.6 (36.7)	1,008.4 (49.0)
Length of Time (min)	106.7 (14.6)	103.2 (11.9)
1 n (%); Mean (SD)

boxplot_distance <- ggplot(gila_transect_data, aes(x = site_id, y = total_length_m)) +
  geom_boxplot() +
  geom_point() +
  ylab ("Total Transect Length (m)") +
  xlab ("Site")

boxplot_time <- ggplot(gila_transect_data, aes(x = site_id, y = tran_time_min)) +
  geom_boxplot() +
  geom_point() +
  ylab ("Transect Time (min)") +
  xlab ("Site") +
  scale_y_continuous(limits = c(75, 150), breaks = c(75, 90, 105, 120, 135, 150))
  
(boxplot_distance + boxplot_time)

ttest_rock_cal <- t.test(data_transect_cal$rock_ind_avg, data_transect_cal$rock_ind_median, paired = TRUE)
ttest_rock_vof <- t.test(data_transect_vof$rock_ind_avg, data_transect_vof$rock_ind_median, paired = TRUE)

ttest_rock_cal

## 
##  Paired t-test
## 
## data:  data_transect_cal$rock_ind_avg and data_transect_cal$rock_ind_median
## t = 1.2914, df = 137, p-value = 0.1987
## alternative hypothesis: true mean difference is not equal to 0
## 95 percent confidence interval:
##  -0.02733214  0.13023069
## sample estimates:
## mean difference 
##      0.05144928

ttest_rock_vof

## 
##  Paired t-test
## 
## data:  data_transect_vof$rock_ind_avg and data_transect_vof$rock_ind_median
## t = -1.4703, df = 148, p-value = 0.1436
## alternative hypothesis: true mean difference is not equal to 0
## 95 percent confidence interval:
##  -0.22842676  0.03352743
## sample estimates:
## mean difference 
##     -0.09744966

table_transect_env <- gila_transect_data %>%
  select(
    site_id,
    elev,
    air_temp,
    gr_temp,
    avg_wind_spd,
    rock_ind_avg,
    shr_dens,
    vap_pres_kPa,
    prey_pres
  ) %>%
  tbl_summary(
    by = site_id,
    missing = "no",
    digits = all_continuous() ~ 1,
    statistic = list(all_continuous() ~ "{mean} ({sd})",
                     all_categorical() ~ "{n} ({p}%)"),
    label = list(
      elev ~ "Elevation (m)",
      air_temp ~ "Air Temperature (C)",
      gr_temp ~ "Ground Temperature (C)",
      avg_wind_spd ~ "Average Wind Speed (km/h)",
      rock_ind_avg ~ "Granularity Index",
      shr_dens ~ "Shrub Density (n/m^2)",
      vap_pres_kPa ~ "Vapor Pressure (kPa)",
      prey_pres ~ "Prey Presence (n)"
      )) %>%
  add_p(pvalue_fun = ~ style_pvalue(.x, digits = 2)) %>%
  modify_caption("Table 3. Transect Environmental Data")

table_transect_env

Table 3. Transect Environmental Data

Characteristic	Calico Basin N = 1381	Valley of Fire N = 1491	p-value2
Elevation (m)	1,225.7 (84.9)	597.4 (35.9)	<0.001
Air Temperature (C)	26.3 (5.0)	30.4 (4.2)	<0.001
Ground Temperature (C)	28.9 (5.1)	33.1 (5.0)	<0.001
Average Wind Speed (km/h)	4.5 (2.4)	3.8 (2.8)	0.036
Granularity Index	3.2 (0.7)	3.7 (1.0)	<0.001
Shrub Density (n/m^2)	0.4 (0.2)	0.2 (0.1)	<0.001
Vapor Pressure (kPa)	2.8 (1.0)	3.6 (1.1)	<0.001
Prey Presence (n)	1.9 (2.6)	0.4 (1.1)	<0.001
1 Mean (SD)
2 Welch Two Sample t-test

gathered_env_data <- gila_transect_data %>%
  select(
    site_id,
    elev,
    air_temp,
    gr_temp,
    avg_wind_spd,
    rock_ind_avg,
    shr_dens,
    vap_pres_kPa,
    prey_pres
  ) %>%
    gather(-site_id, key="var", value = "value")

ggplot(gathered_env_data, aes(x = site_id, y = value)) +
    geom_boxplot() +
    geom_point() +
    facet_wrap(~var, scales = "free") +
    theme_bw()

table_detections_cal <- gila_transect_data %>%
  filter(site_id == "Calico Basin") %>%
  select(
    detection,
    elev,
    air_temp,
    gr_temp,
    avg_wind_spd,
    rock_ind_avg,
    shr_dens,
    vap_pres_kPa,
    prey_pres
  ) %>%
  tbl_summary(
    by = detection,
    missing = "no",
    digits = all_continuous() ~ 1,
    statistic = list(all_continuous() ~ "{mean} ({sd})",
                     all_categorical() ~ "{n} ({p}%)"),
    label = list(
      elev ~ "Elevation (m)",
      air_temp ~ "Air Temperature (C)",
      gr_temp ~ "Ground Temperature (C)",
      avg_wind_spd ~ "Average Wind Speed (km/h)",
      rock_ind_avg ~ "Granularity Index",
      shr_dens ~ "Shrub Density (n/m^2)",
      vap_pres_kPa ~ "Vapor Pressure (kPa)",
      prey_pres ~ "Prey Presence (n)"
      )) %>%
  add_p(test = all_continuous() ~ "t.test",
        pvalue_fun = ~ style_pvalue(.x, digits = 2)) %>%
  modify_fmt_fun(statistic ~ style_sigfig) %>% 
  modify_caption("Table 4. Transect Detections Data for Calico Basin") %>%
  modify_header(
    update = list(
      label ~ '**Calico Basin**',
      stat_1 ~ '**Non-detection**<br>N = {n}',
      stat_2 ~ '**Detection**<br>N = {n}',
      statistic ~ "**t-value**",
      p.value ~ '**P-value**')) %>%
  modify_footnote(everything() ~ NA)
  

table_detections_cal

Table 4. Transect Detections Data for Calico Basin

Calico Basin	Non-detection N = 131	Detection N = 7	t-value	P-value
Elevation (m)	1,227.3 (86.4)	1,194.4 (41.2)	1.9	0.089
Air Temperature (C)	26.2 (5.1)	28.1 (4.5)	-1.1	0.32
Ground Temperature (C)	28.8 (5.1)	30.4 (4.0)	-1.0	0.34
Average Wind Speed (km/h)	4.6 (2.5)	3.4 (2.0)	1.5	0.18
Granularity Index	3.1 (0.7)	3.8 (0.6)	-3.0	0.021
Shrub Density (n/m^2)	0.4 (0.2)	0.5 (0.2)	-0.56	0.59
Vapor Pressure (kPa)	2.8 (1.0)	3.2 (0.8)	-1.1	0.29
Prey Presence (n)	1.8 (2.3)	5.3 (4.7)	-2.0	0.10

table_detections_cal_offtran <- gila_offtransect_data %>%
  filter(site_id == "Calico Basin") %>%
  select(
    detection,
    elev,
    air_temp,
    gr_temp,
    avg_wind_spd,
    rock_ind_avg,
    shr_dens,
    vap_pres_kPa,
    prey_pres
  ) %>%
  tbl_summary(
    by = detection,
    missing = "no",
    digits = all_continuous() ~ 1,
    statistic = list(all_continuous() ~ "{mean} ({sd})",
                     all_categorical() ~ "{n} ({p}%)"),
    label = list(
      elev ~ "Elevation (m)",
      air_temp ~ "Air Temperature (C)",
      gr_temp ~ "Ground Temperature (C)",
      avg_wind_spd ~ "Average Wind Speed (km/h)",
      rock_ind_avg ~ "Granularity Index",
      shr_dens ~ "Shrub Density (n/m^2)",
      vap_pres_kPa ~ "Vapor Pressure (kPa)",
      prey_pres ~ "Prey Presence (n)"
      )) %>%
  add_p(test = all_continuous() ~ "t.test",
        pvalue_fun = ~ style_pvalue(.x, digits = 2)) %>%
  modify_fmt_fun(statistic ~ style_sigfig) %>% 
  modify_caption("Table 4. Transect Detections Data for Calico Basin with off-transect data") %>%
  modify_header(
    update = list(
      label ~ '**Calico Basin**',
      stat_1 ~ '**Non-detection**<br>N = {n}',
      stat_2 ~ '**Detection**<br>N = {n}',
      statistic ~ "**t-value**",
      p.value ~ '**P-value**')) %>%
  modify_footnote(everything() ~ NA)
  

table_detections_cal_offtran

Table 4. Transect Detections Data for Calico Basin with off-transect data

Calico Basin	Non-detection N = 131	Detection N = 19	t-value	P-value
Elevation (m)	1,227.3 (86.4)	1,156.9 (42.5)	5.7	<0.001
Air Temperature (C)	26.2 (5.1)	27.7 (4.3)	-1.4	0.18
Ground Temperature (C)	28.8 (5.1)	29.6 (4.1)	-0.82	0.42
Average Wind Speed (km/h)	4.6 (2.5)	3.8 (2.0)	1.5	0.14
Granularity Index	3.1 (0.7)	4.2 (1.1)	-4.2	<0.001
Shrub Density (n/m^2)	0.4 (0.2)	0.7 (0.7)	-1.9	0.071
Vapor Pressure (kPa)	2.8 (1.0)	3.1 (0.9)	-1.2	0.25
Prey Presence (n)	1.8 (2.3)	2.3 (3.7)	-0.58	0.57

table_detections_vof <- gila_transect_data %>%
  filter(site_id == "Valley of Fire") %>%
  select(
    detection,
    elev,
    air_temp,
    gr_temp,
    avg_wind_spd,
    rock_ind_avg,
    shr_dens,
    vap_pres_kPa,
    prey_pres
  ) %>%
  tbl_summary(
    by = detection,
    missing = "no",
    digits = all_continuous() ~ 1,
    statistic = list(all_continuous() ~ "{mean} ({sd})",
                     all_categorical() ~ "{n} ({p}%)"),
    label = list(
      elev ~ "Elevation (m)",
      air_temp ~ "Air Temperature (C)",
      gr_temp ~ "Ground Temperature (C)",
      avg_wind_spd ~ "Average Wind Speed (km/h)",
      rock_ind_avg ~ "Granularity Index",
      shr_dens ~ "Shrub Density (n/m^2)",
      vap_pres_kPa ~ "Vapor Pressure (kPa)",
      prey_pres ~ "Prey Presence (n)"
      )) %>%
  add_p(test = all_continuous() ~ "t.test",
        pvalue_fun = ~ style_pvalue(.x, digits = 2)) %>%
  modify_fmt_fun(statistic ~ style_sigfig) %>% 
  modify_caption("Table 5. Transect Detections Data for Valley of Fire") %>%
  modify_header(
    update = list(
      label ~ '**Valley of Valley**',
      stat_1 ~ '**Non-detection**<br>N = {n}',
      stat_2 ~ '**Detection**<br>N = {n}',
      statistic ~ "**t-value**",
      p.value ~ '**P-value**')) %>%
  modify_footnote(everything() ~ NA)
  

table_detections_vof

Table 5. Transect Detections Data for Valley of Fire

Valley of Valley	Non-detection N = 134	Detection N = 15	t-value	P-value
Elevation (m)	598.8 (36.4)	585.5 (29.6)	1.6	0.12
Air Temperature (C)	30.3 (4.3)	31.9 (2.7)	-2.1	0.047
Ground Temperature (C)	33.2 (5.0)	32.5 (4.2)	0.55	0.59
Average Wind Speed (km/h)	3.8 (2.7)	4.0 (3.2)	-0.21	0.83
Granularity Index	3.6 (1.0)	4.4 (0.9)	-3.0	0.008
Shrub Density (n/m^2)	0.2 (0.1)	0.2 (0.1)	0.56	0.58
Vapor Pressure (kPa)	3.6 (1.1)	3.9 (0.9)	-1.2	0.23
Prey Presence (n)				>0.99
0	99 (74%)	12 (80%)
1	23 (17%)	2 (13%)
2	7 (5.2%)	1 (6.7%)
3	3 (2.2%)	0 (0%)
4	1 (0.7%)	0 (0%)
11	1 (0.7%)	0 (0%)

table_detections_vof_offtran <- gila_offtransect_data %>%
  filter(site_id == "Valley of Fire") %>%
  select(
    detection,
    elev,
    air_temp,
    gr_temp,
    avg_wind_spd,
    rock_ind_avg,
    shr_dens,
    vap_pres_kPa,
    prey_pres
  ) %>%
  tbl_summary(
    by = detection,
    missing = "no",
    digits = all_continuous() ~ 1,
    statistic = list(all_continuous() ~ "{mean} ({sd})",
                     all_categorical() ~ "{n} ({p}%)"),
    label = list(
      elev ~ "Elevation (m)",
      air_temp ~ "Air Temperature (C)",
      gr_temp ~ "Ground Temperature (C)",
      avg_wind_spd ~ "Average Wind Speed (km/h)",
      rock_ind_avg ~ "Granularity Index",
      shr_dens ~ "Shrub Density (n/m^2)",
      vap_pres_kPa ~ "Vapor Pressure (kPa)",
      prey_pres ~ "Prey Presence (n)"
      )) %>%
  add_p(test = all_continuous() ~ "t.test",
        pvalue_fun = ~ style_pvalue(.x, digits = 2)) %>%
  modify_fmt_fun(statistic ~ style_sigfig) %>% 
  modify_caption("Table 5. Transect Detections Data for Valley of Fire with off-transect data") %>%
  modify_header(
    update = list(
      label ~ '**Valley of Valley**',
      stat_1 ~ '**Non-detection**<br>N = {n}',
      stat_2 ~ '**Detection**<br>N = {n}',
      statistic ~ "**t-value**",
      p.value ~ '**P-value**')) %>%
  modify_footnote(everything() ~ NA)
  

table_detections_vof_offtran

Table 5. Transect Detections Data for Valley of Fire with off-transect data

Valley of Valley	Non-detection N = 134	Detection N = 21	t-value	P-value
Elevation (m)	598.8 (36.4)	589.2 (30.6)	1.3	0.21
Air Temperature (C)	30.3 (4.3)	31.5 (3.0)	-1.7	0.10
Ground Temperature (C)	33.2 (5.0)	32.1 (4.0)	1.1	0.27
Average Wind Speed (km/h)	3.8 (2.7)	4.1 (2.9)	-0.39	0.70
Granularity Index	3.6 (1.0)	4.3 (1.5)	-2.2	0.037
Shrub Density (n/m^2)	0.2 (0.1)	0.2 (0.2)	0.99	0.33
Vapor Pressure (kPa)	3.6 (1.1)	3.8 (0.9)	-1.1	0.28
Prey Presence (n)				0.91
0	99 (74%)	18 (86%)
1	23 (17%)	2 (9.5%)
2	7 (5.2%)	1 (4.8%)
3	3 (2.2%)	0 (0%)
4	1 (0.7%)	0 (0%)
11	1 (0.7%)	0 (0%)

data_transect_cal$detection <- as.factor(data_transect_cal$detection)
gathered_det_cal <- data_transect_cal %>%
  select(
    detection,
    elev,
    air_temp,
    gr_temp,
    avg_wind_spd,
    rock_ind_avg,
    shr_dens,
    vap_pres_kPa,
    prey_pres
  ) %>%
    gather(-detection, key="var", value = "value")


ggplot(gathered_det_cal, aes(x = detection, y = value)) +
    geom_boxplot() +
    geom_point() +
    facet_wrap(~var, scales = "free") +
    theme_bw() +
    scale_x_discrete(labels = labels_det)

data_transect_vof$detection <- as.factor(data_transect_vof$detection)
gathered_det_vof <- data_transect_vof %>%
  select(
    detection,
    elev,
    air_temp,
    gr_temp,
    avg_wind_spd,
    rock_ind_avg,
    shr_dens,
    vap_pres_kPa,
    prey_pres
  ) %>%
    gather(-detection, key="var", value = "value")

ggplot(gathered_det_vof, aes(x = detection, y = value)) +
    geom_boxplot() +
    geom_point() +
    facet_wrap(~var, scales = "free") +
    theme_bw() +
    scale_x_discrete(labels = labels_det)